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. 78 single-end strand-specific RNA-seq libraries were generated from polyA-selected RNA from four organs (brain, heart, kidney and liver) from human, macaque, marmoset, mouse, rat and rabbit samples.启动子（promoter）与增强子（enhancer）所介导的基因表达时空调控，对于生物体的发育、生理功能与行为模式至关重要。长期以来，这两类调控元件一直以功能差异作为区分依据，但近期研究揭示了二者在结构架构与功能特征上的共通之处。此外，相关研究还提出，调控元件的表观遗传修饰与序列环境发生可遗传改变，可能是其核心活性发生演化变化的基础，这一过程可导致其所调控基因的转录谱发生改变，甚至推动新基因的诞生。本研究基于对跨哺乳动物的DNase超敏感位点（DNase hypersensitivity）、染色质修饰（chromatin modification）与转录组数据的整合分析，在灵长类与啮齿类演化支的姊妹物种中检测到445个带有活性转换特征的调控元件（命名为"P/E元件"），为上述假说提供了支持证据。通过与外类群物种的比较，我们明确了活性转换事件的方向性，结果显示绝大多数转换事件均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的转录位点或5'外显子。值得注意的是，P/E元件具有独特的GC序列组成与稳定的5'剪接（U1）调控基序模式，这或许使其在演化过程中更易发生功能重定向。此外，我们还追踪了伴随且可能推动演化活性转换的U1与多聚腺苷酸化信号的密度与分布变化。总体而言，本研究揭示功能重定向是一项重要机制，该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新外显子的产生。本研究从人类、猕猴、狨猴、小鼠、大鼠与家兔的4种器官（大脑、心脏、肾脏与肝脏）中提取聚腺苷酸（polyA）富集RNA，构建了78个单链特异性RNA测序（RNA-seq）文库。