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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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Three types of genes affected by light entrainment.(A) The circadian expression of fast light-induced genes, slow light-induced genes, and dark-induced genes and representatives of each group (per2, cry2a, and aanat1) on the microarrays are shown. (B) The distinct kinetics of per2, cry2a, aanat1, and clock genes upon light or dark exposure in larval zebrafish fertilized and raised under either DD or LL conditions respectively for 20 hours starting at 5 dpf (5DD to LL and 5LL to DD). The larval zebrafish remained in the constant conditions (5DD to DD and 5LL to LL) were used as controls. The lowest log2-transformed expression level for each gene was normalized to zero. Two independent time-series experiments were conducted with error bars shown in the figure.
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pcbi-1002940-g002: Three types of genes affected by light entrainment.(A) The circadian expression of fast light-induced genes, slow light-induced genes, and dark-induced genes and representatives of each group (per2, cry2a, and aanat1) on the microarrays are shown. (B) The distinct kinetics of per2, cry2a, aanat1, and clock genes upon light or dark exposure in larval zebrafish fertilized and raised under either DD or LL conditions respectively for 20 hours starting at 5 dpf (5DD to LL and 5LL to DD). The larval zebrafish remained in the constant conditions (5DD to DD and 5LL to LL) were used as controls. The lowest log2-transformed expression level for each gene was normalized to zero. Two independent time-series experiments were conducted with error bars shown in the figure.

Mentions: Next, we searched for genes having reduced amplitudes as a consequence of either decreased peak levels or elevated trough levels in DD compared to LD. To include the genes that might have lost rhythmicity under DD, we examined 3,677 LD oscillating genes (FDR≤10%) regardless of their rhythmicity under DD. Among them, we identified 464 genes showing decreased peaks and 113 genes showing elevated troughs in DD compared to LD (Materials and Methods). We defined 366 peak decreased genes with LD circadian phases lying in the light period as “light-induced” because their expression increases in the light period in LD but remains at low level in DD (Figure 2A; Table S4). Similarly, 50 trough-increased genes with LD circadian phases lying in the dark period were defined as “dark-induced genes”. Furthermore, we observed that the LD circadian phases of light-induced genes were predominantly distributed around CT5. The expression of these genes increases rapidly after lights-on and reaches a peak after 5 hours in LD. Thus we defined 197 light-induced genes with LD circadian phases between CT2 and CT8 as “fast light-induced genes”. This group includes known light-sensitive genes (e.g. per2, cry5, cry-dash, and tefa). It also contains genes showing significantly enriched expression in epiphysis and the retinal photoreceptive layer (e.g. arrestin 3 (arr3a/b) and interphotoreceptor retinoid-binding protein (irbp)). The remaining light-induced genes show a slow increase in expression during the light period, reaching a peak before lights-off in LD. Accordingly, they were defined as “slow light-induced genes”. This group includes key circadian genes (e.g. cry2a/b, arntl1b, and nfil3-5). The expression of dark-induced genes is repressed during the light period but increases in the dark period reaching peak level after lights-off. Among the dark-induced genes are melatonin synthesizing enzyme (aanat1), dopamine D4 receptor (drd4a) and two genes related to pigmentation (mitfa and slc24a5). In short, there are complex, dynamic responses to light entrainment during circadian gene expression.


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)

Three types of genes affected by light entrainment.(A) The circadian expression of fast light-induced genes, slow light-induced genes, and dark-induced genes and representatives of each group (per2, cry2a, and aanat1) on the microarrays are shown. (B) The distinct kinetics of per2, cry2a, aanat1, and clock genes upon light or dark exposure in larval zebrafish fertilized and raised under either DD or LL conditions respectively for 20 hours starting at 5 dpf (5DD to LL and 5LL to DD). The larval zebrafish remained in the constant conditions (5DD to DD and 5LL to LL) were used as controls. The lowest log2-transformed expression level for each gene was normalized to zero. Two independent time-series experiments were conducted with error bars shown in the figure.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002940-g002: Three types of genes affected by light entrainment.(A) The circadian expression of fast light-induced genes, slow light-induced genes, and dark-induced genes and representatives of each group (per2, cry2a, and aanat1) on the microarrays are shown. (B) The distinct kinetics of per2, cry2a, aanat1, and clock genes upon light or dark exposure in larval zebrafish fertilized and raised under either DD or LL conditions respectively for 20 hours starting at 5 dpf (5DD to LL and 5LL to DD). The larval zebrafish remained in the constant conditions (5DD to DD and 5LL to LL) were used as controls. The lowest log2-transformed expression level for each gene was normalized to zero. Two independent time-series experiments were conducted with error bars shown in the figure.
Mentions: Next, we searched for genes having reduced amplitudes as a consequence of either decreased peak levels or elevated trough levels in DD compared to LD. To include the genes that might have lost rhythmicity under DD, we examined 3,677 LD oscillating genes (FDR≤10%) regardless of their rhythmicity under DD. Among them, we identified 464 genes showing decreased peaks and 113 genes showing elevated troughs in DD compared to LD (Materials and Methods). We defined 366 peak decreased genes with LD circadian phases lying in the light period as “light-induced” because their expression increases in the light period in LD but remains at low level in DD (Figure 2A; Table S4). Similarly, 50 trough-increased genes with LD circadian phases lying in the dark period were defined as “dark-induced genes”. Furthermore, we observed that the LD circadian phases of light-induced genes were predominantly distributed around CT5. The expression of these genes increases rapidly after lights-on and reaches a peak after 5 hours in LD. Thus we defined 197 light-induced genes with LD circadian phases between CT2 and CT8 as “fast light-induced genes”. This group includes known light-sensitive genes (e.g. per2, cry5, cry-dash, and tefa). It also contains genes showing significantly enriched expression in epiphysis and the retinal photoreceptive layer (e.g. arrestin 3 (arr3a/b) and interphotoreceptor retinoid-binding protein (irbp)). The remaining light-induced genes show a slow increase in expression during the light period, reaching a peak before lights-off in LD. Accordingly, they were defined as “slow light-induced genes”. This group includes key circadian genes (e.g. cry2a/b, arntl1b, and nfil3-5). The expression of dark-induced genes is repressed during the light period but increases in the dark period reaching peak level after lights-off. Among the dark-induced genes are melatonin synthesizing enzyme (aanat1), dopamine D4 receptor (drd4a) and two genes related to pigmentation (mitfa and slc24a5). In short, there are complex, dynamic responses to light entrainment during circadian gene expression.

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