An integrated map of p53-binding sites and histone modification in the human ENCODE regions
TP53 (tumor protein p53; p53) regulates its target genes under various cellular stresses. By combining chromatin immunoprecipitation with oligonucleotide microarrays, we have mapped binding sites of p53 (p53-BS) in the genome of HCT116 human colon carcinoma cells, along with those of acetylated H3,...
Gespeichert in:
| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2007-02, Vol.89 (2), p.178-188 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 188 |
|---|---|
| container_issue | 2 |
| container_start_page | 178 |
| container_title | Genomics (San Diego, Calif.) |
| container_volume | 89 |
| creator | Kaneshiro, Kiyofumi Tsutsumi, Shuichi Tsuji, Shingo Shirahige, Katsuhiko Aburatani, Hiroyuki |
| description | TP53 (tumor protein p53; p53) regulates its target genes under various cellular stresses. By combining chromatin immunoprecipitation with oligonucleotide microarrays, we have mapped binding sites of p53 (p53-BS) in the genome of HCT116 human colon carcinoma cells, along with those of acetylated H3, acetylated H4, and methylated H3-K4. We analyzed a 30-Mb portion of the human genome selected as a representative model by the ENCODE Consortium. In the region, we found 37 p53-BS, of which the p53-binding motif was present in 32 (86%). Acetylated histone H3 and H4 were detected at 14 (38%) and 33 (89%) of the p53-BS, respectively. A significant portion (58%) of H4 acetylation in the p53-BS was not accompanied by H3 acetylation. Acetyl H3 were preferentially located at the 5′ and 3′ ends of genes, whereas acetyl H4 were distributed widely across the genome. These results provide novel insights into how p53 binding coordinates with histone modification in human. |
| doi_str_mv | 10.1016/j.ygeno.2006.09.001 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_68422974</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0888754306002618</els_id><sourcerecordid>68422974</sourcerecordid><originalsourceid>FETCH-LOGICAL-c507t-95681b214f091257f3f327a249b15853b4c19d20f7fc1cde5a97e186cb6d466d3</originalsourceid><addsrcrecordid>eNqF0D2PEzEQgGELgbjcwS9AQm6g2zD2-rOgOIUcIJ24BioKy2uPE0dZb1hvkO7fsyGRroPKxTwzsl5C3jBYMmDqw275uMEyLDmAWoJdArBnZMHA2MYooZ6TBRhjGi1Fe0Wua90BgG0Nf0mumAYjgfEF-XlbaC4TbkY_YaS9P9Ah0YNsmy6XmMuG1jxhpb5Eus11GgrSfog55eCnPJyW6bRFuj32vtD1t9XDpzUdcTOP6ivyIvl9xdeX94b8uFt_X31p7h8-f13d3jdBgp4aK5VhHWcigWVc6tSmlmvPhe2YNLLtRGA2ckg6BRYiSm81MqNCp6JQKrY35P357mEcfh2xTq7PNeB-7wsOx-qUEZxbLf4LOcxOtDDD9gzDONQ6YnKHMfd-fHQM3Cm-27m_8d0pvgPr5vjz1tvL-WPXY3zaudSewbsL8DX4fRp9Cbk-OSOkBqFn9_HscK72O-PoashYAsY8YphcHPI_P_IHMiOhzQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20229430</pqid></control><display><type>article</type><title>An integrated map of p53-binding sites and histone modification in the human ENCODE regions</title><source>MEDLINE</source><source>Access via ScienceDirect (Elsevier)</source><source>EZB-FREE-00999 freely available EZB journals</source><creator>Kaneshiro, Kiyofumi ; Tsutsumi, Shuichi ; Tsuji, Shingo ; Shirahige, Katsuhiko ; Aburatani, Hiroyuki</creator><creatorcontrib>Kaneshiro, Kiyofumi ; Tsutsumi, Shuichi ; Tsuji, Shingo ; Shirahige, Katsuhiko ; Aburatani, Hiroyuki</creatorcontrib><description>TP53 (tumor protein p53; p53) regulates its target genes under various cellular stresses. By combining chromatin immunoprecipitation with oligonucleotide microarrays, we have mapped binding sites of p53 (p53-BS) in the genome of HCT116 human colon carcinoma cells, along with those of acetylated H3, acetylated H4, and methylated H3-K4. We analyzed a 30-Mb portion of the human genome selected as a representative model by the ENCODE Consortium. In the region, we found 37 p53-BS, of which the p53-binding motif was present in 32 (86%). Acetylated histone H3 and H4 were detected at 14 (38%) and 33 (89%) of the p53-BS, respectively. A significant portion (58%) of H4 acetylation in the p53-BS was not accompanied by H3 acetylation. Acetyl H3 were preferentially located at the 5′ and 3′ ends of genes, whereas acetyl H4 were distributed widely across the genome. These results provide novel insights into how p53 binding coordinates with histone modification in human.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2006.09.001</identifier><identifier>PMID: 17085012</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>Acetylation ; Base Sequence ; Binding Sites - genetics ; Biological and medical sciences ; Cell Line ; Chromatin ; Chromatin. Chromosome ; Chromosome Mapping ; DNA - genetics ; DNA - metabolism ; Fundamental and applied biological sciences. Psychology ; Genes, p53 ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Human ; HCT116 cells ; Histone ; Histones - genetics ; Histones - metabolism ; Human ; Humans ; Molecular and cellular biology ; Molecular genetics ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide microarrays ; TP53 protein ; Transcriptional Activation ; Tumor Suppressor Protein p53 - metabolism</subject><ispartof>Genomics (San Diego, Calif.), 2007-02, Vol.89 (2), p.178-188</ispartof><rights>2006 Elsevier Inc.</rights><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c507t-95681b214f091257f3f327a249b15853b4c19d20f7fc1cde5a97e186cb6d466d3</citedby><cites>FETCH-LOGICAL-c507t-95681b214f091257f3f327a249b15853b4c19d20f7fc1cde5a97e186cb6d466d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2006.09.001$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18457047$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17085012$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kaneshiro, Kiyofumi</creatorcontrib><creatorcontrib>Tsutsumi, Shuichi</creatorcontrib><creatorcontrib>Tsuji, Shingo</creatorcontrib><creatorcontrib>Shirahige, Katsuhiko</creatorcontrib><creatorcontrib>Aburatani, Hiroyuki</creatorcontrib><title>An integrated map of p53-binding sites and histone modification in the human ENCODE regions</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>TP53 (tumor protein p53; p53) regulates its target genes under various cellular stresses. By combining chromatin immunoprecipitation with oligonucleotide microarrays, we have mapped binding sites of p53 (p53-BS) in the genome of HCT116 human colon carcinoma cells, along with those of acetylated H3, acetylated H4, and methylated H3-K4. We analyzed a 30-Mb portion of the human genome selected as a representative model by the ENCODE Consortium. In the region, we found 37 p53-BS, of which the p53-binding motif was present in 32 (86%). Acetylated histone H3 and H4 were detected at 14 (38%) and 33 (89%) of the p53-BS, respectively. A significant portion (58%) of H4 acetylation in the p53-BS was not accompanied by H3 acetylation. Acetyl H3 were preferentially located at the 5′ and 3′ ends of genes, whereas acetyl H4 were distributed widely across the genome. These results provide novel insights into how p53 binding coordinates with histone modification in human.</description><subject>Acetylation</subject><subject>Base Sequence</subject><subject>Binding Sites - genetics</subject><subject>Biological and medical sciences</subject><subject>Cell Line</subject><subject>Chromatin</subject><subject>Chromatin. Chromosome</subject><subject>Chromosome Mapping</subject><subject>DNA - genetics</subject><subject>DNA - metabolism</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, p53</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Human</subject><subject>HCT116 cells</subject><subject>Histone</subject><subject>Histones - genetics</subject><subject>Histones - metabolism</subject><subject>Human</subject><subject>Humans</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Oligonucleotide microarrays</subject><subject>TP53 protein</subject><subject>Transcriptional Activation</subject><subject>Tumor Suppressor Protein p53 - metabolism</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0D2PEzEQgGELgbjcwS9AQm6g2zD2-rOgOIUcIJ24BioKy2uPE0dZb1hvkO7fsyGRroPKxTwzsl5C3jBYMmDqw275uMEyLDmAWoJdArBnZMHA2MYooZ6TBRhjGi1Fe0Wua90BgG0Nf0mumAYjgfEF-XlbaC4TbkY_YaS9P9Ah0YNsmy6XmMuG1jxhpb5Eus11GgrSfog55eCnPJyW6bRFuj32vtD1t9XDpzUdcTOP6ivyIvl9xdeX94b8uFt_X31p7h8-f13d3jdBgp4aK5VhHWcigWVc6tSmlmvPhe2YNLLtRGA2ckg6BRYiSm81MqNCp6JQKrY35P357mEcfh2xTq7PNeB-7wsOx-qUEZxbLf4LOcxOtDDD9gzDONQ6YnKHMfd-fHQM3Cm-27m_8d0pvgPr5vjz1tvL-WPXY3zaudSewbsL8DX4fRp9Cbk-OSOkBqFn9_HscK72O-PoashYAsY8YphcHPI_P_IHMiOhzQ</recordid><startdate>20070201</startdate><enddate>20070201</enddate><creator>Kaneshiro, Kiyofumi</creator><creator>Tsutsumi, Shuichi</creator><creator>Tsuji, Shingo</creator><creator>Shirahige, Katsuhiko</creator><creator>Aburatani, Hiroyuki</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><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>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20070201</creationdate><title>An integrated map of p53-binding sites and histone modification in the human ENCODE regions</title><author>Kaneshiro, Kiyofumi ; Tsutsumi, Shuichi ; Tsuji, Shingo ; Shirahige, Katsuhiko ; Aburatani, Hiroyuki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c507t-95681b214f091257f3f327a249b15853b4c19d20f7fc1cde5a97e186cb6d466d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Acetylation</topic><topic>Base Sequence</topic><topic>Binding Sites - genetics</topic><topic>Biological and medical sciences</topic><topic>Cell Line</topic><topic>Chromatin</topic><topic>Chromatin. Chromosome</topic><topic>Chromosome Mapping</topic><topic>DNA - genetics</topic><topic>DNA - metabolism</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, p53</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Human</topic><topic>HCT116 cells</topic><topic>Histone</topic><topic>Histones - genetics</topic><topic>Histones - metabolism</topic><topic>Human</topic><topic>Humans</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Oligonucleotide microarrays</topic><topic>TP53 protein</topic><topic>Transcriptional Activation</topic><topic>Tumor Suppressor Protein p53 - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kaneshiro, Kiyofumi</creatorcontrib><creatorcontrib>Tsutsumi, Shuichi</creatorcontrib><creatorcontrib>Tsuji, Shingo</creatorcontrib><creatorcontrib>Shirahige, Katsuhiko</creatorcontrib><creatorcontrib>Aburatani, Hiroyuki</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><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>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>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kaneshiro, Kiyofumi</au><au>Tsutsumi, Shuichi</au><au>Tsuji, Shingo</au><au>Shirahige, Katsuhiko</au><au>Aburatani, Hiroyuki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>An integrated map of p53-binding sites and histone modification in the human ENCODE regions</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2007-02-01</date><risdate>2007</risdate><volume>89</volume><issue>2</issue><spage>178</spage><epage>188</epage><pages>178-188</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>TP53 (tumor protein p53; p53) regulates its target genes under various cellular stresses. By combining chromatin immunoprecipitation with oligonucleotide microarrays, we have mapped binding sites of p53 (p53-BS) in the genome of HCT116 human colon carcinoma cells, along with those of acetylated H3, acetylated H4, and methylated H3-K4. We analyzed a 30-Mb portion of the human genome selected as a representative model by the ENCODE Consortium. In the region, we found 37 p53-BS, of which the p53-binding motif was present in 32 (86%). Acetylated histone H3 and H4 were detected at 14 (38%) and 33 (89%) of the p53-BS, respectively. A significant portion (58%) of H4 acetylation in the p53-BS was not accompanied by H3 acetylation. Acetyl H3 were preferentially located at the 5′ and 3′ ends of genes, whereas acetyl H4 were distributed widely across the genome. These results provide novel insights into how p53 binding coordinates with histone modification in human.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>17085012</pmid><doi>10.1016/j.ygeno.2006.09.001</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0888-7543 |
| ispartof | Genomics (San Diego, Calif.), 2007-02, Vol.89 (2), p.178-188 |
| issn | 0888-7543 1089-8646 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_68422974 |
| source | MEDLINE; Access via ScienceDirect (Elsevier); EZB-FREE-00999 freely available EZB journals |
| subjects | Acetylation Base Sequence Binding Sites - genetics Biological and medical sciences Cell Line Chromatin Chromatin. Chromosome Chromosome Mapping DNA - genetics DNA - metabolism Fundamental and applied biological sciences. Psychology Genes, p53 Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome, Human HCT116 cells Histone Histones - genetics Histones - metabolism Human Humans Molecular and cellular biology Molecular genetics Oligonucleotide Array Sequence Analysis Oligonucleotide microarrays TP53 protein Transcriptional Activation Tumor Suppressor Protein p53 - metabolism |
| title | An integrated map of p53-binding sites and histone modification in the human ENCODE regions |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-20T08%3A24%3A38IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=An%20integrated%20map%20of%20p53-binding%20sites%20and%20histone%20modification%20in%20the%20human%20ENCODE%20regions&rft.jtitle=Genomics%20(San%20Diego,%20Calif.)&rft.au=Kaneshiro,%20Kiyofumi&rft.date=2007-02-01&rft.volume=89&rft.issue=2&rft.spage=178&rft.epage=188&rft.pages=178-188&rft.issn=0888-7543&rft.eissn=1089-8646&rft_id=info:doi/10.1016/j.ygeno.2006.09.001&rft_dat=%3Cproquest_cross%3E68422974%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=20229430&rft_id=info:pmid/17085012&rft_els_id=S0888754306002618&rfr_iscdi=true |