title: Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes.
abstract: From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network.
authors.affiliation: Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America.
authors.forename: Greg
authors.initials: G
authors.lastname: Boyle
authors.affiliation: Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Richter
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America.
authors.forename: Henry D
authors.initials: HD
authors.lastname: Priest
authors.affiliation: Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America.
authors.forename: David
authors.initials: D
authors.lastname: Traver
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.affiliation: Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America.
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Chang
authors.affiliation: Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Steve A
authors.initials: SA
authors.lastname: Kay
authors.affiliation: Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America.
authors.forename: Ghislain
authors.identifier: http://orcid.org/0000-0001-6400-3858
authors.initials: G
authors.lastname: Breton
mesh_terms: D000818:Animals; D057906:Circadian Clocks / Q000235:genetics; D002940:Circadian Rhythm / Q000235:genetics*; D004625:Embryo, Nonmammalian; D020869:Gene Expression Profiling; D008099:Liver / Q000378:metabolism; D008297:Male; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D059467:Transcriptome; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish