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Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish.

Li Y, Li G, Wang H, Du J, Yan J - PLoS Comput. Biol. (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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.

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Related in: MedlinePlus

Circadian expression profiles of 14 tissue-specific TFs.The expression levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs were measured by real-time PCR in 5 dpf clock morphants (red) compared to WT (blue) or control (green) morphants. The lowest log2-transformed expression level for each TF was normalized to zero. The reduction in oscillation amplitude, loss of rhythmicity, and increase or decrease in baseline expression levels in clock morphants compared to WT or control morphants were annotated for each gene.
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pcbi-1002940-g005: Circadian expression profiles of 14 tissue-specific TFs.The expression levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs were measured by real-time PCR in 5 dpf clock morphants (red) compared to WT (blue) or control (green) morphants. The lowest log2-transformed expression level for each TF was normalized to zero. The reduction in oscillation amplitude, loss of rhythmicity, and increase or decrease in baseline expression levels in clock morphants compared to WT or control morphants were annotated for each gene.

Mentions: Our network analysis shows that clock is at the center of the regulatory network and all other circadian TFs are under its control either directly or indirectly. In order to validate this experimentally, we generated clock morpholino (MO) knock-down larvae. We measured circadian mRNA levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs by real-time PCR in 5 dpf clock morphants compared to WT or control morphants (Figure 5). In WT and controls, the circadian peak times of these genes show high consistency between real-time PCR and arrays. In clock morphants, bhlhe40/41, per3, smad3a, and hnf1a continue to oscillate but show significant reductions in oscillation amplitudes. The remaining genes show loss of rhythmicity except for crx in clock morphants. Furthermore, smad1 and myog show significant up-regulation (p<0.001), whereas ppargc1b, maf, mef2a show significant down-regulation in baseline levels in clock morphants compared to the WT and controls (Primers used for real-time PCR are in Table S5).


Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish.

Li Y, Li G, Wang H, Du J, Yan J - PLoS Comput. Biol. (2013)

Circadian expression profiles of 14 tissue-specific TFs.The expression levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs were measured by real-time PCR in 5 dpf clock morphants (red) compared to WT (blue) or control (green) morphants. The lowest log2-transformed expression level for each TF was normalized to zero. The reduction in oscillation amplitude, loss of rhythmicity, and increase or decrease in baseline expression levels in clock morphants compared to WT or control morphants were annotated for each gene.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585402&req=5

pcbi-1002940-g005: Circadian expression profiles of 14 tissue-specific TFs.The expression levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs were measured by real-time PCR in 5 dpf clock morphants (red) compared to WT (blue) or control (green) morphants. The lowest log2-transformed expression level for each TF was normalized to zero. The reduction in oscillation amplitude, loss of rhythmicity, and increase or decrease in baseline expression levels in clock morphants compared to WT or control morphants were annotated for each gene.
Mentions: Our network analysis shows that clock is at the center of the regulatory network and all other circadian TFs are under its control either directly or indirectly. In order to validate this experimentally, we generated clock morpholino (MO) knock-down larvae. We measured circadian mRNA levels of bhlhe40/41 and per3 together with 11 circadian tissue-specific TFs by real-time PCR in 5 dpf clock morphants compared to WT or control morphants (Figure 5). In WT and controls, the circadian peak times of these genes show high consistency between real-time PCR and arrays. In clock morphants, bhlhe40/41, per3, smad3a, and hnf1a continue to oscillate but show significant reductions in oscillation amplitudes. The remaining genes show loss of rhythmicity except for crx in clock morphants. Furthermore, smad1 and myog show significant up-regulation (p<0.001), whereas ppargc1b, maf, mef2a show significant down-regulation in baseline levels in clock morphants compared to the WT and controls (Primers used for real-time PCR are in Table S5).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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.

Show MeSH
Related in: MedlinePlus