Noncoding origins of anthropoid traits and a new null model of transposon functionalization.
Noncoding origins of anthropoid traits and a new null model of transposon functionalization.
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DOI：
10.1101/gr.168963.113
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发表时间：
2014-09
期刊：
影响因子：
7
通讯作者：
Prabhakar S
中科院分区：
文献类型：
--
作者：
del Rosario RC;Rayan NA;Prabhakar S
关于驱动灵长类动物出现的新遗传因素，人们知之甚少。我们利用对绒猴基因组的测序来鉴定23，849个绒猴特异性约束（ASC）区域，并证实了它们强大的功能特征。在ASC碱基对中，99.7%是非编码的，这表明新的类胡萝卜素功能元件绝大多数是顺式调节的。ASCs高度富集在与胎儿脑发育、运动协调、神经传递和视觉相关的基因座中，从而为探索标志性灵长类性状的分子基础提供了大量候选元素。我们验证了ASC192作为发育中大脑增殖区的灵长类动物特异性增强子。出乎意料的是，转座因子（TE）占ASC的56%以上，几乎所有TE家族都显示出与非重复DNA相似的功能潜力。三个L1PA重复衍生的ASC显示出连贯的眼增强子功能，从而证明TE功能化的“基因电池”模型适用于体内增强子。我们的研究提供了基因组进化的基本见解和原始表型的起源，并支持一个优雅简单的新的零模型TE exaptation。
Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission, and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of nonrepetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the “gene-battery” model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes and supports an elegantly simple new null model of TE exaptation.
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