wave of nascent transcription on activated human genes
Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-α (TNFα) and monitored (using microarra...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2009-10, Vol.106 (43), p.18357-18361 |
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| creator | Wada, Youichiro Ohta, Yoshihiro Xu, Meng Tsutsumi, Shuichi Minami, Takashi Inoue, Kenji Komura, Daisuke Kitakami, Jun'ichi Oshida, Nobuhiko Papantonis, Argyris Izumi, Akashi Kobayashi, Mika Meguro, Hiroko Kanki, Yasuharu Mimura, Imari Yamamoto, Kazuki Mataki, Chikage Hamakubo, Takao Shirahige, Katsuhiko Aburatani, Hiroyuki Kimura, Hiroshi Kodama, Tatsuhiko Cook, Peter R Ihara, Sigeo |
| description | Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-α (TNFα) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at ≈3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites. |
| doi_str_mv | 10.1073/pnas.0902573106 |
| format | Article |
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To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-α (TNFα) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at ≈3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0902573106</identifier><identifier>PMID: 19826084</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Antisense elements ; Binding Sites ; Biological Sciences ; CCCTC-Binding Factor ; Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; Cells, Cultured ; Chromatin Immunoprecipitation ; Chromosomal Proteins, Non-Histone - genetics ; Chromosomal Proteins, Non-Histone - metabolism ; Cohesins ; DNA-Binding Proteins ; Fluorescence in situ hybridization ; Genes ; Genomics ; Histones ; Humans ; In Situ Hybridization ; Introns ; Nuclear Proteins - genetics ; Nuclear Proteins - metabolism ; Nucleotides ; Oligonucleotide Array Sequence Analysis ; Phosphoproteins - genetics ; Phosphoproteins - metabolism ; Repressor Proteins - genetics ; Repressor Proteins - metabolism ; RNA ; RNA polymerase ; RNA Polymerase II - metabolism ; RNA probes ; RNA Splicing ; RNA, Messenger - biosynthesis ; Signal detection ; Splicing ; Tiling ; Transcription, Genetic ; Transcriptional Activation ; Tumor Necrosis Factor-alpha - genetics</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2009-10, Vol.106 (43), p.18357-18361</ispartof><rights>Copyright National Academy of Sciences Oct 27, 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c665t-6fad2e4e88e6fbb13076c3042768fa551f0a3d80e61b87be6574a1dd4c78534f3</citedby><cites>FETCH-LOGICAL-c665t-6fad2e4e88e6fbb13076c3042768fa551f0a3d80e61b87be6574a1dd4c78534f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/106/43.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25593011$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25593011$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,315,729,782,786,805,887,27931,27932,53798,53800,58024,58257</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19826084$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wada, Youichiro</creatorcontrib><creatorcontrib>Ohta, Yoshihiro</creatorcontrib><creatorcontrib>Xu, Meng</creatorcontrib><creatorcontrib>Tsutsumi, Shuichi</creatorcontrib><creatorcontrib>Minami, Takashi</creatorcontrib><creatorcontrib>Inoue, Kenji</creatorcontrib><creatorcontrib>Komura, Daisuke</creatorcontrib><creatorcontrib>Kitakami, Jun'ichi</creatorcontrib><creatorcontrib>Oshida, Nobuhiko</creatorcontrib><creatorcontrib>Papantonis, Argyris</creatorcontrib><creatorcontrib>Izumi, Akashi</creatorcontrib><creatorcontrib>Kobayashi, Mika</creatorcontrib><creatorcontrib>Meguro, Hiroko</creatorcontrib><creatorcontrib>Kanki, Yasuharu</creatorcontrib><creatorcontrib>Mimura, Imari</creatorcontrib><creatorcontrib>Yamamoto, Kazuki</creatorcontrib><creatorcontrib>Mataki, Chikage</creatorcontrib><creatorcontrib>Hamakubo, Takao</creatorcontrib><creatorcontrib>Shirahige, Katsuhiko</creatorcontrib><creatorcontrib>Aburatani, Hiroyuki</creatorcontrib><creatorcontrib>Kimura, Hiroshi</creatorcontrib><creatorcontrib>Kodama, Tatsuhiko</creatorcontrib><creatorcontrib>Cook, Peter R</creatorcontrib><creatorcontrib>Ihara, Sigeo</creatorcontrib><title>wave of nascent transcription on activated human genes</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-α (TNFα) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at ≈3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites.</description><subject>Antisense elements</subject><subject>Binding Sites</subject><subject>Biological Sciences</subject><subject>CCCTC-Binding Factor</subject><subject>Cell Cycle Proteins - genetics</subject><subject>Cell Cycle Proteins - metabolism</subject><subject>Cells, Cultured</subject><subject>Chromatin Immunoprecipitation</subject><subject>Chromosomal Proteins, Non-Histone - genetics</subject><subject>Chromosomal Proteins, Non-Histone - metabolism</subject><subject>Cohesins</subject><subject>DNA-Binding Proteins</subject><subject>Fluorescence in situ hybridization</subject><subject>Genes</subject><subject>Genomics</subject><subject>Histones</subject><subject>Humans</subject><subject>In Situ Hybridization</subject><subject>Introns</subject><subject>Nuclear Proteins - 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| ispartof | Proceedings of the National Academy of Sciences - PNAS, 2009-10, Vol.106 (43), p.18357-18361 |
| issn | 0027-8424 1091-6490 |
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| recordid | cdi_pubmed_primary_19826084 |
| source | MEDLINE; JSTOR Archive Collection A-Z Listing; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Antisense elements Binding Sites Biological Sciences CCCTC-Binding Factor Cell Cycle Proteins - genetics Cell Cycle Proteins - metabolism Cells, Cultured Chromatin Immunoprecipitation Chromosomal Proteins, Non-Histone - genetics Chromosomal Proteins, Non-Histone - metabolism Cohesins DNA-Binding Proteins Fluorescence in situ hybridization Genes Genomics Histones Humans In Situ Hybridization Introns Nuclear Proteins - genetics Nuclear Proteins - metabolism Nucleotides Oligonucleotide Array Sequence Analysis Phosphoproteins - genetics Phosphoproteins - metabolism Repressor Proteins - genetics Repressor Proteins - metabolism RNA RNA polymerase RNA Polymerase II - metabolism RNA probes RNA Splicing RNA, Messenger - biosynthesis Signal detection Splicing Tiling Transcription, Genetic Transcriptional Activation Tumor Necrosis Factor-alpha - genetics |
| title | wave of nascent transcription on activated human genes |
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