Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae

doi:10.1093/molbev/msaa036

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	Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae
	Li, Liang 1,2; Zhang, Sheng 1,2; Li, Lei M.1,2,3
	2020-06-01
发表期刊	MOLECULAR BIOLOGY AND EVOLUTION
ISSN	0737-4038
卷号	37 期号:6 页码:1679-1693
摘要	To understand the genomic basis accounting for the phenotypic differences between human and apes, we compare the matrices consisting of the cis-element frequencies in the proximal regulatory regions of their genomes. One such frequency matrix is represented by a robust singular value decomposition. For each singular value, the negative and positive ends of the sorted motif eigenvector correspond to the dual ends of the sorted gene eigenvector, respectively, comprising a dual eigen-module defined by cis-regulatory element frequencies (CREF). The CREF eigen-modules at levels 1, 2, 3, and 6 are highly conserved across humans, chimpanzees, and orangutans. The key biological processes embedded in the top three CREF eigen-modules are reproduction versus embryogenesis, fetal maturation versus immune system, and stress responses versus mitosis. Although the divergence at the nucleotide level between the chimpanzee and human genome was small, their cis-element frequency matrices crossed a singularity point, at which the fourth and fifth singular values were identical. The CREF eigen-modules corresponding to the fourth and fifth singular values were reorganized along the evolution from apes to human. Interestingly, the fourth sorted gene eigenvector encodes the phenotypes unique to human such as long-term memory, language development, and social behavior. The number of motifs present on Alu elements increases substantially at the fourth level. The motif analysis together with the cases of human-specific Alu insertions suggests that mutations related to Alu elements play a critical role in the evolution of the human-phenotypic gene eigenvector.
关键词	cis-element frequency dual eigenmodule polarized eigenvector Alu element cognition
DOI	10.1093/molbev/msaa036
收录类别	SCI
语种	英语
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13040600] ; National Natural Science Foundation of China[11871462] ; National Natural Science Foundation of China[91530105] ; National Center for Mathematics and Interdisciplinary Sciences of the Chinese Academy of Sciences ; Key Laboratory of Systems and Control of the Chinese Academy of Sciences ; National Key Research and Development Program of China[2017YFC0908400]
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000569060900012
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/52197
专题	中国科学院数学与系统科学研究院
通讯作者	Li, Lei M.
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Li, Liang,Zhang, Sheng,Li, Lei M.. Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae[J]. MOLECULAR BIOLOGY AND EVOLUTION,2020,37(6):1679-1693.
APA	Li, Liang,Zhang, Sheng,&Li, Lei M..(2020).Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae.MOLECULAR BIOLOGY AND EVOLUTION,37(6),1679-1693.
MLA	Li, Liang,et al."Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae".MOLECULAR BIOLOGY AND EVOLUTION 37.6(2020):1679-1693.