Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions
The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide p...
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creator | Goldberg, Aaron D. Banaszynski, Laura A. Noh, Kyung-Min Lewis, Peter W. Elsaesser, Simon J. Stadler, Sonja Dewell, Scott Law, Martin Guo, Xingyi Li, Xuan Wen, Duancheng Chapgier, Ariane DeKelver, Russell C. Miller, Jeffrey C. Lee, Ya-Li Boydston, Elizabeth A. Holmes, Michael C. Gregory, Philip D. Greally, John M. Rafii, Shahin Yang, Chingwen Scambler, Peter J. Garrick, David Gibbons, Richard J. Higgs, Douglas R. Cristea, Ileana M. Urnov, Fyodor D. Zheng, Deyou Allis, C. David |
description | The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.
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► H3.3 localization at specific genes and regulatory regions is cell-type specific ► Hira controls H3.3 localization to genes and some regulatory regions ► H3.3 localization to many regulatory elements and telomeres is Hira independent ► Atrx is required for H3.3 telomeric localization, and for telomeric RNA repression |
doi_str_mv | 10.1016/j.cell.2010.01.003 |
format | Article |
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► H3.3 localization at specific genes and regulatory regions is cell-type specific ► Hira controls H3.3 localization to genes and some regulatory regions ► H3.3 localization to many regulatory elements and telomeres is Hira independent ► Atrx is required for H3.3 telomeric localization, and for telomeric RNA repression</description><identifier>ISSN: 0092-8674</identifier><identifier>EISSN: 1097-4172</identifier><identifier>DOI: 10.1016/j.cell.2010.01.003</identifier><identifier>PMID: 20211137</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Animals ; Binding Sites ; Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; DNA ; Embryonic Stem Cells - metabolism ; Genome ; Histone Chaperones - genetics ; Histone Chaperones - metabolism ; Histones - analysis ; Histones - genetics ; Histones - metabolism ; Mice ; Mice, Inbred C57BL ; PROTEINS ; STEMCELL ; Telomere - chemistry ; Telomere - metabolism ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription Initiation Site</subject><ispartof>Cell, 2010-03, Vol.140 (5), p.678-691</ispartof><rights>2010 Elsevier Inc.</rights><rights>(c) 2010 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c601t-4e565f4d44bd7dc7fb073e3c9a4923f1886d65521511da6e06784f382327b14d3</citedby><cites>FETCH-LOGICAL-c601t-4e565f4d44bd7dc7fb073e3c9a4923f1886d65521511da6e06784f382327b14d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0092867410000048$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20211137$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Goldberg, Aaron D.</creatorcontrib><creatorcontrib>Banaszynski, Laura A.</creatorcontrib><creatorcontrib>Noh, Kyung-Min</creatorcontrib><creatorcontrib>Lewis, Peter W.</creatorcontrib><creatorcontrib>Elsaesser, Simon J.</creatorcontrib><creatorcontrib>Stadler, Sonja</creatorcontrib><creatorcontrib>Dewell, Scott</creatorcontrib><creatorcontrib>Law, Martin</creatorcontrib><creatorcontrib>Guo, Xingyi</creatorcontrib><creatorcontrib>Li, Xuan</creatorcontrib><creatorcontrib>Wen, Duancheng</creatorcontrib><creatorcontrib>Chapgier, Ariane</creatorcontrib><creatorcontrib>DeKelver, Russell C.</creatorcontrib><creatorcontrib>Miller, Jeffrey C.</creatorcontrib><creatorcontrib>Lee, Ya-Li</creatorcontrib><creatorcontrib>Boydston, Elizabeth A.</creatorcontrib><creatorcontrib>Holmes, Michael C.</creatorcontrib><creatorcontrib>Gregory, Philip D.</creatorcontrib><creatorcontrib>Greally, John M.</creatorcontrib><creatorcontrib>Rafii, Shahin</creatorcontrib><creatorcontrib>Yang, Chingwen</creatorcontrib><creatorcontrib>Scambler, Peter J.</creatorcontrib><creatorcontrib>Garrick, David</creatorcontrib><creatorcontrib>Gibbons, Richard J.</creatorcontrib><creatorcontrib>Higgs, Douglas R.</creatorcontrib><creatorcontrib>Cristea, Ileana M.</creatorcontrib><creatorcontrib>Urnov, Fyodor D.</creatorcontrib><creatorcontrib>Zheng, Deyou</creatorcontrib><creatorcontrib>Allis, C. David</creatorcontrib><title>Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions</title><title>Cell</title><addtitle>Cell</addtitle><description>The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.
[Display omitted]
► H3.3 localization at specific genes and regulatory regions is cell-type specific ► Hira controls H3.3 localization to genes and some regulatory regions ► H3.3 localization to many regulatory elements and telomeres is Hira independent ► Atrx is required for H3.3 telomeric localization, and for telomeric RNA repression</description><subject>Animals</subject><subject>Binding Sites</subject><subject>Cell Cycle Proteins - genetics</subject><subject>Cell Cycle Proteins - metabolism</subject><subject>DNA</subject><subject>Embryonic Stem Cells - metabolism</subject><subject>Genome</subject><subject>Histone Chaperones - genetics</subject><subject>Histone Chaperones - metabolism</subject><subject>Histones - analysis</subject><subject>Histones - genetics</subject><subject>Histones - metabolism</subject><subject>Mice</subject><subject>Mice, Inbred C57BL</subject><subject>PROTEINS</subject><subject>STEMCELL</subject><subject>Telomere - chemistry</subject><subject>Telomere - metabolism</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription Initiation Site</subject><issn>0092-8674</issn><issn>1097-4172</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUuLFDEUhYMoTjv6B1xI7VxVzc07BSJI60wLDYKP2YZ06taYprrSJukB_fWm6ZlBN7q6kPOdw809hLyk0FGg6mLbeZymjkF9ANoB8EdkQaHXraCaPSYLgJ61RmlxRp7lvAUAI6V8Ss4YMEop1wty_T7kEmZfmkvnS0y5Wca5pDg1qyrEGZtrl4KbS7PiHW_W0bsp_HIlxLlxpfmyRx_G4JsrnOOuzs94U6X8nDwZ3ZTxxd08J98uP3xdrtr1p6uPy3fr1iugpRUolRzFIMRm0IPX4wY0R-57J3rGR2qMGpSUjEpKB6cQlDZi5IZxpjdUDPycvD3l7g-bHQ4e6-5usvsUdi79tNEF-7cyh-_2Jt5aZow03NSA13cBKf44YC52F_LxrG7GeMhWC0WlUBL-T3LORS8lryQ7kT7FnBOOD_tQsMfm7NYejfbYnAVqa3PV9OrPnzxY7quqwJsTgPWetwGTzT7g7HEICX2xQwz_yv8NlpypkQ</recordid><startdate>20100305</startdate><enddate>20100305</enddate><creator>Goldberg, Aaron D.</creator><creator>Banaszynski, Laura A.</creator><creator>Noh, Kyung-Min</creator><creator>Lewis, Peter W.</creator><creator>Elsaesser, Simon J.</creator><creator>Stadler, Sonja</creator><creator>Dewell, Scott</creator><creator>Law, Martin</creator><creator>Guo, Xingyi</creator><creator>Li, Xuan</creator><creator>Wen, Duancheng</creator><creator>Chapgier, Ariane</creator><creator>DeKelver, Russell C.</creator><creator>Miller, Jeffrey C.</creator><creator>Lee, Ya-Li</creator><creator>Boydston, Elizabeth A.</creator><creator>Holmes, Michael C.</creator><creator>Gregory, Philip D.</creator><creator>Greally, John M.</creator><creator>Rafii, Shahin</creator><creator>Yang, Chingwen</creator><creator>Scambler, Peter J.</creator><creator>Garrick, David</creator><creator>Gibbons, Richard J.</creator><creator>Higgs, Douglas R.</creator><creator>Cristea, Ileana M.</creator><creator>Urnov, Fyodor D.</creator><creator>Zheng, Deyou</creator><creator>Allis, C. David</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><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>5PM</scope></search><sort><creationdate>20100305</creationdate><title>Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions</title><author>Goldberg, Aaron D. ; Banaszynski, Laura A. ; Noh, Kyung-Min ; Lewis, Peter W. ; Elsaesser, Simon J. ; Stadler, Sonja ; Dewell, Scott ; Law, Martin ; Guo, Xingyi ; Li, Xuan ; Wen, Duancheng ; Chapgier, Ariane ; DeKelver, Russell C. ; Miller, Jeffrey C. ; Lee, Ya-Li ; Boydston, Elizabeth A. ; Holmes, Michael C. ; Gregory, Philip D. ; Greally, John M. ; Rafii, Shahin ; Yang, Chingwen ; Scambler, Peter J. ; Garrick, David ; Gibbons, Richard J. ; Higgs, Douglas R. ; Cristea, Ileana M. ; Urnov, Fyodor D. ; Zheng, Deyou ; Allis, C. 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David</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><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>PubMed Central (Full Participant titles)</collection><jtitle>Cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Goldberg, Aaron D.</au><au>Banaszynski, Laura A.</au><au>Noh, Kyung-Min</au><au>Lewis, Peter W.</au><au>Elsaesser, Simon J.</au><au>Stadler, Sonja</au><au>Dewell, Scott</au><au>Law, Martin</au><au>Guo, Xingyi</au><au>Li, Xuan</au><au>Wen, Duancheng</au><au>Chapgier, Ariane</au><au>DeKelver, Russell C.</au><au>Miller, Jeffrey C.</au><au>Lee, Ya-Li</au><au>Boydston, Elizabeth A.</au><au>Holmes, Michael C.</au><au>Gregory, Philip D.</au><au>Greally, John M.</au><au>Rafii, Shahin</au><au>Yang, Chingwen</au><au>Scambler, Peter J.</au><au>Garrick, David</au><au>Gibbons, Richard J.</au><au>Higgs, Douglas R.</au><au>Cristea, Ileana M.</au><au>Urnov, Fyodor D.</au><au>Zheng, Deyou</au><au>Allis, C. David</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions</atitle><jtitle>Cell</jtitle><addtitle>Cell</addtitle><date>2010-03-05</date><risdate>2010</risdate><volume>140</volume><issue>5</issue><spage>678</spage><epage>691</epage><pages>678-691</pages><issn>0092-8674</issn><eissn>1097-4172</eissn><abstract>The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.
[Display omitted]
► H3.3 localization at specific genes and regulatory regions is cell-type specific ► Hira controls H3.3 localization to genes and some regulatory regions ► H3.3 localization to many regulatory elements and telomeres is Hira independent ► Atrx is required for H3.3 telomeric localization, and for telomeric RNA repression</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>20211137</pmid><doi>10.1016/j.cell.2010.01.003</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Animals Binding Sites Cell Cycle Proteins - genetics Cell Cycle Proteins - metabolism DNA Embryonic Stem Cells - metabolism Genome Histone Chaperones - genetics Histone Chaperones - metabolism Histones - analysis Histones - genetics Histones - metabolism Mice Mice, Inbred C57BL PROTEINS STEMCELL Telomere - chemistry Telomere - metabolism Transcription Factors - genetics Transcription Factors - metabolism Transcription Initiation Site |
title | Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions |
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