TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed
Identifieur interne : 000B73 ( Istex/Curation ); précédent : 000B72; suivant : 000B74TNFα 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
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Larkin</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Binwei" sort="Deng, Binwei" uniqKey="Deng B" first="Binwei" last="Deng">Binwei Deng</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Short, Patrick" sort="Short, Patrick" uniqKey="Short P" first="Patrick" last="Short">Patrick Short</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, 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Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo</wicri:regionArea></affiliation></author><author><name sortKey="Taylor, Stephen" sort="Taylor, Stephen" uniqKey="Taylor S" first="Stephen" last="Taylor">Stephen Taylor</name><affiliation wicri:level="1"><mods:affiliation>Computational Research Biology Group, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Computational Research Biology Group, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Kanki, Yasuharu" sort="Kanki, Yasuharu" uniqKey="Kanki Y" first="Yasuharu" last="Kanki">Yasuharu Kanki</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for Systems Biology 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of Singapore, Singapore</wicri:regionArea></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"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Ruan, Xiaoan" sort="Ruan, Xiaoan" uniqKey="Ruan X" first="Xiaoan" last="Ruan">Xiaoan Ruan</name><affiliation wicri:level="1"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Aburatani, Hiroyuki" sort="Aburatani, Hiroyuki" uniqKey="Aburatani H" first="Hiroyuki" last="Aburatani">Hiroyuki Aburatani</name><affiliation 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and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Wada, Youichiro" sort="Wada, Youichiro" uniqKey="Wada Y" first="Youichiro" last="Wada">Youichiro Wada</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation><affiliation><mods:affiliation>E-mail: wada-y@lsbm.org</mods:affiliation><wicri:noCountry code="no comma">E-mail: 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Larkin</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Binwei" sort="Deng, Binwei" uniqKey="Deng B" first="Binwei" last="Deng">Binwei Deng</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Short, Patrick" sort="Short, Patrick" uniqKey="Short P" first="Patrick" last="Short">Patrick Short</name><affiliation wicri:level="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation><affiliation wicri:level="1"><mods:affiliation>Department of Applied Mathematics and Quantitative Biology, University of North Carolina, NC, Chapel Hill, USA</mods:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Applied Mathematics and Quantitative Biology, University of North Carolina, NC, Chapel Hill</wicri:regionArea></affiliation></author><author><name sortKey="Tsutsumi, Shuichi" sort="Tsutsumi, Shuichi" uniqKey="Tsutsumi S" first="Shuichi" last="Tsutsumi">Shuichi Tsutsumi</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Taylor, Stephen" sort="Taylor, Stephen" uniqKey="Taylor S" first="Stephen" last="Taylor">Stephen Taylor</name><affiliation wicri:level="1"><mods:affiliation>Computational Research Biology Group, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Computational Research Biology Group, University of Oxford, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Kanki, Yasuharu" sort="Kanki, Yasuharu" uniqKey="Kanki Y" first="Yasuharu" last="Kanki">Yasuharu Kanki</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Kobayashi, Mika" sort="Kobayashi, Mika" uniqKey="Kobayashi M" first="Mika" last="Kobayashi">Mika Kobayashi</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name><affiliation wicri:level="1"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></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"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Ruan, Xiaoan" sort="Ruan, Xiaoan" uniqKey="Ruan X" first="Xiaoan" last="Ruan">Xiaoan Ruan</name><affiliation wicri:level="1"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Aburatani, Hiroyuki" sort="Aburatani, Hiroyuki" uniqKey="Aburatani H" first="Hiroyuki" last="Aburatani">Hiroyuki Aburatani</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Ruan, Yijun" sort="Ruan, Yijun" uniqKey="Ruan Y" first="Yijun" last="Ruan">Yijun Ruan</name><affiliation wicri:level="1"><mods:affiliation>Genome Institute of Singapore, Singapore, Singapore</mods:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Genome Institute of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Kodama, Tatsuhiko" sort="Kodama, Tatsuhiko" uniqKey="Kodama T" first="Tatsuhiko" last="Kodama">Tatsuhiko Kodama</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation></author><author><name sortKey="Wada, Youichiro" sort="Wada, Youichiro" uniqKey="Wada Y" first="Youichiro" last="Wada">Youichiro Wada</name><affiliation wicri:level="1"><mods:affiliation>Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan</mods:affiliation><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></affiliation><affiliation><mods:affiliation>E-mail: wada-y@lsbm.org</mods: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="1"><mods:affiliation>The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Sir William Dunn School of Pathology, University of Oxford, Oxford</wicri:regionArea></affiliation><affiliation><mods:affiliation>E-mail: wada-y@lsbm.org</mods: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></record>Pour manipuler ce document sous Unix (Dilib)
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