Genome-scale profiling of histone H3.3 replacement patterns
Histones of multicellular organisms are assembled into chromatin primarily during DNA replication. When chromatin assembly occurs at other times, the histone H3.3 variant replaces canonical H3. Here we introduce a new strategy for profiling epigenetic patterns on the basis of H3.3 replacement, using...
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| Veröffentlicht in: | Nature genetics 2005-10, Vol.37 (10), p.1090-1097 |
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| creator | Henikoff, Steven Mito, Yoshiko Henikoff, Jorja G |
| description | Histones of multicellular organisms are assembled into chromatin primarily during DNA replication. When chromatin assembly occurs at other times, the histone H3.3 variant replaces canonical H3. Here we introduce a new strategy for profiling epigenetic patterns on the basis of H3.3 replacement, using microarrays covering roughly one-third of the
Drosophila melanogaster
genome at 100-bp resolution. We identified patterns of H3.3 replacement over active genes and transposons. H3.3 replacement occurred prominently at sites of abundant RNA polymerase II and methylated H3 Lys4 throughout the genome and was enhanced on the dosage-compensated male X chromosome. Active genes were depleted of histones at promoters and were enriched in H3.3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin. |
| doi_str_mv | 10.1038/ng1637 |
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Drosophila melanogaster
genome at 100-bp resolution. We identified patterns of H3.3 replacement over active genes and transposons. H3.3 replacement occurred prominently at sites of abundant RNA polymerase II and methylated H3 Lys4 throughout the genome and was enhanced on the dosage-compensated male X chromosome. Active genes were depleted of histones at promoters and were enriched in H3.3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/ng1637</identifier><identifier>PMID: 16155569</identifier><identifier>CODEN: NGENEC</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>Agriculture ; Animal Genetics and Genomics ; Animals ; Biological and medical sciences ; Biomedical and Life Sciences ; Biomedicine ; Cancer Research ; Chromatin - metabolism ; Deoxyribonucleic acid ; DNA ; DNA microarrays ; DNA Transposable Elements ; Drosophila melanogaster ; Drosophila melanogaster - genetics ; Drosophila melanogaster - metabolism ; Epigenesis, Genetic ; Fundamental and applied biological sciences. Psychology ; Gene expression ; Gene Expression Profiling ; Gene Function ; Genes, Insect ; Genes, X-Linked - genetics ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Insect ; Histones ; Histones - metabolism ; Human Genetics ; Male ; Methods ; Oligonucleotide Array Sequence Analysis ; Physiological aspects ; Promoter Regions, Genetic ; RNA Polymerase II - metabolism ; X Chromosome - genetics</subject><ispartof>Nature genetics, 2005-10, Vol.37 (10), p.1090-1097</ispartof><rights>Springer Nature America, Inc. 2005</rights><rights>2006 INIST-CNRS</rights><rights>COPYRIGHT 2005 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Oct 2005</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c619t-12742db05b2e3b1a340676feb5f16bfbd489025a35b0d9c52ce1220a10f5bc423</citedby><cites>FETCH-LOGICAL-c619t-12742db05b2e3b1a340676feb5f16bfbd489025a35b0d9c52ce1220a10f5bc423</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/ng1637$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/ng1637$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27915,27916,41479,42548,51310</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17252397$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16155569$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Henikoff, Steven</creatorcontrib><creatorcontrib>Mito, Yoshiko</creatorcontrib><creatorcontrib>Henikoff, Jorja G</creatorcontrib><title>Genome-scale profiling of histone H3.3 replacement patterns</title><title>Nature genetics</title><addtitle>Nat Genet</addtitle><addtitle>Nat Genet</addtitle><description>Histones of multicellular organisms are assembled into chromatin primarily during DNA replication. When chromatin assembly occurs at other times, the histone H3.3 variant replaces canonical H3. Here we introduce a new strategy for profiling epigenetic patterns on the basis of H3.3 replacement, using microarrays covering roughly one-third of the
Drosophila melanogaster
genome at 100-bp resolution. We identified patterns of H3.3 replacement over active genes and transposons. H3.3 replacement occurred prominently at sites of abundant RNA polymerase II and methylated H3 Lys4 throughout the genome and was enhanced on the dosage-compensated male X chromosome. Active genes were depleted of histones at promoters and were enriched in H3.3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin.</description><subject>Agriculture</subject><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Chromatin - metabolism</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA microarrays</subject><subject>DNA Transposable Elements</subject><subject>Drosophila melanogaster</subject><subject>Drosophila melanogaster - genetics</subject><subject>Drosophila melanogaster - metabolism</subject><subject>Epigenesis, Genetic</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Function</subject><subject>Genes, Insect</subject><subject>Genes, X-Linked - genetics</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Insect</subject><subject>Histones</subject><subject>Histones - metabolism</subject><subject>Human Genetics</subject><subject>Male</subject><subject>Methods</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Physiological aspects</subject><subject>Promoter Regions, Genetic</subject><subject>RNA Polymerase II - metabolism</subject><subject>X Chromosome - genetics</subject><issn>1061-4036</issn><issn>1546-1718</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqN0luL1TAQAOAiintRf4FIcVHxocdMbm3xaVl0d2FhwdtrSNNJ7dKmxyQF_ffm0OLhqKDkIYH5MskMk2VPgGyAsOqN60Cy8l52DILLAkqo7qczkVBwwuRRdhLCHSHAOakeZkcgQQgh6-Ps7SW6acQiGD1gvvWT7Yfedflk8699iJPD_IptWO5xO2iDI7qYb3WM6F14lD2wegj4eN1Ps8_v3326uCpubi-vL85vCiOhjgXQktO2IaKhyBrQjBNZSouNsCAb27S8qgkVmomGtLUR1CBQSjQQKxrDKTvNXi550_e-zRiiGvtgcBi0w2kOSlaSSwb1PyEllIKgJMHnv8G7afYuFaEopZLXFbCEzhbUpdao3tkpem12GdU5VIwDkLpKavMXlVaLY29S_1JD8fDC64MLyUT8Hjs9h6CuP374f3v75dCuxRs_heDRqq3vR-1_KCBqNyNqmZEEn63Fz82I7Z6tQ5HAixXo3VhYr53pw96VVFBW7xK9WlxIIdeh33fxjyefLtLpOHv8lWoN_wQb2dPv</recordid><startdate>20051001</startdate><enddate>20051001</enddate><creator>Henikoff, Steven</creator><creator>Mito, Yoshiko</creator><creator>Henikoff, Jorja G</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><scope>IQODW</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20051001</creationdate><title>Genome-scale profiling of histone H3.3 replacement patterns</title><author>Henikoff, Steven ; Mito, Yoshiko ; Henikoff, Jorja G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c619t-12742db05b2e3b1a340676feb5f16bfbd489025a35b0d9c52ce1220a10f5bc423</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Agriculture</topic><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Cancer Research</topic><topic>Chromatin - metabolism</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA microarrays</topic><topic>DNA Transposable Elements</topic><topic>Drosophila melanogaster</topic><topic>Drosophila melanogaster - genetics</topic><topic>Drosophila melanogaster - metabolism</topic><topic>Epigenesis, Genetic</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Function</topic><topic>Genes, Insect</topic><topic>Genes, X-Linked - genetics</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Insect</topic><topic>Histones</topic><topic>Histones - metabolism</topic><topic>Human Genetics</topic><topic>Male</topic><topic>Methods</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Physiological aspects</topic><topic>Promoter Regions, Genetic</topic><topic>RNA Polymerase II - metabolism</topic><topic>X Chromosome - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Henikoff, Steven</creatorcontrib><creatorcontrib>Mito, Yoshiko</creatorcontrib><creatorcontrib>Henikoff, Jorja G</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Nature genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Henikoff, Steven</au><au>Mito, Yoshiko</au><au>Henikoff, Jorja G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-scale profiling of histone H3.3 replacement patterns</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2005-10-01</date><risdate>2005</risdate><volume>37</volume><issue>10</issue><spage>1090</spage><epage>1097</epage><pages>1090-1097</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><coden>NGENEC</coden><abstract>Histones of multicellular organisms are assembled into chromatin primarily during DNA replication. When chromatin assembly occurs at other times, the histone H3.3 variant replaces canonical H3. Here we introduce a new strategy for profiling epigenetic patterns on the basis of H3.3 replacement, using microarrays covering roughly one-third of the
Drosophila melanogaster
genome at 100-bp resolution. We identified patterns of H3.3 replacement over active genes and transposons. H3.3 replacement occurred prominently at sites of abundant RNA polymerase II and methylated H3 Lys4 throughout the genome and was enhanced on the dosage-compensated male X chromosome. Active genes were depleted of histones at promoters and were enriched in H3.3 from upstream to downstream of transcription units. We propose that deposition and inheritance of actively modified H3.3 in regulatory regions maintains transcriptionally active chromatin.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>16155569</pmid><doi>10.1038/ng1637</doi><tpages>8</tpages></addata></record> |
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| subjects | Agriculture Animal Genetics and Genomics Animals Biological and medical sciences Biomedical and Life Sciences Biomedicine Cancer Research Chromatin - metabolism Deoxyribonucleic acid DNA DNA microarrays DNA Transposable Elements Drosophila melanogaster Drosophila melanogaster - genetics Drosophila melanogaster - metabolism Epigenesis, Genetic Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling Gene Function Genes, Insect Genes, X-Linked - genetics Genetics of eukaryotes. Biological and molecular evolution Genome, Insect Histones Histones - metabolism Human Genetics Male Methods Oligonucleotide Array Sequence Analysis Physiological aspects Promoter Regions, Genetic RNA Polymerase II - metabolism X Chromosome - genetics |
| title | Genome-scale profiling of histone H3.3 replacement patterns |
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