Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish.
Analysis of a gene regulatory cascade mediating circadian rhythm in zebrafish.
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DOI：
10.1371/journal.pcbi.1002940
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发表时间：
2013
影响因子：
4.3
通讯作者：
Yan J
中科院分区：
文献类型：
--
作者：
Li Y;Li G;Wang H;Du J;Yan J
在生物钟的研究中，有限数量的生物钟基因如何控制生理的各个方面一直是一个难题。在这里，我们调查昼夜节律基因表达全基因组使用斑马鱼幼虫作为模型系统。我们利用空间基因表达图谱来研究昼夜节律基因在各种组织和细胞类型中的表达。斑马鱼和小鼠全基因组昼夜节律基因表达数据的比较揭示了一种几乎反相的关系，使我们能够在脊椎动物中检测到新的进化保守的昼夜节律基因。我们确定了三组斑马鱼基因与不同的光诱导反应：快速光诱导基因，慢光诱导基因，和黑暗诱导基因。我们的昼夜节律基因调控网络的计算分析揭示了几个转录因子（TF）通过转录级联参与昼夜节律生理的各个方面。其中，小眼症相关转录因子a（mitfa），黑暗诱导的TF，介导黑色素合成的昼夜节律，这可能涉及斑马鱼的适应日常光周期。我们的研究描述了一种系统的方法来发现以前未识别的参与复杂生物昼夜节律生理学的TF。对于大多数依赖太阳生存的动物来说，生物钟控制着它们的日常行为和生理。在不同的动物中，生物钟控制下的新功能可以进化为适应特定环境。斑马鱼由于其透明的性质，在外部光与其内部生物钟之间表现出非常高的相互作用。在全基因组研究中，我们鉴定了大量的昼夜节律振荡基因以及在斑马鱼中表达对光或暗高度敏感的基因。我们的基因调控网络的计算分析揭示了一些转录因子（TF），介导新的昼夜节律功能。我们深入研究了一个例子，一个关键的TF，它将生物钟的控制传递给黑暗诱导途径中合成黑色素的酶，从而导致斑马鱼色素沉着的每日变化。这种黑暗诱导的昼夜黑素生成可以导致斑马鱼皮肤颜色的预期变化，使斑马鱼能够适应其环境。这种机制使斑马鱼能够更好地躲避捕食者，并有效地调整其色素细胞中的日常光敏感性。我们的研究提供了一个很好的例子，说明生物钟如何适应特定的生物体来控制其行为，从而使生物体的生态位进化适应。
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. For most animals whose lives are dependent on the sun, circadian clocks govern their daily behaviors and physiology. In different animals, novel functions under the circadian clock's control can evolve as adaptations to their specific environment. A zebrafish demonstrates a remarkably high level of interplay between external light and its internal circadian clock due to its transparent nature. In a genome-wide study, we identified a large number of circadian oscillating genes as well as genes whose expression is highly sensitive to the light or dark in zebrafish. Our computational analysis of gene regulatory networks revealed a number of transcription factors (TFs) that mediate novel circadian functions. We investigated one example in depth, a key TF that relays the control of the circadian clock to the enzymes synthesizing melanin in a dark-induced pathway thus causing the daily change of pigmentation in zebrafish. This dark-induced circadian melanogenesis can lead to an anticipatory change in zebrafish skin color allowing zebrafish to adapt to its environment. This mechanism allows zebrafish to better evade predators and effectively adjust its daily light-sensitivity in the pigment cells. Our study provides an excellent example of how the circadian clock is adapted in a specific organism to control its behavior, thus enabling evolutionary adaptation to the organism's ecological niche.
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影响因子：
2.7
作者：
Johnson SL;Nguyen AN;Lister JA
通讯作者：
Lister JA
影响因子：
3.5
作者：
Appelbaum, L;Vallone, D;Gothilf, Y
通讯作者：
Gothilf, Y
影响因子：
9.8
作者：
Kaneko M;Cahill GM
通讯作者：
Cahill GM
影响因子：
11.4
作者：
Chen, Chen-Hui;Ringelberg, Carol S.;Loros, Jennifer J.
通讯作者：
Loros, Jennifer J.
DOI：
10.1016/s1096-4959(02)00194-x
发表时间：
2003-01-01
影响因子：
2.2
作者：
Du, SJ;Gao, J;Anyangwe, V
通讯作者：
Anyangwe, V