IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin
Xiong, Jie1,2; Gao, Shan3,4; Dui, Wen1; Yang, Wentao2; Chen, Xiao3; Taverna, Sean D.5,6; Pearlman, Ronald E.7; Ashlock, Wendy7; Miao, Wei2; Liu, Yifan1
2016-12-01
Source PublicationNUCLEIC ACIDS RESEARCH
ISSN0305-1048
Volume44Issue:21Pages:10091-10105
Abstract

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.

DOI10.1093/nar/gkw684
Funding OrganizationNatural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; 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Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; 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Indexed BySCI
Language英语
Funding ProjectNatural Science Foundation of China[31301930] ; Natural Science Foundation of China[31522051] ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; NIH[R01 GM106024] ; NIH[R01 GM087343] ; Canadian Institutes of Health Research[MOP13347] ; Natural Sciences and Engineering Research Council of Canada[53909] ; Natural Sciences and Engineering Research Council of Canada ; Projects of International Cooperation and Exchanges, Ministry of Science and Technology of China[2013DFG32390] ; NSF[MCB 1411565] ; Department of Pathology at the University of Michigan
WOS Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemistry & Molecular Biology
WOS IDWOS:000393979400012
WOS KeywordBASE-PAIR RESOLUTION ; SACCHAROMYCES-CEREVISIAE ; EUKARYOTIC GENOME ; DNA ELIMINATION ; HISTONE H3 ; NUCLEAR DEVELOPMENT ; START SITES ; R PACKAGE ; IN-VIVO ; ORGANIZATION
PublisherOXFORD UNIV PRESS
Funding OrganizationNatural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Natural Science Foundation of China ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Knowledge Innovation Programof the Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Youth Innovation Promotion Association, Chinese Academy of Sciences ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China ; 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Cited Times:11[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/33058
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorMiao, Wei; Liu, Yifan
Affiliation1.Univ Michigan, Dept Pathol, Ann Arbor, MI 48109 USA
2.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China
3.Ocean Univ China, Inst Evolut & Marine Biodivers, Qingdao 266003, Peoples R China
4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266003, Peoples R China
5.Johns Hopkins Univ, Sch Med, Dept Pharmacol & Mol Sci, Baltimore, MD 21205 USA
6.Johns Hopkins Univ, Sch Med, Ctr Epigenet, Baltimore, MD 21205 USA
7.York Univ, Dept Biol, Toronto, ON M3J 1P3, Canada
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Xiong, Jie,Gao, Shan,Dui, Wen,et al. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin[J]. NUCLEIC ACIDS RESEARCH,2016,44(21):10091-10105.
APA Xiong, Jie.,Gao, Shan.,Dui, Wen.,Yang, Wentao.,Chen, Xiao.,...&Liu, Yifan.(2016).Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.NUCLEIC ACIDS RESEARCH,44(21),10091-10105.
MLA Xiong, Jie,et al."Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin".NUCLEIC ACIDS RESEARCH 44.21(2016):10091-10105.
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