Evolution of regulatory networks associated with traits under selection in cichlids.
Evolution of regulatory networks associated with traits under selection in cichlids.
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DOI：
10.1186/s13059-020-02208-8
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发表时间：
2021-01-08
期刊：
影响因子：
12.3
通讯作者：
Di-Palma F
中科院分区：
文献类型：
--
作者：
Mehta TK;Koch C;Nash W;Knaack SA;Sudhakar P;Olbei M;Bastkowski S;Penso-Dolfin L;Korcsmaros T;Haerty W;Roy S;Di-Palma F
脊椎动物蛋白质进化的精液研究推测，基因调控的变化可以驱动解剖学的创新。然而，很少有人知道基因调控网络（GRN）的进化与表型效应在生态多样性物种。在这里，我们使用一种新的方法比较GRN分析脊椎动物物种的GRN进化研究的代表性物种的最引人注目的例子，适应性辐射，东非慈鲷。我们以前证明了如何爆炸性的表型多样化的东非慈鲷可以归因于不同的分子机制，包括加速调控序列的进化和基因表达的分歧。为了在全基因组范围内研究这些跨物种的机制，我们开发了一种新的计算管道，预测调节器的共现存和祖先的共表达模块沿着一个基因组，和候选人的监管区域与在慈鲷的选择下的性状。作为一个案例研究，我们将我们的方法应用到一个研究充分的适应性特征-视觉系统，我们报告了视觉视蛋白基因网络重新布线的惊人案例，识别离散的监管变体，并调查它们与慈鲷视觉系统进化的关联。在视觉视蛋白基因的调控区，在体外试验证实，转录因子结合位点突变破坏跨物种的监管边缘和隔离，根据湖泊物种发育和生态，这表明GRN重新布线辐射慈鲷。我们的方法揭示了许多新的潜在的候选监管机构和整个慈鲷基因组的监管区域，包括一些新的和一些以前报道的协会已知的适应性进化特征。
Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.
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影响因子：
2.7
作者：
Fraser, Gareth J.;Bloomquist, Ryan F.;Streelman, J. Todd
通讯作者：
Streelman, J. Todd
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
7
作者：
Chen, Jenny;Swofford, Ross;Regev, Aviv
通讯作者：
Regev, Aviv
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS
影响因子：
9.8
作者：
Hofmann CM;O'Quin KE;Marshall NJ;Cronin TW;Seehausen O;Carleton KL
通讯作者：
Carleton KL