Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.
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DOI：
10.1186/s13059-017-1335-7
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发表时间：
2017-10-24
期刊：
影响因子：
12.3
通讯作者：
Veenstra GJC
中科院分区：
文献类型：
--
作者：
Elurbe DM;Paranjpe SS;Georgiou G;van Kruijsbergen I;Bogdanovic O;Gibeaux R;Heald R;Lister R;Huynen MA;van Heeringen SJ;Veenstra GJC
基因组复制在包括脊椎动物在内的许多真核生物谱系的进化中起着关键作用。一种相对较新的脊椎动物基因组复制是非洲爪蟾，它是1700万年前两个关系密切的物种杂交的结果。然而，人们对这种复制在基因组、表观基因组和基因表达水平上的后果知之甚少。松鸡基因组由两个亚基因组组成，称为L（长染色体）和S（短染色体），它们起源于不同的二倍体祖先。在亲本亚基因组中，从基因组复制的角度来看，S染色体的退化速度比L染色体快，直到今天。缺失似乎对假基因的形成和调控区域的丢失有最大的影响。缺失区域富含长DNA重复序列，侧翼区域具有高比对得分，表明非等位基因同源重组在DNA丢失中起重要作用。为了评估热带热带扁虱亚基因组的创新，我们研究了热带扁虱亚基因组特有的p300结合增强子峰。绝大多数新的增强子包含转座元件。最后，为了剖析种间杂交后的早期和晚期事件，我们研究了热带X. X.的表观基因组和增强子景观。Laevis杂交胚胎。引人注目的是，在杂交胚胎中，年轻的热带蓟DNA转座子被抑制并招募p300。结果表明，青松基因和功能调控元件的侵蚀与重复序列和非等位基因同源重组有关，此外，年轻重复序列也有助于杂交和全基因组复制后的p300结合调控景观。本文的在线版本（doi:10.1186/s13059-017-1335-7）包含补充材料，仅供授权用户使用。
Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers comprise transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos. The results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and non-allelic homologous recombination and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole-genome duplication. The online version of this article (doi:10.1186/s13059-017-1335-7) contains supplementary material, which is available to authorized users.
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作者：
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