Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic...
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| Veröffentlicht in: | Nature 2007-08, Vol.448 (7153), p.553-560 |
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| creator | Mikkelsen, Tarjei S. Ku, Manching Jaffe, David B. Issac, Biju Lieberman, Erez Giannoukos, Georgia Alvarez, Pablo Brockman, William Kim, Tae-Kyung Koche, Richard P. Lee, William Mendenhall, Eric O’Donovan, Aisling Presser, Aviva Russ, Carsten Xie, Xiaohui Meissner, Alexander Wernig, Marius Jaenisch, Rudolf Nusbaum, Chad Lander, Eric S. Bernstein, Bradley E. |
| description | We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Chromatin profiling
Although they contain the same set of genes, different cell types in a multicellular organism maintain very different behaviours. These cell states are thought to be related to chromatin state — that is, modifications to histones and other proteins that package the genome. Single-molecule sequencing technology has now been used to construct chromatin-state maps for mouse embryonic stem cells and two other more developmentally advanced cell types, revealing the genome-wide distribution of important chromatin modifications. The study provides pointers for the use of chromatin profiling on mammalian cell populations, including those of abnormal cells, such as cancer.
Single-molecule-based sequencing technology is applied to generate genome-wide maps of chromatin modifications in mammalian cells. Histone marks can discriminate genes that are active, poised for activation, or stably repressed and therefore reflect cell state and developmental potential. |
| doi_str_mv | 10.1038/nature06008 |
| format | Article |
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Chromatin profiling
Although they contain the same set of genes, different cell types in a multicellular organism maintain very different behaviours. These cell states are thought to be related to chromatin state — that is, modifications to histones and other proteins that package the genome. Single-molecule sequencing technology has now been used to construct chromatin-state maps for mouse embryonic stem cells and two other more developmentally advanced cell types, revealing the genome-wide distribution of important chromatin modifications. The study provides pointers for the use of chromatin profiling on mammalian cell populations, including those of abnormal cells, such as cancer.
Single-molecule-based sequencing technology is applied to generate genome-wide maps of chromatin modifications in mammalian cells. Histone marks can discriminate genes that are active, poised for activation, or stably repressed and therefore reflect cell state and developmental potential.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>EISSN: 1476-4679</identifier><identifier>DOI: 10.1038/nature06008</identifier><identifier>PMID: 17603471</identifier><identifier>CODEN: NATUAS</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Alleles ; Animals ; Biological and medical sciences ; Cell Lineage - genetics ; Chromatin ; Chromatin - genetics ; Chromatin - metabolism ; Chromatin. Chromosome ; CpG Islands - genetics ; Deoxyribonucleic acid ; DNA ; Fibroblasts ; Fundamental and applied biological sciences. Psychology ; Gene Expression Regulation, Developmental ; Genome - genetics ; Genomic Imprinting ; Genomics ; Histones - metabolism ; Humanities and Social Sciences ; Male ; Mammals ; Methylation ; Mice ; Molecular and cellular biology ; Molecular genetics ; multidisciplinary ; Pluripotent Stem Cells - cytology ; Pluripotent Stem Cells - metabolism ; Promoter Regions, Genetic - genetics ; Research methodology ; Rodents ; Science ; Science (multidisciplinary) ; Stem cells ; Transcription, Genetic - genetics</subject><ispartof>Nature, 2007-08, Vol.448 (7153), p.553-560</ispartof><rights>Springer Nature Limited 2007</rights><rights>2007 INIST-CNRS</rights><rights>COPYRIGHT 2007 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Aug 2, 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c777t-71f0365d6cd708ef28fbc19979adc7b2a4365c87e85f38eab969710c5cc7b4ed3</citedby><cites>FETCH-LOGICAL-c777t-71f0365d6cd708ef28fbc19979adc7b2a4365c87e85f38eab969710c5cc7b4ed3</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/nature06008$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature06008$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18949592$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17603471$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mikkelsen, Tarjei S.</creatorcontrib><creatorcontrib>Ku, Manching</creatorcontrib><creatorcontrib>Jaffe, David B.</creatorcontrib><creatorcontrib>Issac, Biju</creatorcontrib><creatorcontrib>Lieberman, Erez</creatorcontrib><creatorcontrib>Giannoukos, Georgia</creatorcontrib><creatorcontrib>Alvarez, Pablo</creatorcontrib><creatorcontrib>Brockman, William</creatorcontrib><creatorcontrib>Kim, Tae-Kyung</creatorcontrib><creatorcontrib>Koche, Richard P.</creatorcontrib><creatorcontrib>Lee, William</creatorcontrib><creatorcontrib>Mendenhall, Eric</creatorcontrib><creatorcontrib>O’Donovan, Aisling</creatorcontrib><creatorcontrib>Presser, Aviva</creatorcontrib><creatorcontrib>Russ, Carsten</creatorcontrib><creatorcontrib>Xie, Xiaohui</creatorcontrib><creatorcontrib>Meissner, Alexander</creatorcontrib><creatorcontrib>Wernig, Marius</creatorcontrib><creatorcontrib>Jaenisch, Rudolf</creatorcontrib><creatorcontrib>Nusbaum, Chad</creatorcontrib><creatorcontrib>Lander, Eric S.</creatorcontrib><creatorcontrib>Bernstein, Bradley E.</creatorcontrib><title>Genome-wide maps of chromatin state in pluripotent and lineage-committed cells</title><title>Nature</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Chromatin profiling
Although they contain the same set of genes, different cell types in a multicellular organism maintain very different behaviours. These cell states are thought to be related to chromatin state — that is, modifications to histones and other proteins that package the genome. Single-molecule sequencing technology has now been used to construct chromatin-state maps for mouse embryonic stem cells and two other more developmentally advanced cell types, revealing the genome-wide distribution of important chromatin modifications. The study provides pointers for the use of chromatin profiling on mammalian cell populations, including those of abnormal cells, such as cancer.
Single-molecule-based sequencing technology is applied to generate genome-wide maps of chromatin modifications in mammalian cells. Histone marks can discriminate genes that are active, poised for activation, or stably repressed and therefore reflect cell state and developmental potential.</description><subject>Alleles</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Cell Lineage - genetics</subject><subject>Chromatin</subject><subject>Chromatin - genetics</subject><subject>Chromatin - metabolism</subject><subject>Chromatin. Chromosome</subject><subject>CpG Islands - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Fibroblasts</subject><subject>Fundamental and applied biological sciences. 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Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Psychology</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Research Library (Corporate)</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</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 One Psychology</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>Genetics Abstracts</collection><collection>SIRS Editorial</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mikkelsen, Tarjei S.</au><au>Ku, Manching</au><au>Jaffe, David B.</au><au>Issac, Biju</au><au>Lieberman, Erez</au><au>Giannoukos, Georgia</au><au>Alvarez, Pablo</au><au>Brockman, William</au><au>Kim, Tae-Kyung</au><au>Koche, Richard P.</au><au>Lee, William</au><au>Mendenhall, Eric</au><au>O’Donovan, Aisling</au><au>Presser, Aviva</au><au>Russ, Carsten</au><au>Xie, Xiaohui</au><au>Meissner, Alexander</au><au>Wernig, Marius</au><au>Jaenisch, Rudolf</au><au>Nusbaum, Chad</au><au>Lander, Eric S.</au><au>Bernstein, Bradley E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide maps of chromatin state in pluripotent and lineage-committed cells</atitle><jtitle>Nature</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2007-08-02</date><risdate>2007</risdate><volume>448</volume><issue>7153</issue><spage>553</spage><epage>560</epage><pages>553-560</pages><issn>0028-0836</issn><eissn>1476-4687</eissn><eissn>1476-4679</eissn><coden>NATUAS</coden><abstract>We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Chromatin profiling
Although they contain the same set of genes, different cell types in a multicellular organism maintain very different behaviours. These cell states are thought to be related to chromatin state — that is, modifications to histones and other proteins that package the genome. Single-molecule sequencing technology has now been used to construct chromatin-state maps for mouse embryonic stem cells and two other more developmentally advanced cell types, revealing the genome-wide distribution of important chromatin modifications. The study provides pointers for the use of chromatin profiling on mammalian cell populations, including those of abnormal cells, such as cancer.
Single-molecule-based sequencing technology is applied to generate genome-wide maps of chromatin modifications in mammalian cells. Histone marks can discriminate genes that are active, poised for activation, or stably repressed and therefore reflect cell state and developmental potential.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>17603471</pmid><doi>10.1038/nature06008</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0028-0836 |
| ispartof | Nature, 2007-08, Vol.448 (7153), p.553-560 |
| issn | 0028-0836 1476-4687 1476-4679 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2921165 |
| source | MEDLINE; Springer Nature - Complete Springer Journals; Nature Journals Online |
| subjects | Alleles Animals Biological and medical sciences Cell Lineage - genetics Chromatin Chromatin - genetics Chromatin - metabolism Chromatin. Chromosome CpG Islands - genetics Deoxyribonucleic acid DNA Fibroblasts Fundamental and applied biological sciences. Psychology Gene Expression Regulation, Developmental Genome - genetics Genomic Imprinting Genomics Histones - metabolism Humanities and Social Sciences Male Mammals Methylation Mice Molecular and cellular biology Molecular genetics multidisciplinary Pluripotent Stem Cells - cytology Pluripotent Stem Cells - metabolism Promoter Regions, Genetic - genetics Research methodology Rodents Science Science (multidisciplinary) Stem cells Transcription, Genetic - genetics |
| title | Genome-wide maps of chromatin state in pluripotent and lineage-committed cells |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-02T02%3A04%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20maps%20of%20chromatin%20state%20in%20pluripotent%20and%20lineage-committed%20cells&rft.jtitle=Nature&rft.au=Mikkelsen,%20Tarjei%20S.&rft.date=2007-08-02&rft.volume=448&rft.issue=7153&rft.spage=553&rft.epage=560&rft.pages=553-560&rft.issn=0028-0836&rft.eissn=1476-4687&rft.coden=NATUAS&rft_id=info:doi/10.1038/nature06008&rft_dat=%3Cgale_pubme%3EA185195142%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=204552622&rft_id=info:pmid/17603471&rft_galeid=A185195142&rfr_iscdi=true |