Methods for identifying compounds which modulate circadian rhythm

FIELD OF THE INVENTION

[0002] The field of the invention relates to the regulation of circadian rhythms.

BACKGROUND OF THE INVENTION

[0003] Circadian rhythms in mammals are regulated by a master clock located in the suprachiasmatic nucleus (SCN) of the brain (Klein et al., Suprachiasmatic nucleus: The Mind's Clock, Oxford University Press, New York, 1991; Reppert and Weaver, Cell 89:487-490, 1997). Environmental light-dark cycles entrain the SCN clock to the 24-hr day via direct and indirect retinal projections. The timekeeping capability of the SCN is expressed at the level of single neurons (Welsh et al., Neuron 14:697-706, 1995).

[0004] The SCN clock mechanism is cell-autonomous, possibly based on transcriptional and translational negative feedback loops (Reppert, Neuron 21:1-4, 1998). Precedent for such a mechanism has been described for circadian clocks in the fly Drosophila melanogaster.

[0005] In the fly, autoregulatory transcriptional loops occur in which protein products of clock genes periodically enter the nucleus to suppress their own transcription. This feedback loop involves dynamic regulation of the clock genes period (per) and timeless (Tim). As the levels of PER and TIM rise, they are phosphorylated, form heterodimers, and are then translocated to the nucleus where they negatively regulate their own transcription (Saez and Young, Neuron 17:1-920, 1996; Darlington et al., Science 280:1599-1603, 1998). Negative transcriptional regulation appears to involve interference with drosophila CLOCK:drosophila dBMAL-1 (dCLOCK:dBMAL-1) and may be mediated by direct interaction of PER and TIM with dCLOCK. dCLOCK and dBMAL-1 are positive factors which drive Per and Tim transcriptional activation by binding to CACGTG E-box enhancers in the promoters of Per and Tim (Allada et al., Cell 93:791-804, 1998; Rutila et al., Cell 93:805-814, 1998; Darlington et al., supra; Hao et al., Mol. Cell Biol. 17:3687-3693, 1997). The temporal phosphorylation of PER provides at least part of the time delay between transcription and PER-TIM negative feedback necessary to sustain a 24-hr molecular oscillation in drosophila (Price et al., Cell 94:83-95, 1998).

SUMMARY OF THE INVENTION

[0006] The invention is based, in part, on the discovery that the core clockwork in the SCN is comprised of interacting feedback loops. It was discovered that cryptochrome (CRY) proteins are critical players in the negative limb of the mammalian clock feedback loop and Period 2 (PER2) protein is a critical regulator of the Bmal-1 loop. The CRY proteins and PER2 protein therefore function as important modulators of mammalian circadian rhythm.

[0007] It was discovered that mammalian CRY proteins can translocate from the cytoplasm to the nucleus of a cell and inhibit CLOCK:BMAL-1 induced transcription. It was also discovered that CRY proteins can homodimerize or heterodimerize with other circadian proteins. The ability of CRY to heterodimerize with other proteins provides a mechanism whereby CRY can modulate the activity of other circadian proteins. For example, mouse CRY proteins can function as dimeric and potentially trimeric partners for mouse PER proteins; these interactions lead to the nuclear translocation of PER. Once in the nucleus, PER can inhibit CLOCK:BMAL-1 induced transcription. In addition, it was discovered that mouse CRY can form heterodimeric complexes with mouse TIM. The interaction of TIM with CRY may have a role in modulating the negative feedback of mouse PER and/or mouse CRY rhythms. Thus, the compounds which can disrupt the interaction of CRY with itself and other circadian proteins can be used to reset the circadian clock.

[0008] In addition, it was discovered that PER2 positively regulates transcription of the Bmal-1 gene. The ability of PER2 to positively regulate the transcription of Bmal-1 indicates that PER2 controls the rhythmic regulation of Bmal-1. The availability of BMAL-1 is critical for restarting the circadian clock loop. When BMAL-1 is available, it heterodimerizes with CLOCK, thereby driving the transcription of Per genes (e.g., in the mouse(m), mPER1-3) and Cryptochrome genes (e.g., mouse mCry1 and mCry2). Compounds which can disrupt the ability of PER2 to positively activate Bmal-1, or compounds which can modulate transcription of Bmal-1, can be used to reset the circadian clock.

[0009] Accordingly, the invention includes a method for identifying a compound which binds to a mammalian CRY protein. The method, which is useful as a quick initial screen for CRY agonists and antagonists, includes contacting the CRY protein with a test compound and determining whether the latter binds to the CRY protein. Binding by the test compound to the CRY protein indicates that the test compound is a CRY protein binding compound. For ease of detection, the test compound can be labeled, e.g., radiolabeled. The CRY protein can any mammalian CRY protein such as a CRY from a mouse, rat, rabbit, goat, horse, cow, pig, dog, cat, sheep, pig, non-human, primate, or human. In particular, the CRY protein is a mouse CRY1 or CRY2 or human CRY1 or CRY2.

[0010] The method may further include contacting the test compound with: a CRY protein in the presence of a PER protein; a CRY protein in the presence of a TIM protein; a CRY protein in the presence of a CLOCK:BMAL-1 complex; or a CRY protein in the presence of a BMAL-1 protein; and determining whether the test compound disrupts the association of the CRY protein with the PER, TIM, CLOCK:BMAL-1, or BMAL-1 protein, as the case may be; wherein a decrease in the association in the presence of the test compound compared to the association in the absence of the test compound indicates that the test compound disrupts the association of the CRY protein with the indicated binding partner. The PER protein can any mammalian PER protein such as mouse, rat, rabbit, goat, horse, cow, pig, dog, cat or human. For example, the PER protein may be mouse or human PER1, PER2 or PER3.

[0011] The method can further include contacting the test compound with the first CRY protein in the presence of a second CRY protein and determining whether the test compound disrupts the association of the first CRY protein with the second CRY protein, wherein the second CRY protein has an amino acid sequence the same as or different than the first CRY protein, and wherein a decrease in the association in the presence of the test compound compared to the association in the absence of the test compound indicates that the test compound disrupts the association of the first CRY protein and the second CRY protein. The first and second CRY proteins can be any mammalian CRY protein such as a CRY from a mouse, rat, rabbit, goat, horse, cow, pig, dog, cat, sheep, non-human, primate or human. For example, each CRY protein can be a mouse or human CRY1 or CRY2 and the second CRY protein is a mouse CRY1 or CRY2.

[0012] The method can further include providing a cell or cell-free system which includes a CRY protein, a CLOCK:BMAL-1 complex, and a DNA comprising an E-box operatively linked to a reporter gene. The method includes introducing the test compound into the cell or cell-free system and assaying for transcription of the reporter gene, wherein an increase in transcription in the presence of the compound compared to transcription in the absence of the compound indicates that the compound blocks CRY-induced inhibition of CLOCK:BMAL-1-mediated transcription in a cell. The cell can be any cell type, such as a cultured mammalian cell, e.g., a NIH3T3 cell, a COS7 cell, or a clock neuron. The reporter gene can be a gene that encodes a detectable marker, e.g., luciferase.

[0013] The invention further includes a method for identifying a compound which disrupts the association of a CRY protein and a second protein or protein complex, which can be any of the following: a PER protein, a TIM protein, a BMAL-1 protein, a second CRY protein, or a CLOCK:BMAL-1 complex. The method includes contacting a test compound with the CRY protein in the presence of the second protein (or protein complex) and determining whether the test compound disrupts the association of the CRY protein and the second protein (or protein complex), wherein a decrease in the association in the presence of the test compound compared to the association in the absence of the test compound indicates that the test compound disrupts the association of the CRY protein and the second protein. The first and second CRY proteins can be any mammalian CRY protein such as a CRY protein from a mouse, rat, rabbit, goat, horse, cow, sheep, pig, dog, cat, non-human primate or human, e.g., a mouse or human CRY1 or CRY2. The PER protein can be any mammalian PER protein as described above, e.g., a mouse PER1, PER2 or PER3. The TIM protein can be any mammalian TIM protein as described above, e.g., a mouse or human TIM protein. The CLOCK and the BMAL-1 proteins can be any mammalian CLOCK and BMAL-1 proteins as described above, particularly mouse or human.

[0014] Also within the invention is a method for identifying a compound that blocks CRY-induced inhibition of CLOCK:BMAL-1 transcription in a cell. The method includes providing a cell comprising a CRY protein, a CLOCK:BMAL-1 complex, and a DNA comprising an E-box operatively linked to a reporter gene; introducing the compound into the cell or a cell-free transcription system; and assaying for transcription of the reporter gene, wherein an increase in transcription in the presence of the compound compared to transcription in the absence of the compound indicates that the compound blocks CRY-induced inhibition of CLOCK:BMAL-1-mediated transcription. The cell can be any cell type, such as a cultured mammalian cell, e.g., a NIH3T3 cell, a COS7 cell or a clock neuron. The reporter gene can be gene that encodes a detectable marker, e.g., luciferase.

[0015] The invention further includes a method for identifying a compound that activates or inhibits the transcription of Per2. The method includes providing a cell including a mammalian Per2 regulatory sequence operatively linked to a reporter gene, introducing a test compound into the cell, and assaying for transcription of the reporter gene in the cell. A decrease in transcription in the presence of the compound compared to transcription in the absence of the compound indicates that the compound inhibits Per2 transcription in a cell. Likewise, an increase of transcription in the presence of the compound compared to transcription in the absence of the compound indicates that the compound inhibits Per2 transcription in a cell. The cell can be any cell that can generate circadian rhythms, such as a NIH3T3 cell, a Cos-7 cell or a clock neuron. The reporter gene can be any detectable marker, e.g., a luciferase, a chloramphenicol acetyl transferase, a betagalactosidase, an alkaline phosphate, or a fluorescent protein such as green fluorescent protein. The Per2 regulatory sequence can be any mammalian Per2 regulatory sequence, e.g., from a mouse, a rat, a rabbit, a goat, a horse, a cow, a pig, a dog, a cat, a sheep, a non-human primate, or a human. In particular, the Per2 regulatory sequence can be a mouse Per2 regulatory sequence (SEQ ID NO:3).

[0016] Also within the invention is a method of determining if a candidate compound positively regulates the expression of Bmal-1. The method includes providing a transgenic animal whose somatic and germ cells comprise a disrupted Per2 gene, the disruption being sufficient to inhibit the ability of Per2 to positively regulate Bmal-1, administering a test compound to the mouse, and detecting Bmal-1 expression, wherein an increase in the expression of Bmal-1 indicates that the compound can positively regulate expression of Bmal-1.

[0017] The invention also features a method of modulating circadian-clock controlled rhythms in a cell including comprising introducing into a cell an expression vector encoding a BMAL-1 protein such that an effective amount of the BMAL-1 protein is produced in the cell, thereby modulating circadian-clock controlled rhythms. The BMAL-1 can be any mammalian BMAL-1, e.g., that of a mouse, a rat, a rabbit, a goat, a horse, a cow, a dog, a cat, a sheep, a non-human primate, or a human BMAL-1.

[0018] Also within the invention is a method of modulating circadian-clock controlled rhythms in a cell comprising introducing into the cell an effective amount of an oligonucleotide antisense to a part, or all, of a mammalian Bmal-1, thereby inhibiting expression of Bmal-1 in the cell and modulating circadian-clock rhythms. Oligonucleotides can be antisense to any mammalian Bmal-1, e.g., Bmal-1 from a mouse, a rat, a rabbit, a goat, a horse, a cow, a sheep, a non-human primate, or a human.

[0019] The invention further includes isolated nucleic acid molecules which are at least about 60% (or 65%, 75%, 85%, 95%, or 98%) identical to the nucleotide sequence of mouse TIMELESS (TIM) (SEQ ID NO:1). The invention also features isolated nucleic acid molecules which include a fragment of at least 100 (e.g., at least 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, or 3745) nucleotides of the nucleotide sequence of SEQ ID NO:1, or a complement thereof. The invention also features nucleic acid molecules which include a nucleotide sequence encoding a protein having an amino acid sequence that is at least about 60% (or 70%, 75%, 85%, 95%, or 98%) identical to the amino acid sequence of SEQ ID NO:2. In a preferred embodiment, the isolated nucleic acid molecule has the nucleotide sequence of SEQ ID NO: 1, or a complement thereof.

[0020] Also within the invention is an isolated polypeptide having an amino acid sequence that is at least about 60%, preferably 70%, 75%, 85%, 95%, or 98%, identical to the amino acid sequence of SEQ ID NO:2. Also within the invention are isolated polypeptides encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to the complement of SEQ ID NO: 1.

[0021] The invention also features isolated nucleic acid molecules which are at least about 60% (or 65%, 75%, 85%, 95%, or 98%) identical to the mouse Per2 upstream sequence (SEQ ID NO:3) containing a sequence controlling expression of mouse Per2. The invention also features isolated nucleic acid molecules which include a fragment of at least 100 (e.g., at least 200, 300, 400, 500, 600, 700, 800, 900, or 950) nucleotides of the nucleotide sequence of SEQ ID NO:3, or a complement thereof.

[0022] The invention also includes nucleic acid molecules that hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3. The nucleic acid molecules can be, for example, at least 20 (e.g. at least about 30, 40, 50, 70, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, or 3745) nucleotides in length.

[0023] Another aspect of the invention provides vectors, e.g., recombinant expression vectors, comprising a nucleic acid molecule described herein. The vector or nucleic acid molecule can be provided in a host cell. Such cells may be utilized for producing a polypeptide of the invention by culturing the cells in a suitable medium.

[0024] Also within the invention are a substantially pure preparation of a mouse or human TIM, a mouse or human CRY:PER heterodimer, a CRY:TIM heterodimer, and a mammalian CRY:CRY homodimer.

[0025] Isolated antibodies, which specifically bind to mouse CRY, mouse PER, mouse TIM, mouse BMAL-1 are also within the invention.

[0026] As used herein, “isolated DNA” means either DNA with a non-naturally occurring sequence or DNA free of the genes that flank the DNA in the genome of the organism in which the DNA naturally occurs. The term therefore includes a recombinant DNA incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote. It also includes a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment.

[0027] As used herein, an regulatory sequence which is “operably linked” to a second sequence (or vise versa) means that both are incorporated into a genetic construct so that the regulatory sequence effectively controls expression of a second sequence.

[0028] As used herein, a “substantially pure” protein refers to a protein which either (Klein et al., (1991). Suprachiasmatic nucleus: The Mind's Clock, Oxford University Press, New York. has a non-naturally occurring sequence (e.g., mutated, truncated, chimeric, or completely artificial), or (D. R. Weaver, J. Biol. Rhythms 13, 100 (1998) has a naturally occurring sequence but is not accompanied by or at least partially separated from, components that naturally accompany it. Typically, the protein is substantially pure when it is at least 60% (by weight) free from the proteins and other naturally-occurring organic molecules with which it is naturally associated. Preferably, the purity of the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight. A substantially pure protein can be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding the protein or by chemical synthesis. Purity can be measured by any appropriate method, e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. A chemically synthesized protein or a recombinant protein produced in a cell type other than the cell type in which it naturally occurs is, by definition, substantially free from components that naturally accompany it. Accordingly, substantially pure proteins include those having sequences derived from eukaryotic organisms but synthesized in E. coli or other prokaryotes.

[0029] As used herein, the term “vector” refers to a replicable nucleic acid construct. Examples of vectors include plasmids and viral nucleic acids.

[0030] As used herein, a “circadian protein” refers to a protein that participates in the circadian timing system and controls circadian rhythm. Examples of circadian proteins include PER, TIM, CLOCK, and BMAL-1.

[0031] As used herein, an antibody that “specifically binds” a mouse or human CRY, PER or TIM, respectively, is an antibody that binds only to mouse or human CRY, PER or TIM and does not bind to (i) other molecules in a biological sample or (ii) CRY, PER or TIM of another organism.

[0032] As used herein, a “therapeutically effective amount” is an amount of the nucleic acid of the invention which is capable of producing a medically desirable result in a treated animal.

[0033] As used herein, a “reporter gene” means a gene whose expression can be assayed.

[0034] As used herein, the terms “heterologous DNA” or “heterologous nucleic acid” is meant to include DNA that does not occur naturally as part of the genome in which it is present, or DNA which is found in a location or locations in the genome that differs from that in which it occurs in nature, or occurs extra-chromasomally, e.g., as part of a plasmid.

[0035] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. The preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present document, including definitions, will control. Unless otherwise indicated, materials, methods, and examples described herein are illustrative only and not intended to be limiting.

[0036] Various features and advantages of the invention will be apparent from the following detailed description and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0037]
FIG. 1 is a histogram showing dose-response studies on inhibition of CLOCK:BMAL-1-induced transcription by the mPER and mTIM proteins.

[0038] FIGS. 2A-2B are line graphs showing mouse Cry1 and Cry2 mRNA levels in SCN (FIG. 2A) and mouse Cry1 and Cry2 RNA levels in skeletal muscle (FIG. 2B).

[0039] FIGS. 3A-D is a histogram showing inhibition of CLOCK:BMAL1-mediated transcription from the vasopressin (AVP) promoter (FIGS. 3A, 3C-D) or mPer1 promoter (FIG. 3B) by mPER1, mCRY1 and mCRY2 (250 ng each).

[0040]
FIG. 4 is a schematic representation of epitope-tagged mouse CRY1 and CRY2 proteins evaluated for cellular location and inhibition of Clock:Bmal-1 mediated transcription.

[0041] FIGS. 5A-D are histograms depicting the specificity of mouse PER and mouse CRY in inhibiting transcription of Mop4:Bmal-1 mediated transcription.

[0042]
FIG. 6 is a representation of the nucleotide sequence of mouse TIM (SEQ. ID NO:1).

[0043]
FIG. 7 is a representation of the amino acid sequence of mouse TIM (SEQ. ID NO:2).

[0044]
FIG. 8 is a representation of the nucleotide sequence of the regulatory sequence of mouse Per2 (SEQ. ID NO:3).

[0045]
FIG. 9 is a line graph depicting temporal profiles of Bmal1 RNA levels in the SCN of wild type (solid) and Clock/Clock (dashed) mice. Each value is the mean±SEM of 5-9 animals. Data at CT 2, 3, 22, and 24 are double-plotted. Gray bar, subjective day; black bar, subjective night.

[0046]
FIG. 10 is a line graph depicting CLOCK mRNA levels in the SCN of wild-type (solid line) or Clock/Clock (dashed line) mice. Each value is the mean±SEM of 5-9 animals. Data at CT 2, 3, 22, and 24 are double-plotted. Gray bar, subjective day; black bar, subjective night.

[0047]
FIG. 11 is a line graph depicting temporal profiles of Bmal1 RNA levels in the SCN of wild-type (solid line) and mPER2Brdm1 mutant (dashed line) mice. Each value is the mean±SEM of 4 animals.

[0048]
FIG. 12 is a line graph depicting temporal profiles of mCry1 RNA levels in the SCN of wildtype (solid line) and mPER2Brdm1 mutant (dashed line) mice are shown. Each value is the mean±SEM of 4 animals.

[0049]
FIG. 13 is a schematic representation of different mPER2 constructs with a V5 epitope tagged at the carboxyl terminus of mPER2. Also shown is the cellular location of immunofluorescence of V5-tagged mPER2 constructs expressed in COS-7 cells either with (+) or without (−) mCRY1. The cellular location of immunofluorscence was scored as one of three categories: cytoplasm only (C), both cytoplasm and nucleus (B), or nucleus only (N). Values shown are the mean percentages from two experiments; all values were within 17% of the mean. Gray bars are PAS domain.

[0050]
FIG. 14 is a histogram depicting attenuated peak levels of Bmal1 RNA in mCry-deficient mice. Quantitation of Bmal1 RNA levels in the SCN of wild-type (solid bars) and mCry-deficient (open bars) mice. Values are the mean±SEM of 5 animals. Mice were studied on the first day in DD. * is the significance difference in Bmal1 RNA levels between CT 6 and CT 18 in wild-type mice; P<0.0001.

[0051]
FIG. 15 is a histogram depicting quantitation of Clock RNA levels in the SCN of wildtype (solid bars) and mCry-deficient (open bars) mice. Values are the mean±SEM of 5 animals.

[0052]
FIG. 16 is a histogram depicting the effects of mCRY proteins on transcriptional activation in Drosophila S2 cells. Values are luciferase activity expressed as relative to the response in presence of activators (100%). Each value is the mean±SEM of three replicates from a single assay.

[0053]
FIG. 17 is a histogram depicting the effects of mCRY proteins on transcriptional activation in COS-7 cells. Presence (+) or absence (−) of luciferase reporter (pGL3-Basic) (10 ng) and expression plasmids (0.25 ug mClock, shBmal1, hMop4, dclock; 0.1 ug mCry1, mCry2) is denoted. Values are luciferase activity expressed as relative to the response in presence of activators (100%). Each value is the mean±SEM of three replicates from a single assay. The results shown are representative of three independent experiments.

[0054]
FIG. 18 is a schematic drawing depicting a model of circadian clockwork within an individual SCN neuron.

DETAILED DESCRIPTION

[0055] It has been discovered that members of the mouse PER family (PER1, PER2, and PER3), the mouse CRY family (CRY1, and CRY2) and mouse TIM can interact directly with each other. The ability of these proteins to interact is critically involved in regulating circadian rhythm. More specifically, PER, CRY and TIM control circadian rhythm by inhibiting the transcriptional feedback loop which is at the heart of the mammalian circadian clock.

[0056] It was also discovered that PER2 positively regulates the transcription of Bmal-1, thereby controlling the rhythmic regulation of Bmal-1. BMAL1-1 functions as a positive regulator in the circadian loop. More specifically, BMAL-1 forms a heterodimeric protein with CLOCK, which heterodimer in turn positively regulates the expression of the circadian genes such as PER or CRY.

[0057] Based on the discovery made herein, the SCN clockwork is predicted to include three types of interacting molecular loops (FIG. 18). The Cry genes comprise one loop that has true autoregulatory, negative feedback features, with the protein products feeding back to turn off their transcription. The second loop is that manifested by each of the Per genes and some clock-controlled genes (CCGs) (for example, vasopressin prepropressophysin). This loop type is driven by the same positive elements (CLOCK(C):BMAL1(B)) as the CRY loop, but is not turned off by the respective gene products. Instead, these loops use the CRY proteins as negative regulators, leaving the generated protein products free to transduce other actions. For example, PER2 is used for the positive transcriptional regulation of the Bmal-1 gene. The rhythmic regulation of Bmal-1 comprises the third loop, whose rhythmicity is controlled by the cycling presence and absence of a positive element dependent upon mPER2. This positive feedback loop functions to augment the positive regulation of the first two loops.

[0058] This model of interacting loops proposes that at the start of the circadian day PER and CRY transcription are driven by accumulating CLOCK:BMAL1 heterodimers acting through E box enhancers. After a delay, the PER and CRY proteins are synchronously expressed in the nucleus where the CRY proteins shut off Clock:Bmal1-mediated transcription by directly interacting with these transcription factors. At the same time that the CRY proteins are inhibiting Clock:Bmal-1-mediated transcription, PER2 either shuttles a transcriptional activator into the nucleus or coactivates a transcriptional complex to enhance Bmal-1 transcription. The importance of the Bmal-1 RNA rhythm is to drive a Bmal-1 rhythm after a 4 to 6 hour delay. This delay in the protein rhythm would provide increasingly available CLOCK:BMAL1 heterodimers at the appropriate circadian time to drive Per and Cry transcription, thereby restarting the cycle. It is thus predicted that BMAL-1 availability is rate limiting for heterodimer formation and critical for restarting the loops.

[0059] TIM Nucleic Acid Molecules

[0060] The invention pertains to isolated nucleic acid molecules that encode mouse TIM proteins or biologically active portions thereof, as well as nucleic acid molecules which can serve as hybridization probes to identify TIM-encoding nucleic acids (e.g., TIM mRNA), or as PCR primers for the amplification or mutation of TIM nucleic acid molecules. The nucleic acid encoding mouse TIM (SEQ ID NO:1) (and/or the complement of that nucleic acid) can be used as a probe to identify nucleic acids related to the mouse TIM gene, e.g., other naturally occurring mammalian TIM DNA's.

[0061] Fragments of SEQ ID NO:1 and its complement can be used as probes or primers, so long as they are at least 10, and preferably at least 15 (e.g., at least 18, 20, 25, 50, 100, 150, or 200) nucleotides in length. TIM probes and primers can be produced using any of several standard methods (see, e.g., Ausubel et al., 1989, Current Protocols in Molecular Biology, Vol. 1, Green Publishing Associates, Inc., and John Wiley & Sons, Inc., NY). For example, the probe can be generated using PCR amplification methods in which oligonucleotide primers are used to amplify a portion of SEQ ID NO:1 that can be used as a specific probe. Such probes and primers are part of the invention.

[0062] Hybridization under stringent conditions can be used to identify nucleic acid sequences which encode mouse TIM or other related TIMs, e.g., other mammalian TIM proteins. A related nucleic acid sequence has at least 50% sequence identity to mouse TIM cDNA (SEQ ID NO:1). Standard hybridization conditions (e.g., moderate or highly stringent conditions) are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6, hereby incorporated by reference. Moderate hybridization conditions are defined as equivalent to hybridization in 2×sodium chloride/sodium citrate (SSC) at 30° C., followed by one or more washes in 1×SSC, 0.1% SDS at 60° C. Highly stringent conditions are defined as equivalent to hybridization in 6× sodium chloride/sodium citrate (SSC) at 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C.

[0063] Nucleic acids which hybridize to the above-described probes under stringent conditions can be used as probes themselves to analyze the expression of mouse TIM mRNA in the SCN. These nucleic acids can also be used to express mouse TIM polypeptides or immunogenic fragments thereof for raising mouse TIM antibodies.

[0064] Genomic fragments of the TIM locus that are hybridizable to the above-described probes are also included in the invention. Such fragments are useful starting materials for generating, e.g., knockout constructs that are used to create non-human transgenic mammals containing null mutations at the TIM locus.

[0065] The invention further encompasses nucleic acid molecules that differ from the nucleotide sequence of SEQ ID NO:1 due to degeneracy of the genetic code, and thus encode the same TIM protein as that encoded by the nucleotide sequence shown in SEQ ID NO:1.

[0066] Mutations which change the nucleotide sequence of SEQ ID NO:1 without altering the functional activity of the TIM protein are also within the scope of the invention. For example, one can make nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues. A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of mouse TIM (e.g., the sequence of SEQ ID NO:2) without altering the biological activity, whereas an “essential” amino acid residue is required for biological activity. For example, amino acid residues that are conserved among the TIM proteins of various species are predicted to be particularly unamenable to alteration. These can be identified by sequence comparison among the known TIM proteins (yeast, Drosphylia and now, mouse) Thus, the invention encompasses nucleic acid molecules encoding mouse TIM proteins that contain changes in amino acid residues that are not essential for activity. Such TIM proteins differ in amino acid sequence from SEQ ID NO:2, yet retain biological activity.

[0067] An isolated nucleic acid molecule encoding a TIM protein having a sequence which differs from that of SEQ ID NO:2 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO:1 such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Generally, additions or deletions of nucleotides will be done in multiples of three, so as to avoid a frame shift.

[0068] TIM Polypeptides

[0069] A mouse TIM polypeptide can be isolated and purified from a natural source. Alternatively, it can be produced recombinantly or chemically synthesized by conventional methods. A TIM polypeptide, full-length or truncated, can also be part of a fusion protein, for example, by linking it to an antigenic determinant to facilitate purification. The TIM polypeptides can be prepared for a variety of uses, e.g., generation of antibodies which can be used to detect TIM, and in screening assays which identify compounds that disrupt the association of TIM with CRY.

[0070] Techniques for generating substantially pure polypeptide preparations are well known in the art. A typical method involves transfecting host cells (e.g., bacterial cells such as E. coli, or mammalian cells such as COS7) with an expression vector carrying a nucleic acid that encodes a mouse TIM protein. The recombinant polypeptide so produced can be purified from the culture medium or from lysates of the cells.

[0071] Conventional site-directed mutagenesis techniques can be applied to a TIM coding sequence, e.g., SEQ ID NO:1, to generate TIM sequence variants optimized for expression in a given type of host cell.

[0072] Furthermore, one skilled in the art can prepare not only a natural mouse TIM protein with a naturally occurring sequence (SEQ ID NO:2), but also proteins with substantially the same function as that of the natural protein, by replacing amino acids in the protein. Methods for amino acid alteration include, for example, a site-directed mutagenesis system using PCR (GIBCO-BRL, Gaithersburg, Md.); the oligonucleotide-mediated site-directed mutagenesis method (Kramer, Methods in Enzymol. 154:350-367 1997); and the Kunkel method (Methods Enzymol. 85:2763-2766, 1988). Usually ten or fewer, preferably six or fewer, and more preferably three or fewer amino acids (e.g., one or two) are substituted. Proteins functionally equivalent to the TIM protein can be produced by conservative amino acid substitutions at one or more amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a chemically similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).

[0073] Biologically active portions of a mouse TIM protein include peptides comprising amino acid sequences identical to or derived from the amino acid sequence of the mouse TIM protein (e.g., the amino acid sequence shown in SEQ ID NO:2).

[0074] A TIM protein that has a high sequence identity to SEQ ID NO:2 is also included in the invention. A useful TIM protein has an amino acid sequence at least 60% identical, preferably at least 70%, more preferably at least 80%, and even more preferably at least 90, 95, 96, 97, 98 or 99% identical to the amino acid sequence of SEQ ID NO:2, and retains the functional activity of the TIM protein of SEQ ID NO:2.

[0075] To determine the percent sequence identity of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=# of identical positions/total # of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length.

[0076] To determine percent homology between two sequences, the algorithm of Karlin and Altschul (Proc. Natl. Acad. Sci. USA 87:2264-2268, 1990), modified as in Karlin and Altschul (Proc. Natl. Acad. Sci. USA 90:5873-5877, 1993), is used. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (J. Mol. Biol. 215:403-410, 1990. BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the invention. BLAST protein searches are performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to mouse TIM protein. To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul et al. (Nucleic Acids Res. 25:3389-3402, 1997). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are used. See http://www.ncbi.nlm.nih.gov.

[0077] Per2 Regulatory Sequence

[0078] The invention pertains to an isolated genomic nucleic acid molecule that includes the mouse Per2 regulatory sequence (promoter/enhancer sequence), as well as nucleic acid molecules which can serve as hybridization probes to identify a Per2 regulatory sequence, or as PCR primers for the amplification or mutation of a Per2 regulatory sequence.

[0079] Fragments of mouse Per2 regulatory sequence (SEQ ID NO:3) and its complement can be used as probes or primers, so long as they are at least 10, and preferably at least 15 (e.g., at least 18, 20, 25, 50, 100, 150, or 200) nucleotides in length. PER2 regulatory sequence probes and primers can be produced using any of several standard methods described above. For example, the probe can be generated using PCR amplification methods in which oligonucleotide primers are used to amplify a portion of SEQ ID NO:3 that can be used as a specific probe.

[0080] Other uses for the Per2 regulatory sequence include use as a starting material for generating, e.g., knockout constructs that are used to create non-human transgenic marnmals that contain a disruption in the Per2 regulatory sequence and that are unable to express Per2. Alternatively, the Per2 regulatory sequence may be operably linked to a DNA sequence encoding a polypeptide that is not PER2 (i.e., a heterologous polypeptide).

[0081] Hybridization under stringent conditions can be used to identify nucleic acid sequences that contain a regulatory sequence of mouse PER2, or other related PER2 regulatory seqeuences. A related nucleic acid sequence has at least 50% sequence identity to mouse PER2 regulatory sequence (SEQ ID NO:3). Standard hybridization conditions are described above.

[0082] Circadian Proteins

[0083] The invention includes screening methods which are used to identify compounds which can disrupt the association of mammalian circadian proteins, e.g., the association of TIM with CRY, CRY with CRY, CRY with PER, CRY with BMAL-1, and CRY with CLOCK:BMAL-1. The invention also features antibodies generated against CRY, PER, and TIM proteins. These various uses require a source of CRY, TIM, PER, CLOCK, BMAL-1, and CLOCK:BMAL-1.

[0084] Circadian proteins can be isolated and purified from a natural source. Alternatively, the proteins can be produced recombinantly or chemically synthesized by conventional methods. Typically the proteins will be produced recombinantly. The nucleotide and amino acid sequences of the circadian proteins are publicly available to one skilled in the art, e.g., mouse CRY1 (Genbank accession # AB000777), mouse CRY2 (Genbank Accession # AB003433), mouse TIM (Genbank accession # AF071506), mouse PER3 (Genbank accession # AF050182), CLOCK (Genbank accesssion # AF000998) and BMAL-1 (Genbank accession # AB015203).

[0085] Methods of generating a recombinant circadian protein or a recombinant circadian fusion protein, e.g., CLOCK:GST, are well known in the art. For example, the circadian proteins can be generated by cloning the nucleic acid sequence encoding a circadian protein into an expression vector, where it is operably linked to one or more regulatory sequences. The need for, and identity of, regulatory sequences will vary according to the type of cell in which the circadian protein sequence is to be expressed. Examples of regulatory sequences include transcriptional promoters, enhancers, suitable mRNA ribosomal binding sites, and sequences that terminate transcription and translation. Suitable regulatory sequences can be selected by one of ordinary skill in the art. Standard methods can be used by the skilled person to construct expression vectors. See, generally, Sambrook et al., 1989, Cloning—A Laboratory Manual (2nd Edition), Cold Spring Harbor Press.

[0086] Vectors useful in this invention include plasmid vectors and viral vectors. Viral vectors can be those derived from, for example, retroviruses, adenovirus, adeno-associated virus, SV40 virus, pox viruses, or herpes viruses. Once introduced into a host cell (e.g., bacterial cell, yeast cell, insect cell, or mammalian cell), the vector can remain episomal, or be incorporated into the genome of the host cell.

[0087] In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the gene product being expressed. For example, when a large quantity of such a protein is to be produced, e.g., for studying the interaction of a CRY protein with other proteins or for raising antibodies to the protein, a vector capable of directing the expression of high levels of a fusion protein (e.g., a GST fusion protein) that is readily purified may be desirable. Alternatively, in mammalian host cells, a number of viral-based expression systems can be utilized.

[0088] Construction of GST Fusion Proteins

[0089] In certain screening assays (see below) it may be desirable to immobilize the circadian protein. One method of immobilizing a circadian protein is to express the protein as a fusion protein with GST. To do this a chimeric gene encoding a GST fusion protein can be constructed by fusing DNA encoding a circadian protein to the DNA encoding the carboxyl terminus of GST (see e.g., Smith et al., Gene 67:31, 1988). The fusion construct can be transformed into a suitable expression system, e.g., E. coli XA90 in which expression of the GST fusion protein can be induced with isopropyl-β-D-thiogalactopyranoside (IPTG).

[0090] Purification of GST Fusion Proteins

[0091] After transformation of the construct into a suitable expression system, induction with IPTG should yield the fusion protein as a major constituent of soluble, cellular proteins. The fusion proteins can be purified by methods known to those skilled in the art, including purification by glutathione affinity chromatography. The purity of the product can be assayed by methods known to those skilled in the art, e.g., gel electrophoresis.

[0092] Binding of Circadian Proteins to Immobilized GST

[0093] GST fusion proteins can be complexed to glutathione which is attached to a matrix material, e.g., glutathione Sepharose, by methods known to those skilled in the art.

[0094] Antibodies

[0095] Antibodies which specifically bind to mouse or human CRY, mouse or human TIM, or mouse or human PER, or mouse or human BMAL-1 are also included in the invention. An antibody that specifically binds a mouse or human CRY, PER, TIM, or BMAL-1 is an antibody that binds only to mouse or human CRY, PER, TIM or BMAL-1 and does not bind to (i) other molecules in a biological sample or (ii) CRY, PER, TIM or BMAL-1 of another organism (e.g., Drosophila or yeast).

[0096] Antibodies against mouse or human CRY, PER, TIM or BMAL-1 can be used, for example, to inhibit the interaction between these circadian proteins. Anti-CRY, -TIM or PER antibodies (e.g., monoclonal antibodies) can also be used to isolate a CRY, TIM or -PER protein using techniques well known in the art, such as affinity chromatography or immunoprecipitation. The antibodies are also useful in the screening assays described below. Compounds bound to the immunopreceipitated protein can then be identified.

[0097] Antibodies specific for mouse CRY, TIM, PER or BMAL-1 can be raised by immunizing a suitable subject (e.g., rabbit, goat, mouse or other mammal) with an immunogenic preparation which contains the mouse or human CRY, TIM, PER or BMAL-1 protein. An appropriate immunogenic preparation can contain, for example, a recombinantly expressed or chemically synthesized CRY, or an immunogenic fragment thereof. The preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic CRY, TIM, PER or BMAL-1 preparation induces a polyclonal anti-CRY, TIM, PER or BMAL-1 antibody response.

[0098] The term antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab′)2 fragments, which can be generated by treating the antibody with an enzyme such as pepsin. The term monoclonal antibody or monoclonal antibody composition refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of the polypeptide. A monoclonal antibody composition thus typically displays a single binding affinity for the CRY, TIM or PER with which it immunoreacts.

[0099] Polyclonal anti-CRY, -TIM or -PER antibodies can be prepared by immunizing a suitable subject with a mouse CRY, TIM or PER immunogen. The anti-CRY, -TIM or -PER antibody titer in the immunized subject can be monitored over time by well known techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized polypeptide. If desired, the antibody molecules directed against CRY, TIM, PER or BMAL-1 can be isolated from the mammal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography, to obtain the IgG fraction.

[0100] Monoclonal antibodies can be generated by immunizing a subject with an immunogenic preparation containing a CRY, TIM, PER or BMAL-1. At an appropriate time after immunization, e.g., when the anti-CRY, -TIM, -PER or BMAL-1 antibody titers are highest, antibody-producing cells are obtained from the subject and used to prepare monoclonal antibodies by techniques well known in the art, such as the hybridoma technique originally described by Kohler et al., Nature 256:495-497, 1975, the human B cell hybridoma technique (Kozbor et al., Immunol Today 4:72, 1983), the EBV-hybridoma technique (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing monoclonal antibody hybridomas is well known (see generally Current Protocols in Immunology (1994) Coligan et al. (eds.) John Wiley & Sons, Inc., New York, N.Y.). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with a CRY, TIM, PER or BMAL-1, immunogen as described above, and the culture supernatant of the resulting hybridoma cells that screened to identify a hybridoma producing a monoclonal antibody that binds the CRY, TIM, PER or BMAL-1.

[0101] The anti-CRY, -TIM, -PER or BMAL-1 antibody may be coupled to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, and acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride and phycoerythrin; an example of a luminescent material is luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive materials include 125I, 131I, 35S and 3H.

[0102] Screening Assays

[0103] The invention encompasses methods for identifying compounds that bind to CRY; disrupt the association of TIM:CRY, CRY:CRY, CRY:PER, CRY:BMAL-1, and CRY:CLOCK:BMAL-1; inhibit or activate the transcription of Per2; or positively regulate the transcription of Bmal-1. Candidate compounds that can be screened in accordance with the invention include polypeptides, oligopeptides, antibodies, and monomeric organic compounds, i.e., “small molecules.”

[0104] Identification of a Compound that Binds to CRY

[0105] A useful first step to identifying a compound which disrupts the association between different circadian proteins (e.g., TIM:CRY, CRY:CRY, CRY:PER, CRY:BMAL-1,and CRY:CLOCK:BMAL-1) is to identify a compound that binds to CRY or another circadian protein. Once a circadian binding compound is identified, the ability of the compound to disrupt the association of different circadian proteins can be assayed. Below are a number of assays which can be used to identify a compound which binds to a CRY protein, e.g., CRY1 or CRY2. The examples are not meant to be limiting and the assays can be performed with other circadian proteins, e.g., TIM, PER, CLOCK and BMAL-1.

[0106] Methods of identifying a compound which binds a protein of interest are well known in the art. In one screening method, test compounds are evaluated for their ability to bind CRY, e.g., CRY1 or CRY2. Control reactions which do not contain the compound can be performed in parallel. The method includes immobilizing CRY using methods known in the art such as binding a GST-CRY to a polymeric bead containing glutathione or binding a CRY protein to an anti-CRY antibody which is attached to a solid support. The immobilized CRY is incubated with a test compound for a period of time that permits binding of the test compound to CRY. Following the incubation period, unbound test compound is removed and bound test compound detected. For example, a detectable moiety such as a radionuclide or a fluorescent label can be attached to the compound for ease of detection. Examples of radionuclide and fluorescent labels include 125I, 131I, 35S, 3H, umbelliferone, fluorescein, fluorescein isothiocyanate, and rhodamine.

[0107] Alternatively, the screening method can involve incubating a labeled test compound, with an epitope-tagged CRY protein. Following incubation, the ability of the test compound to bind to the CRY protein is determined using immunoprecipitation with an antibody directed against the epitope tag (e.g., Flag or myc). The recovery of a labeled test compound, e.g., a radioactive compound, following immunoprecipitation indicates that the test compound binds to the CRY protein.

[0108] Display libraries can also be used to identify compounds which bind to a CRY protein. In this approach, the test peptides are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind an appropriate CRY protein, e.g., CRY1 or CRY2, via the displayed product can be detected in a “panning assay” (Ladner et al., WO 88/06630).

[0109] Identifying Compounds which Disrupt the Interaction of CRY:TIM, CRY:CRY CRY:PER, CRY:BMAL-1, and CRY:CLOCK:BMAL-1

[0110] The two-hybrid expression system can be used to screen for compounds capable of disrupting CRY:TIM, CRY:CRY, CRY:PER, CRY:BMAL-1, or CRY:CLOCK:BMAL-1 associations in vivo. In this system, a GAL4 binding site, linked to a reporter gene such as lacZ, is contacted in the presence and absence of a test compound with a GAL4 binding domain linked to a circadian protein, e.g., CRY, TIM, PER, CLOCK or BMAL-1 and a GAL4 transactivation domain linked to a circadian protein, e.g., CRY, TIM, PER, CLOCK, or BMAL-1. Expression of the reporter gene is monitored and a decrease in said expression is an indication that the test compound inhibits the interaction of CRY with TIM, CRY with CRY, CRY with PER, CRY with BMAL-1, or CRY with CLOCK:BMAL-1.

[0111] Another method of identifying compounds which disrupt an association between circadian proteins involves the determination of whether the test compounds can disrupt the ability of, e.g., CRY:PER, to block CLOCK:BMAL-1-mediated transcriptional activation. In this system, an E-box sequence linked to a reporter gene such as a luciferase gene is contacted with a CLOCK:BMAL-1 heterodimer. Binding of the CLOCK:BAML-1 heterodimer to the E-box results in expression of the reporter gene. The system is then contacted with a test compound and a circadian protein (e.g., a CRY protein or a circadian protein complex, e.g., CRY:PER), and expression of the reporter gene is monitored. Since CRY and PER block CLOCK:BMAL-1-mediated transcription, an increase in expression of the reporter gene in the presence of the test compound as compared to the expression in the absence of the compound indicates that the compound disrupts the ability of CRY and PER to block CLOCK:BMAL-1-mediated transcription. The transcription assay can be preformed in any cell that expresses the necessary proteins, either naturally or recombinantly, e.g., NIH 3T3 cells, COS-7 cells, or clock neuron cells.

[0112] In yet another screening method, one of the components of the CRY:TIM, CRY:CRY, CRY:PER, CRY:BMAL-1, or CRY:CLOCK:BMAL-1 binding complex is immobilized. The circadian protein can be immobilized using methods known in the art, such as adsorption onto a plastic microtiter plate or specific binding of a GST-fusion protein to a polymeric bead containing glutathione. For example, to determine a compound which binds CRY:PER, a GST-CRY can be bound to glutathione-Sepharose beads. The immobilized CRY is then contacted with a labeled circadian protein to which it binds (PER in this case) in the presence and absence of a test compound. Unbound PER can then be removed and the complex solubilized and analyzed to determine the amount of bound labeled PER. A decrease in binding is an indication that the test compound inhibits the interaction of CRY with PER.

[0113] A variation of the above-described screening method involves screening for test compounds which are capable of disrupting a previously-formed CRY:TIM, CRY:CRY, CRY:PER, CRY:BMAL-1, or CRY:CLOCK:BMAL-1 interaction. For example, a complex comprising CRY:PER is immobilized as described above and contacted with a test compound. The disassociation of the complex by the test compound correlates with the ability of the test compound to disrupt or inhibit the interaction of CRY with PER.

[0114] Identifying Compounds that Activate Transcription of PER2

[0115] A screening method used to identify a compound that activates or inhibits the transcription of Per2 includes providing a cell that includes a Per2 regulatory sequence operatively linked to a reporter gene. The Per2 regulatory sequence is preferably mammalian, e.g., mouse PER2 (SEQ ID NO:3; see FIG. 8). In one example, the mouse Per2 regulatory sequence is operably linked to a reporter gene such as a luciferase, a chloramphenicol acetyl transferase, a beta-galactosidase, an alkaline phosphate, or a fluorescent protein gene. A test compound is then contacted with the cell and expression of the reporter gene monitored. An increase in expression of the reporter gene in the presence of the test compound as compared to the expression in the absence of the compound indicates that the compound activates Per2 transcription. Alternatively, a decrease in expression of the reporter gene in the presence of the test compound as compared to expression in the absence of the test compound indicates that the compound inhibits Per2 transcription. The transcription assay can be preformed in any cell which undergoes a circadian rhythm, e.g., NIH 3T3 cells, COS-7 cells, or clock neuron cells.

[0116] Identifying Compounds that Positively Regulate Expression of BMAL-1

[0117] A screening method that uses a non-human transgenic animal whose somatic and germ cells comprise a disrupted Per2 gene can be used to identify a compound that regulates expression of Bmal-1. The method includes administering a test compound to the transgenic mouse and detecting Bmal-1 expression. An increase in expression of Bmal-1, compared to a control non-human transgenic animal, indicates that the compound positively regulates expression of Bmal-1. Expression of Bmal-1 can be detected using any appropriate method, e.g., detecting Bmal-1 mRNA levels using Northern blot analysis or BMAL-1 protein levels using a BMAL-1 specific antibody or an activity assay.

[0118] The transgenic non-human animal used in the method described above includes a non-human animal that contains a disruption in the Per2 gene that is sufficient to inhibit the ability of PER2 to positively regulate Bmal-1. A transgenic non-human animal is preferably a mammal such as a rat or mouse, in which one or more of the cells of the animal include a disruption in the Per2 gene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. The transgenic non-human animal is one in which the Per2 gene has been altered, e.g., by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal. Appropriate PER2 transgenic animals which can be used in the method described above are known in the art, e.g., the homozygous mPer2brdm1 described by Zheng et al. (Nature, 400:1667 (1999)) the contents of which are incorporated herein by reference.

[0119] Modulating the Circadian Clock

[0120] Based on the discoveries described herein, it is apparent that expression of Bmal-1 is critical for restarting the circadian loop. The importance of Bmal-1 mRNA rhythm is to drive a Bmal-1 rhythm after a four to six hour delay in the circadian loop. The expression of Bmal-1 makes BMAL-1 available to heterodimerize with CLOCK to drive transcription of circadian proteins, such as Per or Cry. The transcription of Per or Cry restarts the cycle. Therefore, a method of modulating a circadian-clock controlled rhythm includes, for example, altering the endogenous expression of Bmal-1. In one example, an effective amount of a ribozyme, or an oligouncleotide antisense to Bmal-1, can be introduced into a SCN in vivo, thereby inhibiting expression of Bmal-1 in the cell and modulating circadian-clock rhythms.

[0121] Antisense Bmal-1 nucleic acid molecules include molecules which are complementary to a sense nucleic acid encoding a BMAL-1 protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to a mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. Antisense Bmal-1 nucleic acids can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to full length Bmal-1 mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the Bmal-1 mRNA, e.g., part or all of the transcription start site, and/or part or all of the coding region. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.

[0122] The Bmal-1 antisense nucleic acid molecules are typically administered to a subject such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein to thereby inhibit Bmal-1 expression of the protein. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to clock neuron cell surface receptors or antigens. In another example, the antisense nucleic acid molecule is linked to TAT, a HIV leader sequence, that can target the antisense to the SCN (Lisziewicz et al., Hum Gene Ther 11:807-15, 2000).

[0123] Alternatively, an expression vector encoding BMAL-1 protein can be introduced into a clock neuron using gene therapy methods. For example, methods of targeting a vector containing a Bmal-1 sequence into an SCN include using a gene therapy vector which includes a tat sequence operably lined to a Bmal-1 nucleic acid sequence. Expression of TAT targets the vector to the SCN.

[0124] The gene therapy expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which a mammalian BMAL-1 is operably linked to an appropriate regulatory sequence. Examples of suitable viral vectors include recombinant retroviral vectors (Valerio et al., 1989, Gene, 84:419; Scharfman et al., 1991, Proc. Natl. Acad. Sci., USA, 88:462; Miller, D. G. & Buttimore, C., 1986, Mol. Cell. Biol., 6:2895), recombinant adenoviral vectors (Freidman et al., 1986, Mol. Cell. Biol., 6:3791; Levrero et al., 1991, Gene, 101:195), and recombinant Herpes simplex viral vectors. The regulatory sequence can be the same as the endogenous regulatory sequence, or different. It can be inducible or constitutive. Suitable constitutive regulatory sequences include the regulatory sequence of a housekeeping gene such as the α-actin regulatory sequence, or may be of viral origin such as regulatory sequences derived from mouse mammary tumor virus (MMTV) or cytomegalovirus (CMV).

[0125] Utility of the Compounds

[0126] Compounds found to disrupt the interaction of CRY:TIM, CRY:CRY, CRY:PER, CRY:BMAL-1, or CRY:CLOCK:BMAL-1 or bind to CRY can be used to manipulate the circadian clock. For example, the association of PER with CRY in the cytoplasm of a clock neuron is necessary for the translocation of PER into the nucleus of the cell. Once PER is in the nucleus, PER has a negative feedback effect on the circadian loop, i.e., inhibits CLOCK:BMAL-1-mediated transcription. A compound which disrupts the ability of CRY and PER to associate in the cytoplasm would prevent the translocation of PER to the nucleus and would therefore be useful for blocking PER's negative feedback effect on the circadian loop. Similarly, a compound that binds to CRY is potentially useful for blocking CRY's negative feedback effect on the circadian loop.

[0127] Compounds that can modulate the transcription of the Per2 gene can be used to advance or delay restarting the circadian loop. For example, a compound that inhibits transcription of Per2 will inhibit the transcription of Bmal-1. Since BMAL-1 is needed to restart the circadian loop, a compound that inhibits transcription of Per2 will inhibit the restarting of the circadian loop. Moreover, delivery of an expression vector encoding a mammalian Bmal-1 protein to a clock neuron can also be used to manipulate the circadian rhythm and advance restarting of the circadian loop.

[0128] A compound identified as described above is therefore useful as an agent that can reset the circadian clock. The compound can be used to prevent jet lag or facilitate resetting the clock in shift workers. In addition, the compound can be used to improve rhythmicity, i.e., the co-ordinated regulation of outputs from cells within the SCN. Disruption of rhythmicity is common in the elderly and affects the ability to sleep. The compound described herein can be used to improve the interactions between neurons to allow them to arrive at a common phase or directly reset individual neurons to a common phase. Compounds can also be used to alleviate circadian rhythm disorders such as winter depression or seasonal affective disorder.

[0129] Administration

[0130] The compounds described herein can be administered to a subject, e.g., a mammal such as a human, to treat a circadian rhythm disorder, e.g., jet lag, winter depression and shift work disturbance. The compounds can be used to specifically advance or delay the phase of certain circadian rhythms. The ability of a compound to reset the clock to a specified phase will depend on the nature of the agent and its biological half-life.

[0131] The compound can be administered alone, or in a mixture, in the presence of a pharmaceutically acceptable excipient or carrier (e.g., physiological saline). Given that the different CRY and PER proteins are redundant, it is preferable that the compound administered have the specificity to affect all members of a given family, e.g., CRY1 and CRY2 (CRY protein family members) or PER1, PER2 or PER3 (PER protein family members). Alternatively, a combination of compounds specific for each member of a family can be administered.

[0132] Gene therapy vectors can be delivered to a subject by, for example, intravenous injection or local administration (see U.S. Pat. No. 5,328,470). The pharmaceutical preparation of the gene therapy vector will typically include the gene therapy vector in an acceptable carrier.

[0133] The excipient or carrier is selected on the basis of the mode and route of administration. Suitable pharmaceutical carriers, as well as pharmaceutical necessities for use in pharmaceutical formulations, are described in Remington's Pharmaceutical Sciences (E. W. Martin), a well known reference text in this field, and in the USP/NF (United States Pharmacopeia and the National Formularly). A pharmaceutical composition is formulated to be compatible with its intended route of administration. Examples of routes of administration include oral, rectal, and parenteral, e.g., intravenous, intradermal, and subcutaneous, transdermal (topical), and transmucosal, administration. Compounds which are unable to cross the blood-brain barrier are administered locally to the SCN.

[0134] As is well known in the medical arts, dosage for any given patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Dosages for the compounds of the invention will vary, but determination of optimal dosage is well within the abilities of a pharmacologist of ordinary skill.

[0135] Transgenic Animals

[0136] Based on the discovery made herein, Tim is predicted to be essential for embryonic development in animals. In order to delineate the region(s) of Tim essential for development, the invention includes non-human transgenic animals that have a selected region of Tim disrupted. The role of this region in embryonic development can be determined by analyzing homozygous embryos for developmental defects, e.g., determining cellular organization in whole embryos that are fixed and embedded in paraffin around embryonic day 7.5.

[0137] Transgenic non-human animals that have a Tim disruption are also useful for screening for compounds that ameliorate the developmental defects caused by the disruption of Tim, e.g., a test compound can be administered to a female Tim+/Tim− heterozygote non-human animal during and/or subsequent to mating with a male Tim+/Tim−0 heterozygote of the same species. The ability of the test compound to ameliorate Tim-associated defects occurring during embryonic development can be determined by analyzing Tim− homozygous embryos for developmental defects, e.g., determining cellular organization in whole embryos that are fixed and embedded in paraffin around embryonic day 7.5.

[0138] Transgenic Tim animals which overexpress TIM are also be useful for studying the function and/or activity of a TIM protein in circadian rhythm. For example, transgenic non-human animals are generated where an endogenous Tim regulatory element, e.g., a promoter, is replaced with an exogenous regulatory element such that the exogenous regulatory element drives a higher level of expression of TIM in a cell of the transgenic animal as compared to a non-transgenic animal. The cell is preferably a neuron. The role of TIM in circadian rhythm in the transgenic animal can be determined by analyzing circadian rhythms in locomoter activity, e.g., rhythmic wheel turning.

[0139] As used herein, a “transgenic animal” is a non-human animal, the nucleated cells of which include a transgene. The animal is preferably a mammal, e.g., a rodent such as a rat or mouse. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, rabbits, amphibians, and the like. A transgene is exogenous DNA or a rearrangment, e.g., a deletion of endogenous chromosomal DNA, which is integrated into or occurs in the genome of the animal's cells. A transgene can direct the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. Other transgenes, e.g., a knockout, reduce expression. Thus, a transgenic animal can be one in which an endogenous Tim gene has been altered, e.g., by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal. The animal can be heterozygous or homozygous for the transgene.

[0140] Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequence(s) can be operably linked to a transgene of the invention to direct expression of a TIM protein in particular cells. A transgenic founder animal can be identified based upon the presence of a TIM transgene in its genome and/or expression of TIM mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding a TIM protein can further be bred to other transgenic animals carrying other transgenes.

[0141] TIM proteins or polypeptides can be expressed in transgenic animals or plants, e.g., a nucleic acid encoding the protein or polypeptide can be introduced into the genome of an animal. In preferred embodiments, the nucleic acid is placed under the control of a tissue specific promoter, e.g., a milk or egg specific promoter, and recovered from the milk or eggs produced by the animal. Suitable animals are mice, pigs, cows, goats, sheep, and chickens.

[0142] The invention also includes a population of cells from a transgenic animal, as discussed herein.

[0143] Any technique known in the art may be used to generate the transgene non-human animals discussed herein. For a review, see Gordon, 1989, Transgenic Animals, Intl. Rev. Cytol. 115:171-229 and Hogan et al. “Manipulating the Mouse Embryo” (Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1986.

[0144] Experimental Information

EXAMPLE 1

[0145] mPER Proteins Interact in Mammalian Cells

[0146] The importance of mPER:mPER interactions in the negative limb of the clock feedback loop was examined. Previous studies using the yeast two-hybrid assay showed that all of the mPERs interact with one another and that mPER1 and mPER2 can homodimerize (Zylka et al., Neuron 21:1103-1115, 1998). No interactions were detectable between mTIM and any of the mPER proteins in the yeast system. Co-immunoprecipitation experiments were performed in mammalian cells using epitope-tagged proteins expressed in COS7 cells.

[0147] Expression plasmids were constructed that contain full-length coding regions for each mPER protein and mTIM with either a hemaglutinin (HA) or a V5 epitope tag at the carboxyl terminus. For cloning, the coding regions of mPER2 (AF035830), mPER3 (AF050182), and mTIM (AF071506) were ligated into pcDNA 3.1 containing either an N terminal or C terminal HA tag. Full-length coding regions were amplified with Pfu TurboJ (Stratagene, La Jolla, Calif.) from plasmid DNA (mPER1). Correct orientation of each construct was verified by sequence analysis. Clones were also transcribed and translated in vitro using TnT T7 QuickJ (Promega, Madison, Wis.) to confirm that a protein of the correct size was produced. Moreover, clones were transiently transfected into NIH3T3 cells and into COS7 cells. Crude cell extracts were prepared, western blotted and probed with anti-V5 or anti-HA antibodies to detect full-length, epitope-tagged proteins.

[0148] Once the constructs were generated, COS7 cells were transiently cotransfected with expression plasmids encoding mPER3-HA and either mPER1-V5, mPER2-VS, mPER3-V5, or mTIM-VS. Cell lysates were immunoprecipitated with anti-HA antibody, and the immunoprecipitated material was blotted and probed with anti-V5 antibodies to assess interactions. Briefly, co-immunoprecipitations were performed as described by Lee and colleagues (Neuron 21:857-867, 1998) with the following modifications. COS7 cells (5×106) were seeded in 10 cm dishes and transfected the following day with the expression plasmids described above. Forty-eight hours post transfection, the cells were washed twice with PBS, homogenized in binding buffer (20 mM HEPES, pH 7.5, 100 mM KCl, 2.5 mM EDTA, 5 mM DTT, 2.5 mM PMSF, 0.05% Triton X-100, 10% glycerol, 10 μg/ml leupeptin, 10 μg/ml aprotonin) and clarified by centrifugation. Protein concentrations were determined by the Bradford method according to the manufacturer's instructions (Pierce, Iselm, N.J.). Total protein (30 μg) from the clarified supernatant was combined with 15 μl of protein A/G agarose beads (Santa Cruz Biotechnology, Santa Cruz, Calif.) and incubated for 1 hr at 4EC to remove non-specific interactions. The samples were centrifuged and the supernatant was incubated for 3 hrs at 4EC with anti-HA mouse monoclonal antibodies (Babco, 1:50 dilution) and 15 μl of protein A/G agarose beads. Subsequently, the beads were washed four times (400 μl binding buffer for 10 min. per wash), mixed with 5 μl of 4×sodium dodecyl sulfate (SDS) gel loading buffer, boiled, and centrifuged. The supernatant was analyzed by SDS-polyacrylamide gel electrophoresis (PAGE) and western blotted as follows. Total protein (5 μg) from COS7 cells was extracted as described above, separated by SDS-PAGE, and transferred to a nitrocellulose membrane using a semi-dry blotting apparatus. Membranes were blocked with 5% non-fat milk. Blots were incubated with either the mouse anti-HA antibody (1:10,000) or the mouse anti-V5 antibody (1:5,000) overnight at 4EC. A goat anti-mouse horseradish peroxidase secondary antibody (1:10,000) was used in combination with enhanced chemiluminescence (NEN) to detect proteins.

[0149] Following detection of epitope-tagged proteins with one antibody, the blots were stripped in stripping buffer (62.5 mM Tris-HCl (pH 6.7), 100 mM 2-mercaptoethanol, 2% SDS) at 50EC for 30 minutes. The membrane was washed extensively (20 mM Tris, pH 7.6, 137 mM NaCl, 0.05% Tween-20) then blocked again and processed for detection of the second epitope-tagged protein.

[0150] Western blotting of cell lysates prior to immunoprecipitation showed that all four proteins tagged with the V5 epitope were expressed at detectable levels. The co-immunoprecipitation data showed that mPER3 homodimerized and heterodimerized with mPER1 and mPER2, but did not interact at detectable levels with mTIM. When the blot was stripped and re-probed with the anti-HA antibody, similar amounts of mPER3-HA were precipitated in each sample. Thus, the lack of detection of an mPER3:mTIM interaction was not due to a transfection or expression artifact. A similar pattern of interactions was obtained when the coimmunoprecipitation experiments were performed using mPER1-HA in place of mPER3-HA; that is, co-immunoprecipitation of the mPER proteins but not mTIM. These results in mammalian cells confirm the findings in yeast: each mPER can homodimerize with itself or heterodimerize with another mPER but does not detectably interact with mTIM. Our results do not rule out the possibility of biologically relevant mPER:mTIM interactions in the mammalian clockwork. But the data do suggest that such mPER:mTIM interactions must be much weaker than the strong mPER:mPER interactions found in both yeast and mammalian cells.

EXAMPLE 2

[0151] Subcellular Location of mPER3 Changes in the Presence of mPER1 or mPER2

[0152] To determine whether mPER:mPER interactions may be important for the nuclear translocation of the mPERs and their subsequent negative feedback on transcription, mPER:mPER interactions were examined by first evaluating the subcellular location of the HA-and V5-epitope tagged constructs when transfected into NIH3T3 and COS7 cells.

[0153] Immunofluorescence of epitope-tagged proteins was used to observe protein location within cells. Briefly, cells (3×105) were seeded on glass coverslips in 6-well dishes and transfected the following day as described above with 1 μg of total DNA per well. Forty-eight hours after transfection, cells adherent to the coverslip were washed twice with phosphate buffered saline (PBS), fixed with −20EC methanol (10 min), washed, and blocked in 5% normal goat serum/0.1%Triton X-100 in PBS (1 hr). Mouse anti-V5 IgG (1:500; Invitrogen, Calsbad, Calif.) or rabbit anti-HA IgG (1:200; Santa Cruz Biotechnology, Santa Cruz, Calif.) was applied for 1.5 hrs. Cells were washed and then incubated in the dark (1 hr) with secondary antibodies. These consisted of either goat anti-rabbit IgG conjugated to Cy2 (1:200) or goat anti-mouse IgG conjugated to Cy3 (1:200; Jackson ImmunoResearch). Cells were washed, and the nuclei were stained with bisBenzimide and then mounted for fluorescence microscopy. A random population of 30-60 cells from each coverslip was examined by epifluorescence microscopy and the subcellular distributions of the transfected proteins were recorded without knowledge of the treatment. At least three independently transfected coverslips were analysed. The cellular location was scored as one of three categories: both cytoplasm and nucleus, cytoplasm alone, or nucleus alone.

[0154] When expressed singly in NIH3T3 cells, mPER1 and mPER2 were each found predominantly in both cytoplasm and nucleus of individual cells (78% and 61% of transfected cells, respectively; n=3 experiments), but were also detected in the nucleus alone (15% and 29%, respectively). In contrast, mPER3 was mostly in cytoplasm alone (95% of transfected cells), and mTIM was mostly nucleus alone (89%).

[0155] To determine whether co-expression promotes nuclear entry of the proteins, all possible pairwise combinations of the mPER and mTIM plasmids were co-transfected. mTIM co-expressed with any of the mPER proteins did not affect subcellular location of mTIM or the mPER proteins (p>0.05). The most obvious example of this was observed when mPER3 and mTIM were coexpressed: mPER3 remained cytoplasmic, and mTIM remained nuclear. The inability of mTIM to influence subcellular location of the mPER proteins provides further evidence that mTIM does not interact functionally with the mPER proteins in a manner analogous to the interactions of PER and TIM in Drosophila.

[0156] When mPER3 was co-expressed with either mPER1 or mPER2, mPER3 was dramatically redistributed from cytoplasm only to both cytoplasm and nucleus (p<0.01, n=3 experiments). mPER1 was more effective than mPER2 in promoting nuclear entry of mPER3; that is, nucleus-only location was found in 3 times more cells with mPER1 co-transfections, compared with mPER2. The same redistribution profile was observed when the amounts of the mPER1 and mPER3 plasmids transfected were decreased by 75% (from 500 ng to 125 ng). All of the subcellular localization experiments described above in NIH3T3 cells were also performed in COS7 cells with similar results. Despite trying all possible combinations of mPER proteins with mTIM, including adding all four proteins at once, we were unable to induce a “nucleus-only” location of mPER1 or mPER2 in >30% of NIH3T3 cells. Thus, it would appear that the tested combinations do not completely reconstitute mPER function in NIH3T3 cells. This suggested that there are other clockrelevant factors important for the nuclear translocation of the mPER proteins.

EXAMPLE 3

[0157] mPER:mPER Interactions do not Augment Inhibition of CLOCK:BMAL-1-Induced Transcription

[0158] The ability of mPER1/2:mPER3 interactions to promote the nuclear entry of mPER3 and augment the inhibition of CLOCK:BMAL1-induced transcription was examined. For these studies, a luciferase reporter gene assay in NIH3T3 cells was used. The reporter construct utilizes a 200 bp fragment of the promoter region of the mouse arginine vasopressin (prepropressophysin) gene containing a CACGTG E box, as previously described (Jin et al., Cell 96:57-68, 1999). This reporter gene construct is activated by CLOCK and BMAL1 acting together on the E box enhancer (Jin et al., supra). Briefly, luciferase reporter gene assays were performed in NIH3T3 cells as previously described (Gekakis et al., Science 280:1564-1569, 1998; Jin et al., supra). Cells (3×105) were seeded in six-well plates and transfected the following day. Each construct contained the vasopressin promoter (10 ng) or 1.8 kb of the 5′ flanking region of the mPerl, gene each cloned into pGL3 BasicJ (Promega, Madison, Wis.) (10 ng of each reporter) and CMV βgalactosidase (25 ng). cDNAs encoding Mouse CLOCK, hamster BMAL-1 and human MOP4, each subcloned into pcDNA3.1-V5, were each used at 250 ng per transfection. Amounts of the mPER and mTIM constructs transfected varied depending on the experiment. The total amount of DNA per well was adjusted to 1 μg by adding pcDNA 3.1 vector as carrier. Forty-eight hours after transfection, cells were harvested to determine β-galactosidase activity and luciferase activity by luminometry.

[0159] Dose-response studies of inhibition of CLOCK:BMAL-1-induced transcription by the mPER proteins and mTIM are shown in FIG. 1. Data from 16 transcription assays were combined by normalizing the relative luciferase activity values in each experiment to the activity from CLOCK:BMAL-1 alone (set at 100%). The amounts of the mPER or mTIM expression constructs transfected are listed (in ng) at the extremes of the triangles. Individual experiments were done in duplicate or triplicate. Values are plotted as the mean %+SEM when three or more experiments were performed with a given amount of expression construct. All other values represent averages from two experiments.

[0160] Results showed that CLOCK:BMAL-1-induced transcription was maximally inhibited transfection of 250 ng of each of the mPer and mTim constructs. Maximal inhibition reached 55-70% for each construct and was not substantially augmented by any pairwise transfection of the mPer and mTim constructs (at 250 ng each). As the amount of each expression plasmid transfected was decreased, there was decreasing inhibition of CLOCK:BMAL-1 transcription (FIG. 1). From the dose-response curves, the amount of each expression construct that was at the threshold of causing transcriptional inhibition was identified.

[0161] Using threshold amounts of each expression construct, all possible pairwise mPER:mPER and mPER:mTIM combinations were next examined to look for synergistic or additive interactions. In no instance, however, was there observed a consistent augmentation of transcriptional inhibition with low-dose, pairwise combinations of mPER expression constructs or mPER plus mTIM expression constructs (n=4 experiments). Co-expression experiments with low doses of mPER1 and mPER3 did show a consistent trend toward inhibition of CLOCK:BMAL-1-induced transcription, but the effects were significant (p<0.05) in only one of three experiments.

[0162] The data hint that mPER1:mPER3 heterodimers may be functionally relevant for transcriptional inhibition. The endogenous expression of the mPer1, mPER2, mPer3, and mTim genes in NIH3T3 cells may obscure finding a more robust inhibitory effect on transcription. Based on the modest effects of mPER:mPER interactions on nuclear localization and transcriptional inhibition, however, it seemed more likely that there were other factors necessary for nuclear translocation and/or retention of the mPER proteins and for their subsequent inhibition of CLOCK:BMAL-1-induced transcription.

EXAMPLE 4

[0163] mCry1 and mCry2 RNA Levels in the SCN and in Peripheral Clocks are Regulated by CLOCK

[0164] It was next determined if cryptochromes were involved in the CLOCK:BMAL1-driven mPer feedback loop. mCry1 and mCry2 gene expression in wild-type and homozygous Clock mutant mice was examined, because a decrease in gene expression in Clock/Clock mice (i.e., mice homozygous for the mutation) would place the cryptochrome genes within the CLOCK-driven feedback loop.

[0165] Northern analysis was used to examine gene expression of CRY1 and CRY2. Briefly, total RNA was extracted from tissues using the Ultraspec RNA isolation reagent. Polyadenylated (polyA+) RNA was prepared using oligotex poly dT spin columns (Qiagen, Valencia, Calfi.). PolyA+ RNA was separated by electrophoresis through a 1% agarose-formaldehyde gel, blotted onto GenScreenJ (New England Nuclear), and hybridized with random prime-labeled probe (S.A.=2×106 cpm/ml). The blots were hybridized with Express HybridizationJ Solution (Clontech, Palo Alto, Calif.) and washed following the manufacturer's protocol. Probes used were mCry1 (nt 1081-1793 of Act. No. AB000777) and mCry2 (nt 1060-1664 of Act. No. AB003433). Probe for actin was from human B-actin, purchased from Clontech (Palo Alto, Calif.). Blots were exposed at −80EC to film with 2 intensifying screens.

[0166] Four blots were prepared from the RNA samples, with each blot consisting of the eight time-points from one genotype and a standard lane. One microgram of polyA +RNA was loaded per lane for each genotype. Each blot was probed, stripped, then reprobed to detect mCry1, mCry2, and actin. To calculate relative RNA abundance, optical densities of mCry1 and mCry2 hybridization were divided by densities from actin hybridization to the same blot. Normalized values were then averaged for the two replicate blots prepared from a single set of RNA samples. Comparison across blots probed and exposed under similar conditions suggested that the absolute level of expression of the mCry genes was lower in Clock/Clock mice than in wild-type mice. This difference in absolute expression level was confirmed using two additional blots that included selected (peak-trough) RNA samples from the two genotypes side-by-side, and were probed for both mCry1, mCry2, and actin.

[0167] mCry RNA levels in SCN are depicted in FIG. 2A. Panels depict the temporal profiles of mCry1 RNA levels (left) and mCry2 RNA levels (right) in the SCN of wild-type mice (solid lines) and Clock/Clock mice (dashed lines). Each values is the mean+SEM of 4 animals. The horizontal bar at the bottom of the panels represents lighting cycle prior to placement in DD; the stippled areas represent subjective day; and the filled areas represent subjective night. Photomicrographs showed representative autoradiographs of mCry1 and mCry2 gene expression from coronal brain sections (15 μm) at the level of the SCN from wild-type (+/+) and Clock/Clock (CZk/CZk) mice at CT 9. The brain sections were examined by in situ hybridization using cRNA probes as follows. A breeding colony of mice carrying the Clock mutation was established on a BALB/c background. For studies, both males and female mice 5-15 weeks of 24 age were used. Mice were housed in LD, except as noted. Animals were killed by decapitation. Genotypes were determined using a PCR mutagenesis method, as previously described (Jin et al., supra).

[0168] Antisense and sense cRNA probes were generated from each plasmid by in vitro transcription in the presence of 35S-UTP (1200 Ci/mmol). Probe for mCry1 (AB000777) was nucleotides 1081-1793 and for mCry2 (AB003433) was nucleotides 1060-1664. Probe quality and size was confirmed by determining 35S incorporation into TCA-precipitable material, and by gel electrophoresis and subsequent autoradiography of the gel.

[0169] Prehybridization, hybridization, and wash procedures were performed as described by Weaver. Probe (50 μl at 107 cpm/ml) was applied to each slide. Coverslipped slides were then incubated in humidified chambers overnight at 55E C. Following completion of the wash steps, slides were air dried and exposed to Kodak BioMax MR film for 8 days.

[0170] Densitometric analysis of hybridization intensity was accomplished using NIH Image software on a Macintosh computer; data are expressed as absolute optical density values as determined by calibration with Kodak photographic step tablet #3. 14C standards included in each cassette were used to verify that the optical density values measured were within the linear response range of the film.

[0171] The results showed that mCry1 RNA levels exhibited a prominent circadian rhythm in the SCN of wild-type animals (ANOVA, p<0.05; FIG. 2A). The phase of the mCry1 RNA rhythm was most similar to the phase of the mPER2 RNA oscillation in the SCN. In sharp contrast to wild-type mice, no mCry1 RNA rhythm was apparent in the SCN of Clock/Clock mice (ANOVA, p>0.05; FIG. 2A). Thus, the mCry1 RNA rhythm is dependent on a functional CLOCK protein. These results are similar to the finding that the amplitude of RNA rhythms for each of the three mPer genes is markedly reduced in Clock/Clock mice (Jin et al., supra).

[0172] mCry2 RNA levels in the SCN of wild-type animals did not show a circadian rhythm (FIG. 2A; p>0.05). Interestingly, mean steady-state mCry2 RNA levels were nonetheless significantly lower in Clock/Clock mice, compared to those in wildtype controls (ANOVA, p<0.005). This finding suggests that mCry2 transcription is also at least partially dependent on a functional CLOCK protein. It is worth noting that of 5 genes studied whose RNA levels do not manifest a circadian rhythm in the SCN, mCry2 is the only one in which mRNA levels in Clock/Clock animals were observed (see Jin et al., supra). Since circadian clocks also appear to exist in peripheral tissues (Balsalobre et al., Cell 93:929-937, 1998; Zylka et al., Neuron 20:1110, 1998b; Sakamoto et al., J. Biol. Chem. 273:27039-27042, 1998), the temporal profiles of mCry1 and mCry2 RNA levels in skeletal muscle were examined. This tissue was chosen because the three mPer genes manifest robust RNA rhythms there (Zylka et al., 1998b, supra). mCry RNA levels in skeletal muscle are shown in FIG. 2B. Autoradiograms (upper panels) illustrate Northern blots of mCry1 (3.0 kb transcript, left) and mCry2 (4.4 kb transcript, right) RNA levels at each of 8 time points in 12L:12D, with lights on from Zeitgeber Times (ZT) 0-12. The lower panels depict quantitative assessment of mCry1 and mCry2 RNA levels in skeletal muscle of wildtype (solid lines) and Clock/Clock mice (dashed lines). The values are the average relative intensity of two replicate blots with each probe. Data were normalized and expressed relative to hybridization intensity of actin control probe. Data at ZT 21, ZT0/24, and ZT3 are double plotted. In contrast to the situation in the SCN, both mCry1 and mCry2 RNA levels in muscle exhibited a daily rhythm under 12 hrs light:12 hrs dark (LD) (FIG. 2A) and a circadian rhythm under constant darkness. The peak of the mCry2 rhythm preceded that of mCry1 by 6 to 9 hrs, and the mCry1 RNA rhythm was delayed by several hrs relative to the phase of its RNA rhythm in the SCN. A phase delay between the SCN and peripheral oscillations is also observed in the RNA rhythms of the three mPer genes (Zylka et al., 1998b, supra). In skeletal muscle of Clock/Clock animals, the mCry1 RNA rhythm was dampened and phase advanced, while the mCry2 RNA rhythm was abolished (FIG. 2B). For both genes, RNA levels were lower in Clock/Clock animals at all times, compared to wild-type controls.

[0173] Taken together, these data indicate that the transcriptional regulation of mCry 1 and mCry2 is under CLOCK control in both the SCN and in peripheral clocks. These findings provide strong evidence that the mouse cryptochromes are components of the CLOCK: BMAL-1-driven feedback loop. Moreover, the occurrence of a CACGTG E box 300 bp upstream of the mCry1 transcription start site suggests that CLOCK directly participates in rhythmic mCry1 transcription through an E box enhancer in its promoter.

EXAMPLE 5

[0174] mCRY1 and mCRY2 Block CLOCK:BMAL-1-induced Transcription in NIH3T3 Cells

[0175] The involvment of mammalian cryptochrome within the negative limb of the feedback loop was analyzed by determining whether mCRY1 and/or mCRY2 can inhibit CLOCK: BMAL-1-induced transcription. For this phase of study, 14 luciferase reporter gene studies were performed in NIH3T3 cells using either the vasopressin promoter (Jin et al., supra) or 1.8 kb of the 5′ flanking region of the mPer1 gene subcloned into a promoterless luciferase reporter vector.

[0176] Inhibition of CLOCK:BMAL-1-mediated transcription from the vasopressin (AVP) promoter (FIG. 3A) or mPer1 promoter (FIG. 4B) by mPER1, mCRY1 and mCRY2 (250 ng each) was determined. Each value is the mean+SEM of three replicates from a single assay. The results are representative of three independent experiments. Dose-response curves for mCRY1 (Fig. cD) or mCRY2 (FIG. 3D) inhibition of CLOCK:BMAL-1-mediated transcription from the vasopressin (AVP) promoter. Each value is the mean+SEM of three replicates from a single assay. Similar results were found in replicate experiments.

[0177] Results show that when vasopressin and mPer1 promoters were used in the reporter vectors, mPER1 caused a maximal inhibition of 61% and 30%, respectively. mCRY1 and mCRY2, on the other hand, inhibited CLOCK:BMAL-1-induced transcription by >90% from either reporter. This dramatic effect on transcriptional inhibition was dose dependent for each of the two mCRY proteins. These results indicate that mCRY1 and mCRY2 are each potent inhibitors of CLOCK:BMAL-1-mediated transcription. The mCRY-induced transcriptional inhibition must occur through direct or indirect interaction with the CLOCK:BMAL-1:E box complex because this is the only complex common to both the vasopressin and mPer1 promoters

EXAMPLE 6

[0178] Both mCRY1 and mCRY2 are Nuclear Proteins

[0179] For the mCRY proteins to interact with the CLOCK:BMAL-1:E box complex, they must be present in the nucleus. Previous studies have shown that mCRY2 is indeed a nuclear antigen (Kobayashi et al., Nucleic Acids Res. 26:5086-5092, 1998; Thresher et al., Science 282:1490-1494, 1998). The situation with mCRY1 is ambiguous because previous studies of the endogenous protein and green fluorescent protein (GFP)-tagged mCRY1 fragments indicate localization mainly in mitochondria (Kobayashi et al., supra). To determine the localization of CRY1 or CRY2, the CRY proteins were tagged at the ends of the protein with a number of different epitopes. For example, the coding regions of mCRY1 (AB000777) were ligated into the pcDNA 3.1 VS-His expression vector containing either an N terminal or C terminal HA tag. For mCRY2, the nucleotide sequence encoding the amino terminal portion of the coding region was not available in GenBank (partial clone accession no. AB003433). The 5′end of the mCRY2 coding region was thus cloned by 5′rapid amplification of cDNA ends. The full-length coding region was then amplified as described above, sequenced, and deposited in GenBank as Accession Number AF156987. The constructs (FIG. 4) were transfected into NIH3T3 cells and both their cellular localization (by immunofluorescence) and ability to inhibit CLOCK:BMAL-1-induced transcription were assessed.

[0180] The results clearly showed that mCRY1 translocates to the nucleus when tagged with either the V5 or HA epitope. This was true when HA was placed at either the N-terminal or C-terminal ends, as well as when epitope tags were placed on both ends of the protein. In each instance, the protein was nuclear and inhibited CLOCK:BMAL1-induced transcription by >90%. Interestingly, when enhanced (E)GFP was fused to either end of mCRY1, immunofluorescence was found diffusely throughout the cell and there was no transcriptional inhibition. The same diffuse staining and lack of transcriptional inhibition was found with EGFP alone. When EGFP was fused to an N-terminal fragment of mCRY1 containing a putative signal sequence for transport into mitochondria, the cellular location was mainly cytoplasmic, punctate and appeared to be in mitochondria. Using a specific anti-mCRY1 antibody, endogenous mCRY1 protein was shown to be nuclear in non-transfected NIH3T3 cells and in SCN. Thus, mCRY1 is normally a nuclear protein and that GFP fused to CRY alters the location of the native protein by changing its conformation. mCRY2-V5 was found in the nucleus, consistent with previous findings (Kobyashi et al., supra; Tresher et al., supra), and the tagged protein inhibited CLOCK:BMAL-1-induced transcription by >90%.

EXAMPLE 7

[0181] mCRY1 and mCRY2 Directly Interact with the mPER Proteins and Translocate them into the Nucleus

[0182] To evaluate the potential for protein: protein interactions between the mCRY and mPER families, co-immunoprecipitation using epitope-tagged proteins was utilized.

[0183] COS7 cells co-transfected with expression plasmids encoding mCRY 1-HA and either mPER1-V5, mPER2-VS, mPER3-V5, or mTIM-V5 expressed each V5-tagged protein prior to immunoprecipitation. Immunoprecipitation with the HA antibody and analysis of the immunoprecipitated material with anti-V5 antibodies indicated the presence of heterodimeric interactions between mCRY1 and each of the mPER and mTIM proteins. There was no interaction between mCRY1 and βgalactosidase which served as a specificity control. Co-immunoprecipitation experiments using mCRY2-HA instead of mCRY 1-HA similarily showed the presence of heterodimeric interactions between mCRY2 and each of the mPER and mTIM proteins.

[0184] Having shown that mCRY:mPER heterodimers could exist, the ability of such interactions to translocate the mPER proteins to the nucleus was determined. In marked contrast to the lack of effect of any pairwise combination of mPER:mPER or mPER:mTIM interactions to translocate mPER1 and mPER2 to the nucleus, each mCRY protein profoundly changed the location all three mPER proteins in NIH3T3 and COS7 cells. This was most apparent for mPER1 and mPER2 which were almost entirely nuclear after co-transfection with either mCRY1 or mCRY2. Curiously, each mCRY protein changed mPER3 from mainly cytoplasm only (>80%) to both cytoplasm and nucleus (>80%) to a degree similar to that induced by co-transfection of mPER3 with mPER1. When mPER3 was co-transfected with mPER1 and either mCRY1 or mCRY2, however, each of the three protein combinations changed mPER3's location from 13-20% nucleus only to predominantly nucleus only (54-68% of transfected cells). Co-transfection of either mCRY1 or mCRY2 with mTIM did not change the predominantly nucleus only location (>90% of transfected cells) of any of the three proteins.

[0185] These data indicate that the mCRY proteins can heterodimerize with the mPER proteins and mTIM. The mCRY:mPER interactions mimic the in vivo situation where the interaction of mCRY and mPER results in the almost complete translocation of mPER1 and mPER2 to the nucleus. Moreover, trimeric interactions among the mPER and mCRY proteins appear necessary for complete nuclear translocation of mPER3. The data also suggest that the nuclear translocation of the mPER proteins is dependent on mCRY 1 and mCRY2. The mCRY proteins, however, appear to be able to translocate to the nucleus independent of the mPERs. Even with massive overexpression of mCRY proteins in cell culture they are always >90% nuclear.

EXAMPLE 8

[0186] mCRY1 and mCRY2 Levels Express Synchronous Circadian Rhythms in the SCN

[0187] If nuclear entry of mPER1 and mPER2 is dependent on the mCRY proteins as suggested by the cell culture experiments, then similarily synchronous circadian oscillations of endogenous mCRY1 and mCRY2 levels in the nuclei of SCN neurons might be expected. To determine this the oscillations of endogenous CRY in neurons was determined. Briefly, mice entrained to a schedule of 12L:12D were transferred to constant dim red light. Circadian Time (CT) was initially defined relative to predicted lights-off (CT12), and on the day of sampling was confirmed by the coincident onset of group activity, as monitored by passive infra-red movement detectors. After 20 (CT8) to 42 (CT6) hours in constant dim red light, mice were killed with an anesthetic overdose, and perfused (4% paraformaldehyde). Brains were removed, post-fixed, transferred to cryoprotectant buffered sucrose solution (20%) and then sectioned on a freezing microtome. Alternate freefloating sections (40 μm) were incubated with affinity purified anti-mCRY1 or anti-mCRY2 (both at 0.5 μg/ml) primary sera (Alpha Diagnostic International). The sera were raised against synthetic peptides corresponding to specific sequences close to the C-terminals of the mCRY1 (26 amino acids) and mCRY2 (22 amino acids)proteins. To test for specificity of the sera, some SCN sections were incubated with affinity purified sera to which synthetic peptide (10 μg/ml) had been added. Immunoreaction was visualised by avidin-biotin/peroxidase in conjunction with diaminobenzidine chromogen (Vector Labs, Peterborough, U.K.). Counts of the number of immunoreactive nuclear profiles in the SCN were made using an image analysis system as described previously.

[0188] Immunocytochemical analysis of mCRY1 and mCRY2 in the brains of mice sampled at Zeitgeber Time (ZT) 15 (3 h after lights off) identified them both as nuclear antigens in the SCN and elsewhere, including piriform cortex (mCRY2) and hippocampus (mCRY1, mCRY2). The majority of SCN neurons appeared to be immunoreactive for the antigen tested, and the immunoreactivities were specific, being blocked by pre-incubation with the peptide (10 μg/ml) used to raise the respective serum. In contrast, the SCN from animals sampled at ZT3 contained very few mCry1-or mCRY2-immunoreactive nuclei, and those which were evident were located in a dorso-lateral position comparable to that reported for mPER1 immunoreactive nuclei at this phase. Rhythmic expression of mCRY1 and mCRY2 was sustained under free-running conditions, with low levels at Circadian Time (CT)2 and high expression throughout the SCN at CT14 was observed. Quantitative analysis of the number of immunoreactive nuclei in the SCN sampled at 2 h intervals over 24 h in DD showed a clear circadian variation. The abundance of both proteins was low in the early subjective day, rising in later subjective day to peak at CT12-CT16. There was a progressive decline during subjective night to basal counts at CT24. This temporal profile of mCRY1 and mCRY2-immunoreactivity in the SCN is directly comparable with that observed for mPER1 and mPER2, indicative of a synchronous nuclear accumulation of these proteins in the SCN.

[0189] In contrast, expression of mCry1- and mCRY2-immunoreactivity in other areas did not exhibit appreciable circadian variation, consistent with the constitutive expression of mPER proteins in brain sites outside the SCN.

[0190] These in vivo data, in conjunction with our cell culture data, strongly suggest that the mCRY proteins are the dominant movers of the mPER1 and mPER2 proteins from cytoplasm to nucleus. We do not yet know the temporal pattern of mPER3 immunoreactivity in the SCN, but we have no reason to believe it will be any different from that found for mPER1 and mPER2.

EXAMPLE 9

[0191] Dissociation Between the Inhibitory Effects of the mPER Proteins and the mCRY Proteins on Transcription

[0192] By varying the amounts of mPER and mCRY plasmids in co-transfection experiments, we have observed at best additive effects of pairwise combinations of mPER with mCRY proteins on the inhibition of CLOCK:BMAL-1-mediated transcription. Although these studies in cell culture are confounded by the endogenous expression of the mPer1, mPER2, mPer3, mTim, mCry1 and mCry2 genes in the cell lines used, the lack of synergism of pairwise combinations on transcriptional inhibition suggested that the mPER and mCRY proteins have independent effects on the transcriptional machinery. To examine this in more detail, the fact that MOP4:BMAL-1-heterodimers also activate transcription via a CACGTG E box was exploited (Hogenesch et al., Proc. Natl. Acad. Sci. USA 95:5474-5479, 1998).

[0193] CLOCK, MOP4, and BMAL-1 alone or in pairwise combinations were tested for transcriptional activation (FIG. 8A). Significant transcriptional activation was seen only when CLOCK and BMAL-1 (10-fold increase) or MOP4 and BMAL 1 (37-fold increase) were co-expressed. Transcriptional activation was dependent on the E-box, because no transcriptional activation was detected when the vasopressin promoter with a mutated E-box was used. The greater levels of transcriptional activation with MOP4:BMAL-1 than with CLOCK:BMAL-1 appeared due to much higher levels of MOP4 protein expression compared with CLOCK based on western blot analysis of epitope tagged proteins.

[0194] Each mPER alone, mTIM, or each mCRY alone was tested for its ability to inhibit MOP4:BMAL-1-induced transcription. Even though each mPER protein can inhibit CLOCK:BMAL-1-induced transcription, the mPER proteins (500 ng of each plasmid) did not affect MOP4:BMAL-1-induced transcription (FIG. 5B). When the amount of MOP4 was reduced so that the relative luciferase values were equal to those seen with CLOCK and BMAL-1 activation, the mPER expression plasmids were still unable to inhibit transcription. In contrast to the lack of inhibition of the mPER proteins, mTIM (at 500 ng) was able to inhibit MOP4:BMAL-1-induced transcription by about 40% (FIG. 5; p>0.01). Combinations of each mPER and the mTIM expression plasmids, or pairwise combinations of mPER expression plasmids did not inhibit more effectively than when the mTIM plasmid was transfected alone. Remarkably, each mCRY protein (250 ng each) abrogated MOP4:BMAL-1-mediated transcription (FIGS. 5C and 5D).

[0195] These data suggest that the mPER proteins have their action on CLOCK, perhaps as mPER:mCRY heterodimers, while the mCRY proteins appear capable of interacting directly with either BMAL-1 or the CACGTG E box. It is worth noting that MOP4 does not appear to play a major role in circadian function, as its RNA is not detectably expressed in the SCN of either wild-type or Clock-mutant mice.

EXAMPLE 10

[0196] Bmal1 RNA Rhythm in Clock/Clock Mutant Mice

[0197] BMAL-1 RNA rhythm was first documented in mouse SCN using quantitative in situ hybridization (Jin et al., Cell 96:57 (1999)) with an antisense riboprobe that recognizes the two major Bmal1 transcripts in the SCN (Yu et al., Biochem. Biophys. Res. Commun. 260:760 (1999)). Wild-type mice exhibited a robust circadian rhythm in Bmal1 RNA levels, with low levels from circadian time (CT) 6-9 and peak levels from CT 15-18.

[0198] The phase of the Bmal1 rhythm is opposite that of the mouse Per1-3(mPer1-3) RNA rhythms (Zylka et al., Neuron 20:1103 (1998); Oishi et al., Biochem. Biophys. Res. Commun. 268:164 (2000); Honma et al., Biochem. Biophys. Res. Commun. 250:83 (1998)). In addition to driving rhythmic transcription of the mPer and mCry genes (Jin et al., Cell 96: 57 (1999); Kume et al., Cell 98:193 (1999)), it seemed possible that CLOCK:BMAL1 heterodimers might simultaneously negatively regulate Bmal1 gene expression, similar to a proposed model of clock gene regulation in Drosophila. If CLOCK:BMAL1 heterodimers are negatively regulating Bmal1 gene expression and if the mutant CLOCK protein is ineffective in this negative transcriptional activity, then Bmal1 RNA levels should be elevated and less rhythmic in homozygous Clock mutant mice. Compared to wild-types, however, Clock/Clock animals expressed a severely dampened circadian rhythm of Bmal1 RNA levels in the SCN (significant difference between genotypes; ANOVA, P<0.001) (FIG. 9). Trough Bmal1 RNA levels did not differ between Clock/Clock mice and wild-types. The peak level of the RNA rhythm in homozygous Clock mutant mice was only ≈ 30% of the peak value in wild-types. A similar blunting of the Bmal1 RNA rhythm in the SCN of Clock/Clock mice has been reported by others (Oishi et al., Biochem. Biophys. Res. Commun. 268:164 (2000)).

[0199] The temporal profile of Clock RNA levels was examined in the SCN of Clock/Clock mutant animals, since it has been reported that Clock RNA levels (assessed by Northern blot analysis) are decreased in the eye and hypothalamus of Clock/Clock mutant mice (King et al., Cell 89:641 (1991)). Consistent with previous reports (Tei et al., Nature 389:512 (1997); Shearman et al., Neuroscience 89:387 (1999) Clock RNA levels did not manifest a circadian oscillation in mouse SCN. Surprisingly, Clock RNA levels in the SCN of Clock/Clock mutant mice were not significantly different from those in the SCN of wild-type animals (FIG. 10; ANOVA, P>0.05). Thus, the Clock mutation appears to alter regulation of Bmal1 gene expression in SCN, but not the regulation of the Clock gene itself. Clock expression may be decreased in other hypothalamic regions.

[0200] The low levels of Bmal1 RNA in the SCN of homozygous Clock mutant animals show that CLOCK is not required for the negative regulation of Bmal1. Instead, these data indicate that CLOCK is actually necessary for the positive regulation of Bmal1. The positive effect of CLOCK on Bmal1 levels is probably indirect and may occur via the mPER and/or mCRY proteins, which are expressed in the nucleus of SCN neurons at the appropriate circadian time to enhance Bmal1 gene expression (Kume et al., Cell 98:193 (1999); Field et al., Neuron 25:437 (2000)). In addition, the mPer1-3 and mCry1-2 RNA oscillations are all down-regulated in Clock/Clock mutant mice (Jin et al., Cell 96:57 (1999); Kume et al., Cell 98:193 (1999)). Reduced levels of the protein products of one or more of these genes may lead to the reduced levels of Bmal1 in the mutant mice, through loss of a positive drive on Bmal1 transcription.

EXAMPLE 11

[0201] Bmal1 and mCry1 RNA Rhythms in mPER2Brdm1 Mutant Mice

[0202] Homozygous mPER2Brdm1 mutant animals have depressed mPer1 and mPER2 RNA rhythms (Zheng et al., Nature 400:167 (1999)). The Bmal1 rhythm in homozygous mPER2Brdm1 mutants was examined to determine whether the positive drive on the Bmal1 feedback loop might come from the mPER2 protein. The effects of this mutation on the mCry1 RNA rhythm were also examined.

[0203] The temporal profiles of gene expression were analyzed at six time points over the first day in DD in homozygous mPER2Brdm1 mutant mice and wild-type littermates. The Bmal1 RNA rhythm expressed in the SCN of wild-type animals was substantially altered in the SCN of mutant mice (ANOVA, P<0.05)(FIG. 11). Trough RNA levels did not differ between wild-type and mutant animals, but the increase in Bmal1 RNA levels was advanced and truncated in the mutants, compared to the wild-type rhythm.

[0204] The mCry1 RNA rhythm was also significantly altered. In the SCN of mPER2Brdm1 mutant mice (ANOVA, P<0.0001)(FIG. 12), the peak levels of the mCry1 RNA rhythm were suppressed by ≈50%, as reported for mPer1 and mPER2 RNA rhythms in this mouse line (Zheng et al., Nature 400:167 (1999)).

[0205] These data suggest that maintenance of a normal Bmal1 RNA rhythm is important for the positive transcriptional regulation of the mPer and mCry feedback loops. Thus, rhythmic Bmal1 RNA levels may drive rhythmic BMAL 1 levels which, in turn, regulate CLOCK:BMAL1-mediated transcriptional enhancement in the master clock. Indeed, mPer1, mPER2, and mCry1 RNA rhythms are all blunted in the SCN of mPER2Brdm1 mutant mice, in which the Bmal1 rhythm is also blunted. In addition, the homozygous mPER2Brdm1 mutation is associated with a shortened circadian period and ensuing arrhythmicity in constant darkness (DD).

[0206] These data, along with the fact that Clock RNA levels are unaltered in the SCN of homozygous mPER2Brdm1 mutants (Zheng et al., Nature 400:167 (1999), also provide evidence that mPER2 is a positive regulator of the Bmal1 RNA rhythm. This effect may be unique to mPER2. For example, the diurnal oscillation in mPer2 RNA is not altered in the SCN of mPer1-deficient mice, and mPer1, mPer2, and Bmal1 RNA circadian rhythms are not altered in the SCN of mPer3-deficient mice. Moreover, circadian rhythms in behavior are sustained in mice deficient in either mPer1 or mPer3.

EXAMPLE 12

[0207] mCRY-Mediated Nuclear Translocation of mPER2 is PAS-Independent

[0208] There are at least two ways that the mPER2Brdm1 mutation could alter the positive drive of the clock feedback loops. The mutation could disrupt mPER:mCRY interactions important for the synchronous oscillations of their nuclear localization and/or alter the protein's ability to interact with other proteins (e.g., transcription factors). We examined whether the PAS domain is necessary for functionally relevant mPER2:mCRY interactions, using immunofluorescence of epitope-tagged proteins in COS-7 cells. Briefly, COS-7 cells (3×105) were seeded on glass coverslips in 6-well dishes and transfected with Lipofectamine Plus™ (Gibco BRL) with 0.5 ug of total DNA per well. Forty-eight hrs after transfection, cells were processed as described (Sangoram et al., Neuron 21:1101 (1998)). A random population of 30-60 cells from each covership was examined by epiflourescence microscopy and the subcellular distribution of expressed proteins was recorded without knowledge of treatment. At least three independently transfected coverslips were analyzed.

[0209] Coexpression of mPER1 or mPER2 with either mCRY1 or mCRY2 in COS-7 cells translocates >90% of mPER1 and mPER2 into the nucleus (Kume et al., Cell 98:193 (1999)). To determine whether the PAS domain of mPER2 is required for this translocation an mPER2 fragment containing residues 1-337 of PER2 (mPER21-337), which includes the PAS domain, was examined in COS-7 cells. mPER21-337 was localized to both cytoplasm and nucleus (89% of transfected cells)(FIG. 13) and the localization was not changed by co-expression with mCRY1. Co-expression of mPER2338-1257 with mCRY1, however, dramatically changed the cellular location of the mPER2338-1257 fragment from cytoplasm only (12%) to nucleus only (85%). Co-expression of mPER2Brdm1 (missing residues 348-434) with mCRY1 also moved mutant mPER2Brdm1 into the nucleus, from cytoplasm only (100% when expressed alone) to predominantly both cytoplasm and nucleus (81%) when co-expressed with mCRY1 (FIG. 13). The same patterns of cellular localization were found when mCRY2 was co-expressed with these mPER2 constructs instead of mCRY1. Thus, functional mPER2:mCRY interactions are not mediated through the PAS domain. Similarly, the PAS domain was not important for the mCRY-mediated nuclear translocation of mPER1 in COS-7 cells.

[0210] The data show mPER:mCRY interactions necessary for nuclear transport of the mPER1 and mPER2 proteins occur through domains outside the PAS region. Thus, the PAS domain of an mPER2:mCRY heterodimer might be free to bind to an activator (e.g., transcription factor) and shuttle it into the nucleus to activate Bmal1 transcription. Alternatively, once in the nucleus, mPER2:mCRY heterodimers or mPER2 monomers could coactivate Bmal1 transcription through a PAS-mediated interaction with a transcription factor (Glossop et al., Science 286:766 (1999)). mPER2 itself does not possess a DNA binding motif (Shearman et al., Neuron 19:1261 (1997)).

EXAMPLE 13

[0211] Bmal1 RNA Levels in Mice Lacking mCry1 and mCry2

[0212] The tonic mid-to-high mPer1 and mPer2 RNA levels in mCRY-deficient mice (van der Horst et al., Nature 398:627 (1999) suggest that CLOCK:BMAL1 heterodimers might be constantly driving mPer1 and mPer2 gene expression in the absence of transcriptional inhibition by the mCRY proteins. To examine whether Bmal1 RNA levels would also be modestly elevated, Bmal1 RNA levels in the SCN of mCRY-deficient mice were compared to those in the SCN of wild-type mice of the same genetic background at CT 6 and at CT 18 on the first day in DD. The mCRY-deficient (double mutant) colony of mice had a C57BL/6 X 129 hybrid background, and wild-type controls were of the same genetic background (van der Horst et al., Neuroreport 10:3165 (1999)). Sex ratios of male and female mice were balanced across time points. We also examined Clock RNA levels in these animals.

[0213] In wild-type animals, the typical circadian variation in Bmal1 RNA levels was apparent with high levels at CT 18 and low levels at CT 6 (P<0.001)(FIG. 14). In mCry-deficient mice, on the other hand, Bmal1 RNA levels were low at both circadian times (P>0.05)(FIG. 15). Clock RNA levels did not differ as a function of circadian time or genotype (P>0.05)(FIG. 15).

[0214] The unexpectedly low Bmal1 gene expression in the SCN of mCry-deficient mice suggests that the Bmal1 feedback loop is disrupted in the mutant animals, with a resultant non-functional circadian clock. Nevertheless, enough Bmal1 gene expression and protein synthesis occurs for heterodimerization with CLOCK so that, without the strong negative feedback normally exerted by the mCRY proteins, mPer1 and mPer2 gene expression is driven sufficiently by the heterodimer to give intermediate to high RNA values (depending on RNA stability).

EXAMPLE 14

[0215] mPER1 and mPER2 Localization in mCry-Deficient Mice

[0216] The mid to high mPer1 and mPer2 RNA levels in the SCN of mCry-deficient mice, and simultaneous low Bmal1 levels, suggests that mPER1 and mPER2 proteins may not be exerting much positive or negative influence on the core feedback loops. To test this, immunocytochemistry was used to determine whether mPER1 and mPER2 were tonically expressed in the nuclei of SCN cells in mCry-deficient mice, since nuclear location is necessary for action on transcription (Kume et al., Cell 98:193 (1999); Field et al., Neuron 25:437 (2000)).

[0217] mPER1 immunoreactivity exhibited a robust rhythm of nuclear staining in the SCN of wild-type mice, with high values at CT 12 (328±3.5, mean±SEM of positive nuclei per 30 μm section, n=3) and significantly lower values at CT 24 (54±5, n=3; P<0.01). These values are very similar to those previously reported in other strains of mice (Field et al., Neuron 25:437 (2000)).

[0218] The pattern of mPER1 immunoreactivity in the SCN of mCry-deficient mice was quite different, however. mPER1 immunoreactivity was detected in the nucleus of a similar number of SCN neurons at each of the two circadian times (CT 12, 140±9, n=3; CT 24, 152±21, n=3), and the counts at each time were at ≈40% of those seen at peak (CT 12) in wild-type animals.

[0219] The double mCry mutation also altered the sub-cellular distribution of mPER1 staining in the SCN. In wild-type mice, mPER1 staining viewed under contrast interference was clearly nuclear with a very condensed immunoreaction and a clear nucleolus. The neuropil of the SCN in wild-types was devoid of mPER1 immunoreactivity. In the SCN of mCry-deficient animals, mPER1 staining was clearly nuclear, but the nuclear profiles were less well defined and less intensely stained, and perinuclear, cytoplasmic immunoreaction could be observed. In addition, the neuropil staining for mPER1 was higher in mCry deficient mice, although dendritic profiles were not discernible. In the same brains, the constitutive nuclear staining for mPER1 normally seen in the piriform cortex was not altered in mCry-deficient animals.

[0220] mPER2-immunoreactivity also exhibited a robust rhythm of nuclear staining in the SCN of wild-type mice, with high counts at CT 12 (371±11, n=3) and significantly lower counts at CT 24 (31±3, n=3; P<0.01), similar to that previously reported in another strain (Field et al., Neuron 25:437 (2000)). In striking contrast, the pattern of mPER2-immunoreactivity in the SCN of mCry-deficient mice was dramatically altered. There were extremely few mPER2-immunoreactive cells in the SCN of mCry-deficient animals at either circadian time (CT 12, 12±1, n=3; CT 24, 8±2, n=3).

[0221] In the wild-type mice, the mPER2 staining profiles were clearly nuclear, with well-defined outlines and nucleoli devoid of reaction product. In the few mPER2-immunoreactive cells in the SCN of mCry-deficient mice, low level mPER2 staining was observed in the nucleus, but the profiles were poorly defined and low intensity perinuclear staining could also be observed. As for mPER1, genotype had no discernible effect on nuclear mPER2 immunoreactivity in the piriform cortex, although there was evidence of a low level of perinuclear immunoreactivity for mPER2 in piriform cortex of mCRY-deficient mice.

[0222] The marked reduction of mPER2 staining in the SCN of mCry-deficient animals suggests that the mCRY proteins are either directly or indirectly important for mPER2 stability, as mPER2 RNA levels are at tonic intermediate to high levels in mCry-deficient mice, similar to those found for mPer1 RNA levels (Okamura et al., Science 286:2531 (1999)). It seems unlikely that our assay is incapable of detecting mPER2 in the cytoplasm of mCry-mutants, since the PER2 antibody can detect cytoplasmically localized antigen in SCN cells (Field et al., Neuron 25:437 (2000)).

[0223] The low levels of mPER2 immunoreactivity in the SCN of mCry-deficient mice, in conjunction with tonically low Bmal1 RNA levels, is consistent with an important role of mPER2 in the positive regulation of the Bmal1 loop. Since mPER1 is present in SCN nuclei in mCry-deficient mice, yet Bmal1 RNA is low, it appears likely that mPER1 likely has little effect on the positive regulation of the Bmal1 feedback loop or negative regulation of the mPer1-3 cycles.

[0224] The immunohistochemical data also indicate that mPER1 and mPER2 can each enter the nucleus even in the absence of mCRY:mPER interactions. mPER1 is expressed in the nucleus of SCN neurons from mCry-deficient mice, and both mPER1 and mPER2 are constitutively expressed in the nucleus of cells in the piriform cortex of mCry-deficient animals. The phosphorylation state of mPER1 dictates its cellular location in the absence of mPER1:mCRY interactions, since its phosphorylation by casein kinase I epsilon leads to cytoplasmic retention in vitro. Thus, the nuclear location of both mPER1 and mPER2 in vivo may depend on several factors, including interactions with mCRY and other proteins and their phosphorylation.

EXAMPLE 15

[0225] mCRY-Induced Inhibition of Transcription

[0226] The intermediate to high levels of mPer1 and mPER2 gene expression throughout the circadian day in mCry-deficient mice (Okamura et al., Science 286:2531 (1999); Vitaterna et al., Proc. Natl. Acad. Sci. USA 96:12114 (1999)) is consistent with a prominent role of the mCRY proteins in negatively regulating CLOCK:BMAL1-mediated transcription, as in vitro data have suggested (Kume et al., Cell 98:193 (1999)). The endogenous expression of the mCry1, mCry2, and mPer1-3 genes in mammalian cell lines, however, has obscured rigorous in vitro analysis of the mechanism. Therefore, an insect cell line, Schneider (S2) cells, a Drosophila cell line that expresses cycle (the Drosophila Bmal1) but not per, Tim, and clock (Saez et al., Neuron 17:911 (1996); Darlington et al., Science 280:1599 (1998)), was used to study the negative regulation of mCRY1 and mCRY2 on E box-mediated transcription with a luciferase reporter that consists of a tandem repeat of the Drosophila per E box (CACGTG) and flanking nucleotides fused to hsp70 driving luciferase (Darlington et al., Science 280: 1599 (1998)). Briefly, S2 cells were transfected with Cellfectin™ (Gibco BRL). Each transfection consisted of 10 to 100 ng of expression plasmid with indicated inserts in pAC5.1-V5, 10 ng luciferase reporter, and 25 ng of β-gal internal control plasmid (driven by baculovirus immediate-early gene, ie-1 promoter). Total DNA for each transfection was normalized using pAC5.1-V5. Cells were harvested 48 hrs after tranfection. Luciferase activity was normalized by determining luciferase:β-gal activity ratios and averaging the values from triplicate wells.

[0227] Since S2 cells express endogenous cyc, transfection with dclock alone caused a large increase in transcriptional activity (265-fold), as described (Darlington et al., Science 280: 1599 (1998)). As for dCRY (Ceriani et al., Science 285:553 (1999)), this activation was not inhibited by either mCRY1 or mCRY2. When co-transfected, mCLOCK and syrian hamster (sh)BMAL1 heterodimers induced a large increase in transcriptional activity (1744-fold) that was reduced by >90% by mCRY1 or mCRY2 (FIG. 16). Moreover, cotransfection of shBmal1 and human (h)Mop4, but not transfection of hMop4 alone, similarly caused a large increase in transcriptional activity in S2 cells (539-fold), like that previously found for hMOP4:shBMAL1 heterodimers in mammalian cells (Hogenesch et al., Proc. Natl. Acad. Sci. USA. 95:5474 (1998); Kume et al., Cell 98:193 (1999)). hMOP4:shBMAL1-mediated transcription was also blocked by either mCRY1 or mCRY2 (FIG. 16). The mCLOCK:shBMAL1- and hMOP4:shBMAL1-induced transcription in S2 cells was dependent on an intact CACGTG E box, because neither heterodimer caused an increase in transcription when a mutated E box reporter was used in the transcriptional assay. Immunofluorescence of epitope-tagged mCRY1 or mCRY2 expressed in S2 cells showed that each was >90% nuclear in location, as in mammalian cells (Kume et al., Cell 98:193 (1999)).

[0228] These data indicate that mCRY1 and mCRY2 are nuclear proteins that can each inhibit mCLOCK:shBMAL1-induced transcription independent of the mPER and mTIM proteins and of each other. The results also show that the inhibitory effect is not mediated by the interaction of either mCRY1 or mCRY2 with the E box itself, since E box-mediated transcription was not blocked by the mCRY proteins when transcription was activated by dCLOCK:CYC heterodimers. It thus appears that the mCRY proteins inhibit mCLOCK:shBMAL1-mediated transcription by interacting with either or both of the transcription factors, since a similar inhibition was found with hMOP4:shBMAL1-induced transcription. The system was performed as described in Gekakis et al. (Science 270:811 (1995)). Yeast two-hybrid assays revealed strong interactions of each mCRY protein with mCLOCK and shBMAL1. Weaker interactions were detected between each mCRY protein and hMOP4. This is further evidence of functionally relevant associations of each mCRY protein with each of the three transcription factors (Griffin et al., Science 286:768 (1999)).

[0229] Next it was determined whether the mCRY-induced inhibition of transcription was through interaction with CLOCK and/or BMAL1. Since neither mCRY1 or mCRY2 inhibited dCLOCK:CYC mediated transcription, the ability of each to inhibit dCLOCK:shBMAL1-mediated transcription was examined. This aspect of study could not be examined in S2 cells, because of the strong activation induced by transfecting dclock alone in S2 cells where there is strong endogenous cyc expression. Briefly, luciferase reporter gene assays were performed in COS-7 cells as described (Jin et al., Cell 96:57 (1999)). mCRY1 and mCRY2 completely inhibited mCLOCK:shBMAL1- and hMOP4:shBMAL1-induced transcription in COS-7 cells (FIG. 17, Left and Middle, respectively), while the cryptochromes did not inhibit dCLOCK:shBMAL1-mediated transcription by more than 20% (FIG. 17). Thus, mCRY inhibits mCLOCK:shBMAL1-induced transcription through interaction with either mCLOCK alone or through an association with both mCLOCK and BMAL1 in a multiprotein complex. Unfortunately, the examination of the inhibition of mCLOCK:CYC heterodimers was not possible, because co-transfection of mClock and cyc did not activate transcription in either insect cells or mammalian cells, even though strong interactions between mCLOCK and CYC were detected in yeast.

EXAMPLE 16

[0230] Identifying a Role for Mouse Tim

[0231] To delineate potential functions for mTim, the gene was disrupted by targeted mutagenesis. A targeting vector was designed from a 15 kb genomic clone in which a portion of the gene was replaced with a PGK-Neo cassette; this deletion-insertion disrupts mTIM after codon 178 (of 1197). Homologous recombination of the targeted allele was obtained in 129/Sv J1 embryonic stem cells, and two clones were microinjected into C57BL/6 mouse blastocysts. Chimeric offspring were mated and germline transmission was obtained.

[0232] When heterozygous animals were crossed, the resulting litters contained a 1:2 ratio of wild-type to heterozygous offspring, but no homozygous mutants. Of the offspring analyzed by Southern blotting, 29 contained only the wild-type allele and 58 were heterozygous for the mTim mutation. These results are consistent with mTim being essential for mouse survival.

[0233] Heterozygous mTim mutant embryos had reduced mTIM protein levels, confirming the targeting event; wild-type levels=8.04±2.07 (mean±SEM; n=4) versus heterozygote levels=2.98±0.61 (n=5; p<0.05, unpaired t test). Heterozygous mTim mutants had no obvious developmental or behavioral abnormalities.

[0234] Heterozygous mTim mutant animals displayed circadian rhythms in locomotor activity indistinguishable from wild-type mice of isogenic background. Rhythmic wheel-running activity of both groups persisted in constant conditions (>25 days). Furthermore, the period of locomotor activity was unchanged; wild-type mice displayed a period of 23.52±0.22 hrs (n=4) vs. 23.73±0.13 hrs (n=8) for heterozygotes (p>0.05, Student's t-test). The lack of period change in heterozygotes does not rule out a clock-relevant function for mTim, because the null Tim mutation in Drosophila is recessive.

[0235] The mortality rate of homozygous mTim mutant embryos at different gestational ages was next determined. Histological analysis of embryos from 13 litters from heterozygous mTim mutant crosses spanning embryonic day (ED) 6.5 to 11.5 showed a mortality rate of 41%. When corrected for naturally occurring prenatal attrition (14%, determined from heterozygous female X wild-type male matings), the lethality rate was 25.5%, consistent with the predicted Mendelian rate for a mutation that is lethal when homozygous.

[0236] Developmental defects due to the mTim mutation were striking at ED 7.5. At this stage, presumptive homozygous embryos lack any cellular organization, with necrotic cell debris filling the amniotic cavity, and resorption by surrounding maternal tissues has already begun. Developmental abnormalities were observed in embryos as early as ED 5.5 (data not shown), indicating that mTim is essential for development around the time of implantation. The mechanism behind the essential role of mTIM for mouse development is currently not known. At ED 7.5, in situ hybridization showed that mTim RNA is expressed throughout the embryo, particularly in the embryonic germ cell layers and in the ectoplacental cone.

[0237] The results show that mTim is essential for embryonic development.

	Number	Date	Country
	60203005	May 2000	US
	60145363	Jul 1999	US

	Number	Date	Country
Parent	09618425	Jul 2000	US
Child	10245175	Sep 2002	US

Methods for identifying compounds which modulate circadian rhythm

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