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转座元件的沉默可能不是灵长类 iPS 细胞调控进化的主要驱动力。

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.

机构信息

Department of Human Genetics, University of Chicago, Chicago, United States.

Department of Medicine, University of Chicago, Chicago, United States.

出版信息

Elife. 2018 Apr 12;7:e33084. doi: 10.7554/eLife.33084.

DOI:10.7554/eLife.33084
PMID:29648536
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5943035/
Abstract

Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from 10 human and 7 chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across 6 million years of primate evolution.

摘要

转座元件 (TEs) 约占灵长类基因组的一半，其异常调控可能导致有害影响。在多能干细胞中，快速进化的 KRAB-ZNF 基因通过 H3K9me3 将 TEs 靶向沉默。为了研究 TE 沉默的进化，我们在来自 10 个人类和 7 只黑猩猩个体的诱导多能干细胞中进行了 H3K9me3 ChIP-seq 实验。我们鉴定了四百万个直系同源 TE，并发现 SVA 和 ERV 家族最常被 H3K9me3 标记。我们几乎没有发现 TE 沉默在物种间存在差异的证据，多达 82%的假定沉默 TE 在人类和黑猩猩中以相似的水平被标记。在一个物种中优先沉默的 TE 与在两个物种中沉默的 TE 具有相似的年龄，并且不太可能与附近直系同源基因的表达差异相关联。我们的数据表明，在 600 万年的灵长类进化过程中，TE 沉默的物种特异性有限。

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Nat Commun. 2017 Mar 28;8:14550. doi: 10.1038/ncomms14550.
6
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks.KRAB 锌指蛋白有助于基因调控网络的进化。
Nature. 2017 Mar 23;543(7646):550-554. doi: 10.1038/nature21683. Epub 2017 Mar 8.
7
Conserved expression of transposon-derived non-coding transcripts in primate stem cells.转座子衍生的非编码转录本在灵长类干细胞中的保守表达。
BMC Genomics. 2017 Feb 28;18(1):214. doi: 10.1186/s12864-017-3568-y.
8
TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells.TRIM28 在人神经祖细胞中控制基于内源性逆转录病毒的基因调控网络。
Cell Rep. 2017 Jan 3;18(1):1-11. doi: 10.1016/j.celrep.2016.12.010.
9
Regulatory activities of transposable elements: from conflicts to benefits.转座元件的调控活动：从冲突到益处
Nat Rev Genet. 2017 Feb;18(2):71-86. doi: 10.1038/nrg.2016.139. Epub 2016 Nov 21.
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The DNA methyltransferase DNMT3C protects male germ cells from transposon activity.DNA 甲基转移酶 DNMT3C 可保护精原细胞免受转座子活性的影响。
Science. 2016 Nov 18;354(6314):909-912. doi: 10.1126/science.aah5143.