Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin
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 nucle...
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| Veröffentlicht in: | Nucleic acids research 2016-12, Vol.44 (21), p.10091-10105 |
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| creator | Xiong, Jie Gao, Shan Dui, Wen Yang, Wentao Chen, Xiao Taverna, Sean D Pearlman, Ronald E Ashlock, Wendy Miao, Wei Liu, Yifan |
| description | 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. |
| doi_str_mv | 10.1093/nar/gkw684 |
| format | Article |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkw684</identifier><identifier>PMID: 27488188</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Chromatin - genetics ; Chromatin - metabolism ; DNA Polymerase II - genetics ; DNA Polymerase II - metabolism ; Gene regulation, Chromatin and Epigenetics ; Macronucleus - genetics ; Macronucleus - metabolism ; Micrococcal Nuclease - genetics ; Micrococcal Nuclease - metabolism ; Micronucleus, Germline - genetics ; Nucleosomes - genetics ; Nucleosomes - metabolism ; RNA Splice Sites ; Tetrahymena thermophila - genetics ; Transcription Initiation Site</subject><ispartof>Nucleic acids research, 2016-12, Vol.44 (21), p.10091-10105</ispartof><rights>The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2016. 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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.</description><subject>Chromatin - genetics</subject><subject>Chromatin - metabolism</subject><subject>DNA Polymerase II - genetics</subject><subject>DNA Polymerase II - metabolism</subject><subject>Gene regulation, Chromatin and Epigenetics</subject><subject>Macronucleus - genetics</subject><subject>Macronucleus - metabolism</subject><subject>Micrococcal Nuclease - genetics</subject><subject>Micrococcal Nuclease - metabolism</subject><subject>Micronucleus, Germline - genetics</subject><subject>Nucleosomes - genetics</subject><subject>Nucleosomes - metabolism</subject><subject>RNA Splice Sites</subject><subject>Tetrahymena thermophila - genetics</subject><subject>Transcription Initiation Site</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkc9uEzEQxi0EoqFw4QGQjwhpqb3r2M4FCZW_UiUu5WzN2rOJYW0H21uUd-FhcZsSldNIM9_3mxl9hLzk7C1nm-EiQr7Y_vwttXhEVnyQfSc2sn9MVmxg644zoc_Is1J-MMYFX4un5KxXQmuu9Yr8-eBLQVt93NKMM1R_g9SmWLMfl-pTLDRN1PrSUYiO1gyxdA4r5uAjxFpoTTQudsZUUkDqfDlZ6XhoqLCHfEu_xmbeHQJGoAFsTncuyHfc4B807C6n0C6Jz8mTCeaCL-7rOfn-6eP15Zfu6tvnr5fvrzo7iL52XI1cTxaFnRyTio9CKuemCSVIiTiCE2umR6GEAtDMKQl9rznHDTohJxzOybsjd7-MAZ3F9j7MZp99gHwwCbz5fxL9zmzTjVnzQYmeN8Dre0BOvxYs1QRfLM4zRExLMVz3UomBcdWkb47S9nApGafTGs7MbZymxWmOcTbxq4eHnaT_8hv-AjbLpBA</recordid><startdate>20161201</startdate><enddate>20161201</enddate><creator>Xiong, Jie</creator><creator>Gao, Shan</creator><creator>Dui, Wen</creator><creator>Yang, Wentao</creator><creator>Chen, Xiao</creator><creator>Taverna, Sean D</creator><creator>Pearlman, Ronald E</creator><creator>Ashlock, Wendy</creator><creator>Miao, Wei</creator><creator>Liu, Yifan</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161201</creationdate><title>Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin</title><author>Xiong, Jie ; Gao, Shan ; Dui, Wen ; Yang, Wentao ; Chen, Xiao ; Taverna, Sean D ; Pearlman, Ronald E ; Ashlock, Wendy ; Miao, Wei ; Liu, Yifan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c342t-17b18fce4cfd0671b467ddffe6a66eebad4508b4747aa80d76a22811e9ed46fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Chromatin - genetics</topic><topic>Chromatin - metabolism</topic><topic>DNA Polymerase II - genetics</topic><topic>DNA Polymerase II - metabolism</topic><topic>Gene regulation, Chromatin and Epigenetics</topic><topic>Macronucleus - genetics</topic><topic>Macronucleus - metabolism</topic><topic>Micrococcal Nuclease - genetics</topic><topic>Micrococcal Nuclease - metabolism</topic><topic>Micronucleus, Germline - genetics</topic><topic>Nucleosomes - genetics</topic><topic>Nucleosomes - metabolism</topic><topic>RNA Splice Sites</topic><topic>Tetrahymena thermophila - genetics</topic><topic>Transcription Initiation Site</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xiong, Jie</creatorcontrib><creatorcontrib>Gao, Shan</creatorcontrib><creatorcontrib>Dui, Wen</creatorcontrib><creatorcontrib>Yang, Wentao</creatorcontrib><creatorcontrib>Chen, Xiao</creatorcontrib><creatorcontrib>Taverna, Sean D</creatorcontrib><creatorcontrib>Pearlman, Ronald E</creatorcontrib><creatorcontrib>Ashlock, Wendy</creatorcontrib><creatorcontrib>Miao, Wei</creatorcontrib><creatorcontrib>Liu, Yifan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xiong, Jie</au><au>Gao, Shan</au><au>Dui, Wen</au><au>Yang, Wentao</au><au>Chen, Xiao</au><au>Taverna, Sean D</au><au>Pearlman, Ronald E</au><au>Ashlock, Wendy</au><au>Miao, Wei</au><au>Liu, Yifan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2016-12-01</date><risdate>2016</risdate><volume>44</volume><issue>21</issue><spage>10091</spage><epage>10105</epage><pages>10091-10105</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>27488188</pmid><doi>10.1093/nar/gkw684</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Chromatin - genetics Chromatin - metabolism DNA Polymerase II - genetics DNA Polymerase II - metabolism Gene regulation, Chromatin and Epigenetics Macronucleus - genetics Macronucleus - metabolism Micrococcal Nuclease - genetics Micrococcal Nuclease - metabolism Micronucleus, Germline - genetics Nucleosomes - genetics Nucleosomes - metabolism RNA Splice Sites Tetrahymena thermophila - genetics Transcription Initiation Site |
| title | Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin |
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