Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

CORC > 昆明动物研究所 > 昆明动物研究所 > 动物模型与人类重大疾病机理重点实验室 > 动物活性蛋白多肽组学

	Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
	Farre, M; Kim, J; Proskuryakova, AA; Zhang, Y; Kulemzina, AI; Li, QY; Zhou, Y; Xiong, YQ; Johnson, JL; Perelman, PL
刊名	GENOME RESEARCH
	2019
卷号	29 期号:4 页码:576-589
ISSN号	1088-9051
英文摘要	The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.
语种	英语
内容类型	期刊论文
源URL	[http://ir.kiz.ac.cn:8080/handle/152453/12593]
专题	昆明动物研究所_动物活性蛋白多肽组学
推荐引用方式 GB/T 7714	Farre, M,Kim, J,Proskuryakova, AA,et al. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks[J]. GENOME RESEARCH,2019,29(4):576-589.
APA	Farre, M.,Kim, J.,Proskuryakova, AA.,Zhang, Y.,Kulemzina, AI.,...&Larkin, DM.(2019).Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.GENOME RESEARCH,29(4),576-589.
MLA	Farre, M,et al."Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks".GENOME RESEARCH 29.4(2019):576-589.