Circadian expression patterns of nuclear receptors

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

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Circadian expression of clock and putative clock-controlled genes in skeletal muscle of the zebrafish

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00367.2011 ◽

2012 ◽

Vol 302 (1) ◽

pp. R193-R206 ◽

Cited By ~ 37

Author(s):

Ian P. G. Amaral ◽

Ian A. Johnston

Keyword(s):

Skeletal Muscle ◽

Expression Patterns ◽

Light Period ◽

Rhythmic Pattern ◽

Circadian Pattern ◽

Continuous Darkness ◽

Peak Expression ◽

Circadian Expression ◽

Separate Control ◽

Food Content

To identify circadian patterns of gene expression in skeletal muscle, adult male zebrafish were acclimated for 2 wk to a 12:12-h light-dark photoperiod and then exposed to continuous darkness for 86 h with ad libitum feeding. The increase in gut food content associated with the subjective light period was much diminished by the third cycle, enabling feeding and circadian rhythms to be distinguished. Expression of zebrafish paralogs of mammalian transcriptional activators of the circadian mechanism ( bmal1, clock1, and rora) followed a rhythmic pattern with a ∼24-h periodicity. Peak expression of rora paralogs occurred at the beginning of the subjective light period [Zeitgeber time (ZT)07 and ZT02 for roraa and rorab], whereas the highest expression of bmal1 and clock paralogs occurred 12 h later (ZT13–15 and ZT16 for bmal and clock paralogs). Expression of the transcriptional repressors cry1a, per1a/1b, per2, per3, nr1d2a/2b, and nr1d1 also followed a circadian pattern with peak expression at ZT0–02. Expression of the two paralogs of cry2 occurred in phase with clock1a/1b. Duplicated genes had a high correlation of expression except for paralogs of clock1, nr1d2, and per1, with cry1b showing no circadian pattern. The highest expression difference was 9.2-fold for the activator bmal1b and 51.7-fold for the repressor per1a. Out of 32 candidate clock-controlled genes, only myf6, igfbp3, igfbp5b, and hsf2 showed circadian expression patterns. Igfbp3, igfbp5b, and myf6 were expressed in phase with clock1a/1b and had an average of twofold change in expression from peak to trough, whereas hsf2 transcripts were expressed in phase with cry1a and had a 7.2-fold-change in expression. The changes in expression of clock and clock-controlled genes observed during continuous darkness were also observed at similar ZTs in fish exposed to a normal photoperiod in a separate control experiment. The role of circadian clocks in regulating muscle maintenance and growth are discussed.

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The Circadian Clock of the Unicellular Eukaryotic Model Organism Chlamydomonas reinhardtii

Biological Chemistry ◽

10.1515/bc.2003.077 ◽

2003 ◽

Vol 384 (5) ◽

pp. 689-695 ◽

Cited By ~ 21

Author(s):

M. Mittag ◽

V. Wagner

Keyword(s):

Circadian Clock ◽

Chlamydomonas Reinhardtii ◽

Rna Binding ◽

Outer Space ◽

Expression Patterns ◽

Model Organism ◽

Nuclear Genome ◽

Circadian System ◽

Transcriptional Level ◽

Circadian Expression

Abstract The green unicellular alga Chlamydomonas reinhardtii, also called 'green yeast', emerged in the past years as a model organism for specific scientific questions such as chloroplast biogenesis and function, the composition of the flagella including its basal apparatus, or the mechanism of the circadian clock. Sequencing of its chloroplast and mitochondrial genomes have already been completed and a first draft of its nuclear genome has also been released recently. In C. reinhardtii several circadian rhythms are physiologically well characterized, and one of them has even been shown to operate in outer space. Circadian expression patterns of nuclear and plastid genes have been studied. The mode of regulation of these genes occurs at the transcriptional level, although there is also evidence for posttranscriptional control. A clock-controlled, phylogenetically conserved RNA-binding protein was characterized in this alga, which interacts with several mRNAs that all contain a common cis-acting motif. Its function within the circadian system is currently under investigation. This review summarizes the current state of the knowledge about the circadian system in C. reinhardtii and points out its potential for future studies.

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Circadian Regulation of Diverse Gene Products Revealed by mRNA Expression Profiling of Synchronized Fibroblasts

Journal of Biological Chemistry ◽

10.1074/jbc.m107499200 ◽

2001 ◽

Vol 276 (50) ◽

pp. 46751-46758 ◽

Cited By ~ 88

Author(s):

Christophe Grundschober ◽

Franck Delaunay ◽

Anja Pühlhofer ◽

Gerard Triqueneaux ◽

Vincent Laudet ◽

...

Keyword(s):

Drug Targets ◽

Expression Patterns ◽

Gene Products ◽

Cellular Functions ◽

Total Period ◽

Circadian Genes ◽

Mrna Profiling ◽

Circadian Expression ◽

Rat Fibroblasts ◽

Mrna Expression Profiling

Genes under a 24-h regulation period may represent drug targets relevant to diseases involving circadian dysfunctions. As a testing model of the circadian clock system, we have used synchronized rat fibroblasts that are known to express at least six genes in a circadian fashion. We have determined the expression patterns of 9957 transcripts every 4 h over a total period of 76 h using high density oligonucleotide microarrays. The spectral analysis of our mRNA profiling data indicated that ∼2% (85 genes) of all expressed genes followed a robust circadian pattern. We have confirmed the circadian expression of previously known clock or clock-driven genes, and we identified 81 novel circadian genes. The majority of the circadian-regulated gene products are known and are involved in diverse cellular functions. We have classified these circadian genes in seven clusters according to their phase of cycling. Our pathway analysis of the mRNA profiling data strongly suggests a direct link between circadian rhythm and cell cycle.

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Circadian expression patterns ofvrillein peripheral tissues of mutants inDrosophila melanogaster

Biological Rhythm Research ◽

10.1080/09291010802402477 ◽

2009 ◽

Vol 40 (4) ◽

pp. 337-345

Author(s):

R. Sivaperumal ◽

P. Subramanian ◽

K. V. Pugalendi

Keyword(s):

Expression Patterns ◽

Peripheral Tissues ◽

Circadian Expression

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A Pair of Partially Overlapping Arabidopsis Genes with Antagonistic Circadian Expression

International Journal of Plant Genomics ◽

10.1155/2012/349527 ◽

2012 ◽

Vol 2012 ◽

pp. 1-7 ◽

Cited By ~ 5

Author(s):

Andrea Kunova ◽

Elena Zubko ◽

Peter Meyer

Keyword(s):

Antisense Transcript ◽

Expression Patterns ◽

Antisense Transcription ◽

Antisense Gene ◽

Transcript Levels ◽

Sense Transcript ◽

Circadian Expression ◽

Plant Genes ◽

Dna Insertion ◽

Partial Overlap

A large number of plant genes are aligned with partially overlapping genes in antisense orientation. Transcription of both genes would therefore favour the formation of double-stranded RNA, providing a substrate for the RNAi machinery, and enhanced antisense transcription should therefore reduce sense transcript levels. We have identified a gene pair that resembles a model for antisense-based gene regulation as a T-DNA insertion into the antisense gene causes a reduction in antisense transcript levels and an increase in sense transcript levels. The same effect was, however, also observed when the two genes were inserted as transgenes into different chromosomal locations, independent of the sense and antisense gene being expressed individually or jointly. Our results therefore indicate that antagonistic changes in sense/antisense transcript levels do not necessarily reflect antisense-mediated regulation. More likely, the partial overlap of the two genes may have favoured the evolution of antagonistic expression patterns preventing RNAi effects.

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