title: Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish.
abstract: In the study of circadian rhythms, it has been a puzzle how a limited number of circadian clock genes can control diverse aspects of physiology. Here we investigate circadian gene expression genome-wide using larval zebrafish as a model system. We made use of a spatial gene expression atlas to investigate the expression of circadian genes in various tissues and cell types. Comparison of genome-wide circadian gene expression data between zebrafish and mouse revealed a nearly anti-phase relationship and allowed us to detect novel evolutionarily conserved circadian genes in vertebrates. We identified three groups of zebrafish genes with distinct responses to light entrainment: fast light-induced genes, slow light-induced genes, and dark-induced genes. Our computational analysis of the circadian gene regulatory network revealed several transcription factors (TFs) involved in diverse aspects of circadian physiology through transcriptional cascade. Of these, microphthalmia-associated transcription factor a (mitfa), a dark-induced TF, mediates a circadian rhythm of melanin synthesis, which may be involved in zebrafish's adaptation to daily light cycling. Our study describes a systematic method to discover previously unidentified TFs involved in circadian physiology in complex organisms.
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.forename: Guang
authors.initials: G
authors.lastname: Li
authors.forename: Haifang
authors.initials: H
authors.lastname: Wang
authors.forename: Jiulin
authors.initials: J
authors.lastname: Du
authors.forename: Jun
authors.initials: J
authors.lastname: Yan
mesh_terms: D000818:Animals; D002940:Circadian Rhythm / Q000235:genetics / Q000502:physiology*; D056925:Circadian Rhythm Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D030562:Databases, Protein; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D007814:Larva; D008027:Light; D008543:Melanins / Q000737:chemistry / Q000378:metabolism; D051379:Mice; D014157:Transcription Factors; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
chemical_list: D056925:Circadian Rhythm Signaling Peptides and Proteins; D008543:Melanins; D014157:Transcription Factors; D029961:Zebrafish Proteins