TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed
Identifieur interne : 002309 ( Main/Exploration ); précédent : 002308; suivant : 002310TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed
Auteurs : Argyris Papantonis [Royaume-Uni] ; Takahide Kohro [Japon] ; Sabyasachi Baboo [Royaume-Uni] ; Joshua D. Larkin [Royaume-Uni] ; Binwei Deng [Royaume-Uni] ; Patrick Short [Royaume-Uni, États-Unis] ; Shuichi Tsutsumi [Japon] ; Stephen Taylor [Royaume-Uni] ; Yasuharu Kanki [Japon] ; Mika Kobayashi [Japon] ; Guoliang Li [Singapour] ; Huay-Mei Poh [Singapour] ; Xiaoan Ruan [Singapour] ; Hiroyuki Aburatani [Japon] ; Yijun Ruan [Singapour] ; Tatsuhiko Kodama [Japon] ; Youichiro Wada [Japon] ; Peter R. Cook [Royaume-Uni]Source :
- The EMBO Journal [ 0261-4189 ] ; 2012-11-28.
English descriptors
- Teeft :
- Active genes, Binding sites, Biol, Biology organization, Cell biol, Chromatin, Chromatin interaction analysis, Chromosome, Chromosome conformation, Colocalization, Colocalize, Conformation, Conventional sequencing, Cytokine, Different chromosomes, Different genes, Embo, Embo journal, Encoding, England biolabs, Ets2, Exact test, Ext1, Ezna microelute, Fewer contacts, Frequent contacts, Gene, Genes encoding mirnas, Genet, Genic, Genic contacts, Genome, Green foci, Hindiii, Human genes, Human genome, Huvecs, Intron, Intronic, Intronic probes, Koinuma, Microarray, Mirna, Mirna genes, Mirnas, More contacts, Mrna, Mrna levels, Multiplexed, Nascent, Nascent rnas, Nascent transcripts, Nfkb, Nuclear factor kappa, Other genes, Papantonis, Phosphorylation, Polymerase, Promoter, Rank order, Reference genes, Reference points, Responsive, Responsive gene, Responsive genes, Responsive promoters, Rna, Samd4a, Samd4a intron, Samd4a libraries, Same strategy, Sequencing, Specialized factories, Specialized transcription factories, Subunit, Supplementary, Supplementary figure, Supplementary figures, Supplementary table, Supplementary tables, Tgfb, Tnfa, Tnfa stimulation, Transcribing, Transcription, Transcription factories, Upregulated, Upregulated genes, Wada.
Abstract
Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired‐end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete ‘NFκB factories’. Some factories further specialize in transcribing responsive genes encoding micro‐RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories.
TNFα alpha treatment induces congregation of both coding and non‐coding NFκB target genes in discrete transcription factories, leading to coordinated gene expression.
Url:
DOI: 10.1038/emboj.2012.288
Affiliations:
- Japon, Royaume-Uni, Singapour, États-Unis
- Angleterre, Oxfordshire, Région de Kantō
- Oxford, Tokyo
- Université d'Oxford, Université de Tokyo
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uniqKey="Kanki Y" first="Yasuharu" last="Kanki">Yasuharu Kanki</name><affiliation wicri:level="4"><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Kobayashi, Mika" sort="Kobayashi, Mika" uniqKey="Kobayashi M" first="Mika" last="Kobayashi">Mika Kobayashi</name><affiliation wicri:level="4"><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name><affiliation wicri:level="1"><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Poh, Huay Ei" sort="Poh, Huay Ei" uniqKey="Poh H" first="Huay-Mei" last="Poh">Huay-Mei Poh</name><affiliation wicri:level="1"><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Ruan, Xiaoan" sort="Ruan, Xiaoan" uniqKey="Ruan X" first="Xiaoan" last="Ruan">Xiaoan Ruan</name><affiliation wicri:level="1"><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Aburatani, Hiroyuki" sort="Aburatani, Hiroyuki" uniqKey="Aburatani H" first="Hiroyuki" last="Aburatani">Hiroyuki Aburatani</name><affiliation wicri:level="4"><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Ruan, Yijun" sort="Ruan, Yijun" uniqKey="Ruan Y" first="Yijun" last="Ruan">Yijun Ruan</name><affiliation wicri:level="1"><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Kodama, Tatsuhiko" sort="Kodama, Tatsuhiko" uniqKey="Kodama T" first="Tatsuhiko" last="Kodama">Tatsuhiko Kodama</name><affiliation wicri:level="4"><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Wada, Youichiro" sort="Wada, Youichiro" uniqKey="Wada Y" first="Youichiro" last="Wada">Youichiro Wada</name><affiliation wicri:level="4"><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation><affiliation></affiliation></author><author><name sortKey="Cook, Peter R" sort="Cook, Peter R" uniqKey="Cook P" first="Peter R" last="Cook">Peter R. Cook</name><affiliation wicri:level="4"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region></placeName><orgName type="university">Université d'Oxford</orgName></affiliation><affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">The EMBO Journal</title><title level="j" type="alt">THE EMBO JOURNAL</title><idno type="ISSN">0261-4189</idno><idno type="eISSN">1460-2075</idno><imprint><biblScope unit="vol">31</biblScope><biblScope unit="issue">23</biblScope><biblScope unit="page" from="4404">4404</biblScope><biblScope unit="page" to="4414">4414</biblScope><biblScope unit="page-count">11</biblScope><publisher>John Wiley & Sons, Ltd</publisher><pubPlace>Chichester, UK</pubPlace><date type="published" when="2012-11-28">2012-11-28</date></imprint><idno type="ISSN">0261-4189</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0261-4189</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Active genes</term><term>Binding sites</term><term>Biol</term><term>Biology organization</term><term>Cell biol</term><term>Chromatin</term><term>Chromatin interaction analysis</term><term>Chromosome</term><term>Chromosome conformation</term><term>Colocalization</term><term>Colocalize</term><term>Conformation</term><term>Conventional sequencing</term><term>Cytokine</term><term>Different chromosomes</term><term>Different genes</term><term>Embo</term><term>Embo journal</term><term>Encoding</term><term>England biolabs</term><term>Ets2</term><term>Exact test</term><term>Ext1</term><term>Ezna microelute</term><term>Fewer contacts</term><term>Frequent contacts</term><term>Gene</term><term>Genes encoding mirnas</term><term>Genet</term><term>Genic</term><term>Genic contacts</term><term>Genome</term><term>Green foci</term><term>Hindiii</term><term>Human genes</term><term>Human genome</term><term>Huvecs</term><term>Intron</term><term>Intronic</term><term>Intronic probes</term><term>Koinuma</term><term>Microarray</term><term>Mirna</term><term>Mirna genes</term><term>Mirnas</term><term>More contacts</term><term>Mrna</term><term>Mrna levels</term><term>Multiplexed</term><term>Nascent</term><term>Nascent rnas</term><term>Nascent transcripts</term><term>Nfkb</term><term>Nuclear factor kappa</term><term>Other genes</term><term>Papantonis</term><term>Phosphorylation</term><term>Polymerase</term><term>Promoter</term><term>Rank order</term><term>Reference genes</term><term>Reference points</term><term>Responsive</term><term>Responsive gene</term><term>Responsive genes</term><term>Responsive promoters</term><term>Rna</term><term>Samd4a</term><term>Samd4a intron</term><term>Samd4a libraries</term><term>Same strategy</term><term>Sequencing</term><term>Specialized factories</term><term>Specialized transcription factories</term><term>Subunit</term><term>Supplementary</term><term>Supplementary figure</term><term>Supplementary figures</term><term>Supplementary table</term><term>Supplementary tables</term><term>Tgfb</term><term>Tnfa</term><term>Tnfa stimulation</term><term>Transcribing</term><term>Transcription</term><term>Transcription factories</term><term>Upregulated</term><term>Upregulated genes</term><term>Wada</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired‐end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete ‘NFκB factories’. Some factories further specialize in transcribing responsive genes encoding micro‐RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories.</div><div type="abstract">TNFα alpha treatment induces congregation of both coding and non‐coding NFκB target genes in discrete transcription factories, leading to coordinated gene expression.</div></front></TEI><affiliations><list><country><li>Japon</li><li>Royaume-Uni</li><li>Singapour</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Oxfordshire</li><li>Région de Kantō</li></region><settlement><li>Oxford</li><li>Tokyo</li></settlement><orgName><li>Université d'Oxford</li><li>Université de Tokyo</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Papantonis, Argyris" sort="Papantonis, Argyris" uniqKey="Papantonis A" first="Argyris" last="Papantonis">Argyris Papantonis</name></region><name sortKey="Baboo, Sabyasachi" sort="Baboo, Sabyasachi" uniqKey="Baboo S" first="Sabyasachi" last="Baboo">Sabyasachi Baboo</name><name sortKey="Cook, Peter R" sort="Cook, Peter R" uniqKey="Cook P" first="Peter R" last="Cook">Peter R. Cook</name><name sortKey="Deng, Binwei" sort="Deng, Binwei" uniqKey="Deng B" first="Binwei" last="Deng">Binwei Deng</name><name sortKey="Larkin, Joshua D" sort="Larkin, Joshua D" uniqKey="Larkin J" first="Joshua D" last="Larkin">Joshua D. Larkin</name><name sortKey="Short, Patrick" sort="Short, Patrick" uniqKey="Short P" first="Patrick" last="Short">Patrick Short</name><name sortKey="Taylor, Stephen" sort="Taylor, Stephen" uniqKey="Taylor S" first="Stephen" last="Taylor">Stephen Taylor</name></country><country name="Japon"><region name="Région de Kantō"><name sortKey="Kohro, Takahide" sort="Kohro, Takahide" uniqKey="Kohro T" first="Takahide" last="Kohro">Takahide Kohro</name></region><name sortKey="Aburatani, Hiroyuki" sort="Aburatani, Hiroyuki" uniqKey="Aburatani H" first="Hiroyuki" last="Aburatani">Hiroyuki Aburatani</name><name sortKey="Kanki, Yasuharu" sort="Kanki, Yasuharu" uniqKey="Kanki Y" first="Yasuharu" last="Kanki">Yasuharu Kanki</name><name sortKey="Kobayashi, Mika" sort="Kobayashi, Mika" uniqKey="Kobayashi M" first="Mika" last="Kobayashi">Mika Kobayashi</name><name sortKey="Kodama, Tatsuhiko" sort="Kodama, Tatsuhiko" uniqKey="Kodama T" first="Tatsuhiko" last="Kodama">Tatsuhiko Kodama</name><name sortKey="Tsutsumi, Shuichi" sort="Tsutsumi, Shuichi" uniqKey="Tsutsumi S" first="Shuichi" last="Tsutsumi">Shuichi Tsutsumi</name><name sortKey="Wada, Youichiro" sort="Wada, Youichiro" uniqKey="Wada Y" first="Youichiro" last="Wada">Youichiro Wada</name></country><country name="États-Unis"><noRegion><name sortKey="Short, Patrick" sort="Short, Patrick" uniqKey="Short P" first="Patrick" last="Short">Patrick Short</name></noRegion></country><country name="Singapour"><noRegion><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name></noRegion><name sortKey="Poh, Huay Ei" sort="Poh, Huay Ei" uniqKey="Poh H" first="Huay-Mei" last="Poh">Huay-Mei Poh</name><name sortKey="Ruan, Xiaoan" sort="Ruan, Xiaoan" uniqKey="Ruan X" first="Xiaoan" last="Ruan">Xiaoan Ruan</name><name sortKey="Ruan, Yijun" sort="Ruan, Yijun" uniqKey="Ruan Y" first="Yijun" last="Ruan">Yijun Ruan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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