Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish
- Authors
- Li, Y., Li, G., Wang, H., Du, J., and Yan, J.
- ID
- ZDB-PUB-130402-4
- Date
- 2013
- Source
- PLoS Computational Biology 9(2): e1002940 (Journal)
- Registered Authors
- Du, Jiu Lin
- Keywords
- none
- Datasets
- GEO:GSE37332
- MeSH Terms
-
- Animals
- Circadian Rhythm/genetics
- Circadian Rhythm/physiology*
- Circadian Rhythm Signaling Peptides and Proteins/genetics
- Circadian Rhythm Signaling Peptides and Proteins/metabolism
- Circadian Rhythm Signaling Peptides and Proteins/physiology*
- Databases, Protein
- Gene Regulatory Networks/genetics
- Gene Regulatory Networks/physiology*
- Larva
- Light
- Melanins/chemistry
- Melanins/metabolism
- Mice
- Transcription Factors
- Zebrafish
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
- Zebrafish Proteins/physiology*
- PubMed
- 23468616 Full text @ PLoS Comput. Biol.
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.