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Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
Zoological Letters ( IF 2.7 ) Pub Date : 2019-11-14 , DOI: 10.1186/s40851-019-0148-9
Masahiro Uesaka , Shigeru Kuratani , Hiroyuki Takeda , Naoki Irie

The relationship between development and evolution has been a central theme in evolutionary developmental biology. Across the vertebrates, the most highly conserved gene expression profiles are found at mid-embryonic, organogenesis stages, whereas those at earlier and later stages are more diverged. This hourglass-like pattern of divergence does not necessarily rule out the possibility that gene expression profiles that are more evolutionarily derived appear at later stages of development; however, no molecular-level evidence of such a phenomenon has been reported. To address this issue, we compared putative gene regulatory elements among different species within a phylum. We made a genome-wide assessment of accessible chromatin regions throughout embryogenesis in three vertebrate species (mouse, chicken, and medaka) and estimated the evolutionary ages of these regions to define their evolutionary origins on the phylogenetic tree. In all the three species, we found that genomic regions tend to become accessible in an order that parallels their phylogenetic history, with evolutionarily newer gene regulations activated at later developmental stages. This tendency was restricted only after the mid-embryonic, phylotypic periods. Our results imply a phylogenetic hierarchy of putative regulatory regions, in which their activation parallels the phylogenetic order of their appearance. One evolutionary mechanism that may explain this phenomenon is that newly introduced regulatory elements are more likely to survive if activated at later stages of embryogenesis. Possible relationships between this phenomenon and the so-called recapitulation are discussed.

中文翻译:

脊椎动物染色质可及性的概括性发展过渡

发展与进化之间的关系一直是进化发展生物学的中心主题。在整个脊椎动物中,在胚胎中期,器官发生阶段发现了最高度保守的基因表达谱,而在早期和晚期阶段则更为分散。这种类似沙漏的发散模式并不一定排除在进化的后期出现更进化的基因表达图谱的可能性。但是,尚未报道这种现象的分子水平证据。为了解决这个问题,我们比较了门内不同物种之间的推定基因调控元件。我们对三种脊椎动物物种(小鼠,鸡,和medaka),并估计了这些区域的进化年龄,以在系统发生树上定义它们的进化起源。在所有这三个物种中,我们发现基因组区域趋向于以与它们的系统发生历史相平行的顺序进入,并且在较新的发育阶段激活了进化上更新的基因调控。这种趋势只有在胚胎中期,系统型时期之后才受到限制。我们的结果暗示推定调节区域的系统发育层次,其中它们的激活与它们外观的系统发生顺序平行。可以解释这种现象的一种进化机制是,新引入的调控元件如果在胚胎发生的后期被激活,则更有可能存活。讨论了这种现象与所谓的概括之间的可能关系。
更新日期:2020-04-22
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