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Amphioxus functional genomics and the origins of vertebrate gene regulation

机译：文昌鱼功能基因组学和脊椎动物基因调控的起源

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摘要

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.
机译：脊椎动物极大地阐明了基本的碳酸盐体计划，并进化出高度独特的基因组，该基因组由两次全基因组重复雕刻而成。在这里，我们对地中海两栖动物（Branchiostoma lanceolatum）的基因组进行测序，并表征DNA甲基化，染色质可及性，组蛋白修饰和跨多个发育阶段和成年组织的转录组，以研究调节胆酸盐基因组的进化。与脊椎动物的比较确定了差异甲基化增强子进化的中间阶段，以及两栖动物和脊椎动物之间基因表达的高度保守及其顺式调节逻辑，这种现象在胚胎中期系统型早期就出现了。我们分析了全基因组重复后的调控进化，发现在脊椎动物中，超过80％的广泛表达的基因家族具有源自全基因组重复的多个旁系同源物，其成员限制了它们的祖先表达，并且经历了专业化而非亚功能化。违反直觉的是，限制其表达的旁白增加了其监管范围的复杂性。这些数据为更好地理解作为关键脊椎动物创新基础的监管原则铺平了道路。

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