Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins

Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study, we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph Heliocidaris erythrogramma, a closely related planktotroph H. tuberculata, and a distantly related planktotroph Lytechinus variegatus. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative cis-regulatory elements in H. erythrogramma that have accumulated non-uniformly thro...

动物胚胎发育过程中，染色质构象（Chromatin configuration）具有高度动态性，在转录调控（transcriptional regulation）中发挥着关键的调控作用。然而，关于染色质构象的进化变化对基因表达及生物性状进化的作用，现有信息极为有限。全基因组染色质构象分析（Genome-wide assays of chromatin configuration）结合全基因组比对（whole-genome alignments），可从多方面填补这一知识空白。本研究对三种具有不同生活史的海胆物种胚胎发生全过程中的调控元件序列及可及性进行了比较分析：卵黄营养型（lecithotroph）的Heliocidaris erythrogramma、与其近缘的浮游营养型（planktotroph）H. tuberculata，以及远缘的浮游营养型Lytechinus variegatus。我们发现，H. erythrogramma中推定的顺式调控元件（putative cis-regulatory elements）功能的进化修饰具有独特的表观遗传及突变特征，这些特征在...过程中非均匀积累。