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cryptochrome 1a


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GeneName cry1a
Aliases ENSDARG:ENSDARG00000045768; cryptochrome 1a; zcry1a, zgc:153885
Description cryptochrome 1a
GenomicLocation chromosome 4 11077567-11091060 forward strand
ExternalIDs Entrez:100003956; EMBL:BC124762; UniGene:82313; ZFIN:ZDB-GENE-010426-2;
TranscriptID ENSDART:ENSDART00000067281; ENSDART:ENSDART00000130692; ENSDART:ENSDART00000034401
mRNA NCBI:NM_001077297

GeneFunction Kobayashi et al. (2000) reported that zebrafish have six rhythmically expressed cryptochrome genes.Gregory M. Cahill (2002) described how phylogenetic analysis has shown that four of Cry1 genes (Cry1a, Cry1b, Cry2a, and Cry2b) are most similar to mCry1. Each of these four zebrafish CRY proteins can inhibit transcriptional activation by mammalian CLOCK:BMAL1 dimers, and all are rhythmically expressed in the eye, brain, and body. The mRNA rhythms of zCry1a and zCry1b peak during the daytime, whereas rhythms of zCry2a and zCry2b peak later, in the evening suggesting that they are not entirely redundant. A fifth gene, Cry3, also clusters with mCrys in phylogenetic analyses. However, the product of this gene does not inhibit CLOCK:BMAL1-mediated transcription, and Kobayashi et al. (2000) place it in a separate class. The Cry3 gene is expressed rhythmically, with an mRNA peak in the morning. The sequence of the sixth zebrafish cryptochrome (Cry4) is most divergent from all other vertebrate Crys, and its product also does not inhibit CLOCK:BMAL1-mediated transcription. It is however rhythmically expressed, with an mRNA peak during t the day.Hirayama et al. (2002) speculated that the opposite regulation of the subcellular distribution of cry1a is associated with the different transcriptional repression abilities of zCRY1a and zPER2. zCRY1a acts as a potent transcriptional inhibitor by interacting directly with the zCLOCK:zBMAL heterodimer in the nucleus, whereas zPER2 maintains the zCLOCK:zBMAL heterodimer in the cytoplasm, resulting in transactivation repression.Hirayama et al. (2003) identified the sequence elements required for the interaction of CRY with other clock proteins, as well as for regulation of the subcellular distribution and transcriptional repression. The findings for these chimeras show that both the nuclear localization and interaction with the CLOCK:BMAL heterodimer are essential for transcriptional repression by CRY. Hirayama et al. (2005) showed that that in zebrafish light induces the activity of AP-1 (activator protein-1), which in turn controls some specific circadian and cell cycle genes. Thus, a unique light-responsive transcriptional pathway is shared by the two cellular systems of cyclic regulation.Tamai et al. (2007) examined the effect of light on Cry1a induction and phase shifting and establish how the Cry1a protein interacts with the core clock. Results from intensity and PRCs demonstrate a strong correlation between light induction of the Cry1a gene and clock resetting. Overexpression analysis reveals that Cry1a is a potent transcriptional repressor and appears to mimic the effect of sustained light to ‘‘stop’’ the circadian oscillator. Biochemical studies showed that the Cry1a protein binds to multiple domains of central clock components, CLOCK and BMAL. This binding then blocks transactivation, providing a likely mechanism for clock resetting and establishment of high-amplitude rhythms on a LD cycle. Thus, Cry1a appears to play a critical role in the response of the zebrafish clock to light but, interestingly, as part of a signaling pathway to the circadian pacemaker.

GeneStructure This gene encodes three transcripts, out of which one is novel (ENSDART00000067281) consists of 12 exons and is 1,674 bps in length. The protein product (ENSDARP00000067280) consists of 557 residues. (ENSDART00000067282) consists of 14 exons and is 3,168 bps in length. The protein product (ENSDARP00000067281) consists of 619 residues. (ENSDART00000034401) consisting of 12 exons and is 1,839 bps in length. The protein product (ENSDARP00000028955) consists of 612 residues. (NOVEL)
Protein ENSDARP00000067280 ENSDARP00000112452 ENSDARP00000028955
ProteinDomainandFamilies has domain InterPro:IPR006050; InterPro:IPR014729; InterPro:IPR005101;
Motifs has motif PFAM:PF00875; PFAM:PF03441;
Expression ArrayExpress:ENSDARG00000045768
GeneOntology GO:0005575; GO:0005667; GO:0005515; GO:0006281; GO:0016564; GO:0009649; GO:0003913; GO:0042542; GO:0009416; GO:0005634;

VariationAndRepeats RSID:rs180035393; RSID:rs180035393; RSID:rs180035393; RSID:rs180035394; RSID:rs180035394; RSID:rs180035394; RSID:rs180035395; RSID:rs180035395; RSID:rs180035395; RSID:rs180035396; RSID:rs180035396; RSID:rs180035396; RSID:rs41107099; RSID:rs41107099; RSID:rs41107099; RSID:rs41211978; RSID:rs41211978; RSID:rs41211978

RelatedPubMedArticles Kobayashi Y.; Ishikawa T.; Hirayama J.; Daiyasu H.; Kanai S.; Toh H.; Fukuda I.; Tsujimura T.; Terada N.; Kamei Y.; Yuba S.; Iwai S.; Todo T.: Molecular analysis of zebrafish photolyase/cryptochrome family: two types of cryptochromes present in zebrafish. Genes Cells. 2000. 5(9):725-38. PMID:10971654 Cahill G. M.: Clock mechanisms in zebrafish. Cell Tissue Res. 2002. 309(1):27-34. Review. PMID:12111534 Tamai T. K.; Carr A. J.; Whitmore D.: Zebrafish circadian clocks: cells that see light. Biochem Soc Trans. 2005. 33(Pt 5):962-6. Review. PMID:16246021 Hirayama J.; Nakamura H.; Ishikawa T.; Kobayashi Y.; and Todo T.: Functional and structural analyses of cryptochrome: Vertebrate CRY regions responsible for interaction with the CLOCK: BMAL1 heterodimer and its nuclear localization. J. Biol. Chem. 2003. 278(37):35630-35628. PMID: 12832412 Hirayama J.; Cardone L.; Doi M.; Sassone-Corsi P.: Common pathways in circadian and cell cycle clocks: light-dependent activation of Fos/AP-1 in zebrafish controls CRY-1a and WEE-1. Proc Natl Acad Sci U S A. 2005. 19;102(29):10194-9. PMID:16000406 Hirayama J.; Cho S.; Sassone-Corsi P.: Circadian control by the reduction/oxidation pathway: catalase represses light-dependent clock gene expression in the zebrafish. Proc Natl Acad Sci U S A. 2007. 104(40):15747-52. PMID:17898172 Tamai T. K..; Young L. C.; Whitmore D.: Light signaling to the zebrafish circadian clock by Cryptochrome 1a. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14712-7. Epub 2007 Sep 4. PMID:17785416NCBI Resource Coordinators.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41(Database issue):D8-D20. 2013. PMID:23193264
Kersey, P. J.; Allen, J. E.; Christensen, M.; et al.: Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2013. PMID:24163254
Sigrist, C. J. A.; de, Castro, E; Cerutti, L; Cuche, B. A.; Hulo, N.; Bridge, A.; Bougueleret, L. Xenarios, I.: New and continuing developments at PROSITE. Nucleic Acids Res. doi: 10.1093/nar/gks1067. 2012. PMID:23161676
Punta, M.; Coggill, P. C.; Eberhardt, et al.: The Pfam protein families database. Nucleic Acids Res. 40(Database Issue):D290-D301. 2012. PMID:22127870
Hunter, S.; Jones P.; Mitchell A.; et al.: Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. doi: 10.1093/nar/gkr948. 2011. PMID:22096229
Carbon, S.; Ireland, A.; Mungall, C. J.; Shu, S.; Marshall, B.; Lewis, S.; AMIGO Hub; Web Presence Working Group.: AMIGO: online access to ontology and annotation data. Bioinformatics. 25(2):288-9. 2009. PMID:19033274
Ashburner, M.; Ball, C. A.; Blake, J. A.; et al. The Gene Ontology Consortium.: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1):25-9. 2000. PMID:10802651
Sherry, S. T.; Ward, M. H.; Kholodov, M.; Baker, J.; Phan, L.; Smigielski, E. M.; Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 1;29(1):308-11. 2001. PMID:11125122
Bradford, Y.; Conlin, T.; Dunn, N.; et al.: ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(suppl 1):D822-D829. 2011. PMID:21036866
Kapushesky, M.; Adamusiak, T.; Burdett, T.; et al.: Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 40(Database isue):D1077-81. 2012. PMID:22064864

Web resources:
NCBI: http://www.ncbi.nlm.nih.gov/
PFAM: http://pfam.sanger.ac.uk/
PROSITE: http://prosite.expasy.org/
Interpro: http://www.ebi.ac.uk/interpro/
ZFIN: http://zfin.org/
Expression Atlas (EMBL): http://www.ebi.ac.uk/gxa/
Ensembl: http://asia.ensembl.org/Danio_rerio/
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine.: http://www.ncbi.nlm.nih.gov/SNP/
PRINTS from Genomenet: http://www.genome.jp/
European Nucleotide Archive: http://www.ebi.ac.uk/ena/home
UNIGENE: http://www.ncbi.nlm.nih.gov/unigene/
AMIGO Gene Ontology: http://amigo.geneontology.org
Topic revision: r2 - 2013-07-26 - ParasSehgal
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