Repurposing of promoters and enhancers during mammalian evolution

The spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 445 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed "P/E" elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of putative ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5' exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5' splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work highlights functional repurposing as a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.启动子（promoter）与增强子（enhancer）对基因表达的时空调控，是个体发育、生理机能与行为表现的核心基础。长期以来，两类调控元件（regulatory elements）依据功能差异加以区分，但近期研究揭示了二者共有的结构与功能特征。另有研究表明，调控元件的表观遗传（epigenetic）与序列背景发生可遗传改变，可能是其核心活性发生演化变化的根源，进而可导致其所调控基因的转录谱（transcriptional profile）改变，甚至推动新基因的诞生。 本研究基于对DNase超敏性（DNase hypersensitivity）、染色质修饰（chromatin modification）及转录数据（transcriptional data）的跨哺乳动物整合分析，通过在灵长类与啮齿类支系（primate and rodent lineages）的姊妹物种（sister species）中检测到445个带有活性周转特征的调控元件（命名为“P/E元件（P/E element）”），为该假说提供了支持。通过与外类群物种（outgroup species）的比较，我们明确了周转事件的方向性，结果显示多数事件为推定的祖先增强子向启动子的转化，进而催生了物种特异性转录位点或5'外显子。 值得注意的是，P/E元件具有独特的GC序列组成与稳定5'剪接（U1）的调控基序模式，这或使其在演化过程中易于发生功能重定向。此外，我们追踪了伴随演化活性转换并可能推动其发生的U1基序与多聚腺苷酸化信号（polyadenylation signal）的密度及分布变化。 综上，本研究凸显了功能重定向作为一种重要机制，可能在哺乳动物演化过程中推动了调控创新以及新基因与外显子的起源。