Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions
AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present...
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| Veröffentlicht in: | Genes & development 2014-11, Vol.28 (22), p.2492-2497 |
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| creator | Lorch, Yahli Maier-Davis, Barbara Kornberg, Roger D |
| description | AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences. |
| doi_str_mv | 10.1101/gad.250704.114 |
| format | Article |
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We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences.</description><identifier>ISSN: 0890-9369</identifier><identifier>EISSN: 1549-5477</identifier><identifier>DOI: 10.1101/gad.250704.114</identifier><identifier>PMID: 25403179</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Adenosine Triphosphate - metabolism ; Base Sequence ; Chromatin Assembly and Disassembly - genetics ; Chromatin Assembly and Disassembly - physiology ; Nucleosomes - metabolism ; Poly dA-dT - metabolism ; Research Paper ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism</subject><ispartof>Genes & development, 2014-11, Vol.28 (22), p.2492-2497</ispartof><rights>2014 Lorch et al.; Published by Cold Spring Harbor Laboratory Press.</rights><rights>2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c489t-1ddef2cce1997861c24c5a6c747d6ab2c78ea4bd7556f55ba61df749984213ba3</citedby><cites>FETCH-LOGICAL-c489t-1ddef2cce1997861c24c5a6c747d6ab2c78ea4bd7556f55ba61df749984213ba3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233242/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233242/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25403179$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lorch, Yahli</creatorcontrib><creatorcontrib>Maier-Davis, Barbara</creatorcontrib><creatorcontrib>Kornberg, Roger D</creatorcontrib><title>Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions</title><title>Genes & development</title><addtitle>Genes Dev</addtitle><description>AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences.</description><subject>Adenosine Triphosphate - metabolism</subject><subject>Base Sequence</subject><subject>Chromatin Assembly and Disassembly - genetics</subject><subject>Chromatin Assembly and Disassembly - physiology</subject><subject>Nucleosomes - metabolism</subject><subject>Poly dA-dT - metabolism</subject><subject>Research Paper</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><issn>0890-9369</issn><issn>1549-5477</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1LxDAQxYMouq5ePUqPXromaT6aiyB-gyiIHjyFNJnuVtpEk67gf2-WVdGbl0yG95vHDA-hA4JnhGByPDduRjmWmOWebaAJ4UyVnEm5iSa4VrhUlVA7aDelF4yxwEJsox3KGa6IVBP0_BB6KEJbnN-dFgneluAtFJ0v7CKGwYz5F2EIDvrOzwvjXTEuoGhDXGnBryb90vYQUhigbCNA5udZSXtoqzV9gv2vOkVPlxePZ9fl7f3VzdnpbWlZrcaSOActtRaIUrIWxFJmuRFWMumEaaiVNRjWOMm5aDlvjCCulUypmlFSNaaaopO17-uyGcBZ8GM0vX6N3WDihw6m038V3y30PLxrRquK5meKjr4MYsj3p1EPXbLQ98ZDWCZNhBSVYFSyf6BUECEoFhmdrVEbQ0oR2p-NCNar6HSOTq-jy_3K-_D3HT_4d1bVJ6qpleY</recordid><startdate>20141115</startdate><enddate>20141115</enddate><creator>Lorch, Yahli</creator><creator>Maier-Davis, Barbara</creator><creator>Kornberg, Roger D</creator><general>Cold Spring Harbor Laboratory 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>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20141115</creationdate><title>Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions</title><author>Lorch, Yahli ; Maier-Davis, Barbara ; Kornberg, Roger D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c489t-1ddef2cce1997861c24c5a6c747d6ab2c78ea4bd7556f55ba61df749984213ba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adenosine Triphosphate - metabolism</topic><topic>Base Sequence</topic><topic>Chromatin Assembly and Disassembly - genetics</topic><topic>Chromatin Assembly and Disassembly - physiology</topic><topic>Nucleosomes - metabolism</topic><topic>Poly dA-dT - metabolism</topic><topic>Research Paper</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lorch, Yahli</creatorcontrib><creatorcontrib>Maier-Davis, Barbara</creatorcontrib><creatorcontrib>Kornberg, Roger D</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>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes & development</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lorch, Yahli</au><au>Maier-Davis, Barbara</au><au>Kornberg, Roger D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions</atitle><jtitle>Genes & development</jtitle><addtitle>Genes Dev</addtitle><date>2014-11-15</date><risdate>2014</risdate><volume>28</volume><issue>22</issue><spage>2492</spage><epage>2497</epage><pages>2492-2497</pages><issn>0890-9369</issn><eissn>1549-5477</eissn><abstract>AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. 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| source | MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Adenosine Triphosphate - metabolism Base Sequence Chromatin Assembly and Disassembly - genetics Chromatin Assembly and Disassembly - physiology Nucleosomes - metabolism Poly dA-dT - metabolism Research Paper Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism |
| title | Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions |
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