RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis
RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in Arabidopsis . We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Mo...
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| Veröffentlicht in: | Nature plants 2018-12, Vol.4 (12), p.1112-1123 |
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| creator | Zhu, Jiafu Liu, Min Liu, Xiaobin Dong, Zhicheng |
| description | RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in
Arabidopsis
. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.
RNA polymerase II (Pol II) catalyses the transcription of DNA in the nucleus eukaryotic cells. Now two approaches, global run-on and native elongating transcript sequencing (initially developed for mammalian cells), are used to determine the transcriptional landscape of Pol II in
Arabidopsis
. The similarities and differences of Pol II dynamics among various eukaryotes are also analysed. |
| doi_str_mv | 10.1038/s41477-018-0280-0 |
| format | Article |
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Arabidopsis
. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.
RNA polymerase II (Pol II) catalyses the transcription of DNA in the nucleus eukaryotic cells. Now two approaches, global run-on and native elongating transcript sequencing (initially developed for mammalian cells), are used to determine the transcriptional landscape of Pol II in
Arabidopsis
. The similarities and differences of Pol II dynamics among various eukaryotes are also analysed.</description><identifier>ISSN: 2055-0278</identifier><identifier>EISSN: 2055-0278</identifier><identifier>DOI: 10.1038/s41477-018-0280-0</identifier><identifier>PMID: 30374093</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/1 ; 38/91 ; 631/1647/2017 ; 631/208/514/2254 ; 631/449 ; Arabidopsis ; Arabidopsis - enzymology ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Biomedical and Life Sciences ; Catalytic Domain - genetics ; DNA-directed RNA polymerase ; Eukaryotes ; Gene expression ; Genome, Plant - genetics ; Genomes ; Life Sciences ; Plant Sciences ; Polyadenylation ; Promoter Regions, Genetic - genetics ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA polymerase II ; RNA Polymerase II - genetics ; RNA Polymerase II - metabolism ; RNA, Plant - genetics ; Sequence Analysis, RNA ; Species Specificity ; Spliceosomes ; Transcription ; Transcription Initiation Site ; Transcription, Genetic</subject><ispartof>Nature plants, 2018-12, Vol.4 (12), p.1112-1123</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Limited 2018</rights><rights>Copyright Nature Publishing Group Dec 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c438t-5d0f781985b4f234f02b8773447f87f14ccd399f8195f208202edb6af6e52123</citedby><cites>FETCH-LOGICAL-c438t-5d0f781985b4f234f02b8773447f87f14ccd399f8195f208202edb6af6e52123</cites><orcidid>0000-0003-2909-5720</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30374093$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhu, Jiafu</creatorcontrib><creatorcontrib>Liu, Min</creatorcontrib><creatorcontrib>Liu, Xiaobin</creatorcontrib><creatorcontrib>Dong, Zhicheng</creatorcontrib><title>RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis</title><title>Nature plants</title><addtitle>Nature Plants</addtitle><addtitle>Nat Plants</addtitle><description>RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in
Arabidopsis
. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.
RNA polymerase II (Pol II) catalyses the transcription of DNA in the nucleus eukaryotic cells. Now two approaches, global run-on and native elongating transcript sequencing (initially developed for mammalian cells), are used to determine the transcriptional landscape of Pol II in
Arabidopsis
. The similarities and differences of Pol II dynamics among various eukaryotes are also analysed.</description><subject>38/1</subject><subject>38/91</subject><subject>631/1647/2017</subject><subject>631/208/514/2254</subject><subject>631/449</subject><subject>Arabidopsis</subject><subject>Arabidopsis - enzymology</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>Biomedical and Life Sciences</subject><subject>Catalytic Domain - genetics</subject><subject>DNA-directed RNA polymerase</subject><subject>Eukaryotes</subject><subject>Gene expression</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Life Sciences</subject><subject>Plant Sciences</subject><subject>Polyadenylation</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>RNA polymerase II</subject><subject>RNA Polymerase II - genetics</subject><subject>RNA Polymerase II - metabolism</subject><subject>RNA, Plant - genetics</subject><subject>Sequence Analysis, RNA</subject><subject>Species Specificity</subject><subject>Spliceosomes</subject><subject>Transcription</subject><subject>Transcription Initiation Site</subject><subject>Transcription, Genetic</subject><issn>2055-0278</issn><issn>2055-0278</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>AFKRA</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><recordid>eNp1kE1rAjEQhkNpqWL9Ab2UQC-9bDv52sSjiLWWoiDeQ3Y3KSvr7pqo4L9vrPaDQk8zQ555JzwI3RJ4JMDUU-CES5kAUQlQBQlcoC4FIeIk1eWvvoP6IawAgEghWArXqMOASQ4D1kWvi9kQt011WFtvgsXTKTb5ttyX2wP2dm9NZQucHfBkMU-C3WBTF7idjZefQ1njoTdZWTRtKMMNunKmCrZ_rj20fB4vRy_J23wyHQ3fkpwztU1EAU4qMlAi444y7oBmSkrGuXRKOsLzvGCDgYuIcBQUBWqLLDUutYISynro4RTb-mazs2Gr12XIbVWZ2ja7oCMjKZA0PaL3f9BVs_N1_FykBAiilJKRIicq900I3jrd-nJt_EET0EfV-qRaR9X6qFpD3Lk7J--ytS2-N77ERoCegBCf6nfrf07_n_oBQeGFOw</recordid><startdate>20181201</startdate><enddate>20181201</enddate><creator>Zhu, Jiafu</creator><creator>Liu, Min</creator><creator>Liu, Xiaobin</creator><creator>Dong, Zhicheng</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><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>7SN</scope><scope>AFKRA</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>HCIFZ</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-2909-5720</orcidid></search><sort><creationdate>20181201</creationdate><title>RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis</title><author>Zhu, Jiafu ; Liu, Min ; Liu, Xiaobin ; Dong, Zhicheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c438t-5d0f781985b4f234f02b8773447f87f14ccd399f8195f208202edb6af6e52123</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>38/1</topic><topic>38/91</topic><topic>631/1647/2017</topic><topic>631/208/514/2254</topic><topic>631/449</topic><topic>Arabidopsis</topic><topic>Arabidopsis - enzymology</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis Proteins - metabolism</topic><topic>Biomedical and Life Sciences</topic><topic>Catalytic Domain - genetics</topic><topic>DNA-directed RNA polymerase</topic><topic>Eukaryotes</topic><topic>Gene expression</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Life Sciences</topic><topic>Plant Sciences</topic><topic>Polyadenylation</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA polymerase</topic><topic>RNA polymerase II</topic><topic>RNA Polymerase II - genetics</topic><topic>RNA Polymerase II - metabolism</topic><topic>RNA, Plant - genetics</topic><topic>Sequence Analysis, RNA</topic><topic>Species Specificity</topic><topic>Spliceosomes</topic><topic>Transcription</topic><topic>Transcription Initiation Site</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhu, Jiafu</creatorcontrib><creatorcontrib>Liu, Min</creatorcontrib><creatorcontrib>Liu, Xiaobin</creatorcontrib><creatorcontrib>Dong, Zhicheng</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>SciTech Premium Collection</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><jtitle>Nature plants</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhu, Jiafu</au><au>Liu, Min</au><au>Liu, Xiaobin</au><au>Dong, Zhicheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis</atitle><jtitle>Nature plants</jtitle><stitle>Nature Plants</stitle><addtitle>Nat Plants</addtitle><date>2018-12-01</date><risdate>2018</risdate><volume>4</volume><issue>12</issue><spage>1112</spage><epage>1123</epage><pages>1112-1123</pages><issn>2055-0278</issn><eissn>2055-0278</eissn><abstract>RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in
Arabidopsis
. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.
RNA polymerase II (Pol II) catalyses the transcription of DNA in the nucleus eukaryotic cells. Now two approaches, global run-on and native elongating transcript sequencing (initially developed for mammalian cells), are used to determine the transcriptional landscape of Pol II in
Arabidopsis
. The similarities and differences of Pol II dynamics among various eukaryotes are also analysed.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>30374093</pmid><doi>10.1038/s41477-018-0280-0</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0003-2909-5720</orcidid></addata></record> |
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| subjects | 38/1 38/91 631/1647/2017 631/208/514/2254 631/449 Arabidopsis Arabidopsis - enzymology Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Biomedical and Life Sciences Catalytic Domain - genetics DNA-directed RNA polymerase Eukaryotes Gene expression Genome, Plant - genetics Genomes Life Sciences Plant Sciences Polyadenylation Promoter Regions, Genetic - genetics Ribonucleic acid RNA RNA polymerase RNA polymerase II RNA Polymerase II - genetics RNA Polymerase II - metabolism RNA, Plant - genetics Sequence Analysis, RNA Species Specificity Spliceosomes Transcription Transcription Initiation Site Transcription, Genetic |
| title | RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis |
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