Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP
Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments term...
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| Veröffentlicht in: | Nature communications 2015-08, Vol.6 (1), p.7921-7921, Article 7921 |
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| creator | Hauer, Christian Curk, Tomaz Anders, Simon Schwarzl, Thomas Alleaume, Anne-Marie Sieber, Jana Hollerer, Ina Bhuvanagiri, Madhuri Huber, Wolfgang Hentze, Matthias W. Kulozik, Andreas E. |
| description | Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.
Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) can map RNA binding sites of RNA-binding proteins (RBPs). Here, the authors report an analysis tool that improves the binding site assignment for some RBPs that have length-dependent broader distribution for their iCLIP fragments. |
| doi_str_mv | 10.1038/ncomms8921 |
| format | Article |
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Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) can map RNA binding sites of RNA-binding proteins (RBPs). Here, the authors report an analysis tool that improves the binding site assignment for some RBPs that have length-dependent broader distribution for their iCLIP fragments.</description><identifier>ISSN: 2041-1723</identifier><identifier>EISSN: 2041-1723</identifier><identifier>DOI: 10.1038/ncomms8921</identifier><identifier>PMID: 26260686</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/1647/48 ; 631/337 ; 631/45/612/1230 ; 96 ; Binding Sites ; Crosslinking ; Fragmentation ; Fragments ; Gene sequencing ; HeLa Cells ; Humanities and Social Sciences ; Humans ; Immunoprecipitation ; multidisciplinary ; Next-generation sequencing ; Nucleic Acid Amplification Techniques ; Peptide mapping ; Protein Binding ; Protein interaction ; Proteins ; Reverse transcription ; Ribonucleic acid ; Ribonucleoproteins - chemistry ; Ribonucleoproteins - metabolism ; RNA ; RNA - metabolism ; RNA-binding protein ; RNA-Binding Proteins - chemistry ; RNA-Binding Proteins - metabolism ; RNA-protein interactions ; Science ; Science (multidisciplinary) ; Ultraviolet radiation</subject><ispartof>Nature communications, 2015-08, Vol.6 (1), p.7921-7921, Article 7921</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Aug 2015</rights><rights>Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c508t-e84f1bff4351bb7df51f7ad9dec0a4fd5829c05d8fa66f9958f7eb4b38df0d383</citedby><cites>FETCH-LOGICAL-c508t-e84f1bff4351bb7df51f7ad9dec0a4fd5829c05d8fa66f9958f7eb4b38df0d383</cites><orcidid>0000-0003-4868-1805</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918375/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918375/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26260686$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hauer, Christian</creatorcontrib><creatorcontrib>Curk, Tomaz</creatorcontrib><creatorcontrib>Anders, Simon</creatorcontrib><creatorcontrib>Schwarzl, Thomas</creatorcontrib><creatorcontrib>Alleaume, Anne-Marie</creatorcontrib><creatorcontrib>Sieber, Jana</creatorcontrib><creatorcontrib>Hollerer, Ina</creatorcontrib><creatorcontrib>Bhuvanagiri, Madhuri</creatorcontrib><creatorcontrib>Huber, Wolfgang</creatorcontrib><creatorcontrib>Hentze, Matthias W.</creatorcontrib><creatorcontrib>Kulozik, Andreas E.</creatorcontrib><title>Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP</title><title>Nature communications</title><addtitle>Nat Commun</addtitle><addtitle>Nat Commun</addtitle><description>Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.
Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) can map RNA binding sites of RNA-binding proteins (RBPs). Here, the authors report an analysis tool that improves the binding site assignment for some RBPs that have length-dependent broader distribution for their iCLIP fragments.</description><subject>631/1647/48</subject><subject>631/337</subject><subject>631/45/612/1230</subject><subject>96</subject><subject>Binding Sites</subject><subject>Crosslinking</subject><subject>Fragmentation</subject><subject>Fragments</subject><subject>Gene sequencing</subject><subject>HeLa Cells</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Immunoprecipitation</subject><subject>multidisciplinary</subject><subject>Next-generation sequencing</subject><subject>Nucleic Acid Amplification Techniques</subject><subject>Peptide mapping</subject><subject>Protein Binding</subject><subject>Protein interaction</subject><subject>Proteins</subject><subject>Reverse transcription</subject><subject>Ribonucleic acid</subject><subject>Ribonucleoproteins - chemistry</subject><subject>Ribonucleoproteins - metabolism</subject><subject>RNA</subject><subject>RNA - metabolism</subject><subject>RNA-binding protein</subject><subject>RNA-Binding Proteins - chemistry</subject><subject>RNA-Binding Proteins - metabolism</subject><subject>RNA-protein interactions</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Ultraviolet radiation</subject><issn>2041-1723</issn><issn>2041-1723</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpl0cGK1TAUBuAgijOMs_EBJOBGlGrSpGm6EYaLoxcuKqLrkDYnvRnapCbtwOx8B99wnsSUO45XzSaB8_HnJAehp5S8poTJN74L45hkU9IH6LQknBa0LtnDo_MJOk_piuTFGio5f4xOSlEKIqQ4RbAdpxiuweDWeeN8j5ObAeuUXO9H8DNub_De9fsiQgrDMrvg8ainaaXB4i8fL25__MwRMziPnZ8h6m5FCS9pNW6z235-gh5ZPSQ4v9vP0LfLd183H4rdp_fbzcWu6Coi5wIkt7S1lrOKtm1tbEVtrU1joCOaW1PJsulIZaTVQtimqaStoeUtk8YSwyQ7Q28PudPSjmC63H_Ug5qiG3W8UUE79XfFu73qw7Xi-WdYXeWAF3cBMXxfIM1qdKmDYdAewpIUrQmrCWmEyPT5P_QqLNHn562qlJwJWWb18qC6GFKKYO-boUStA1R_Bpjxs-P27-nvcWXw6gBSLvke4tGd_8f9ArXVqcU</recordid><startdate>20150811</startdate><enddate>20150811</enddate><creator>Hauer, Christian</creator><creator>Curk, Tomaz</creator><creator>Anders, Simon</creator><creator>Schwarzl, Thomas</creator><creator>Alleaume, Anne-Marie</creator><creator>Sieber, Jana</creator><creator>Hollerer, Ina</creator><creator>Bhuvanagiri, Madhuri</creator><creator>Huber, Wolfgang</creator><creator>Hentze, Matthias W.</creator><creator>Kulozik, Andreas E.</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>3V.</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T5</scope><scope>7T7</scope><scope>7TM</scope><scope>7TO</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4868-1805</orcidid></search><sort><creationdate>20150811</creationdate><title>Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP</title><author>Hauer, Christian ; Curk, Tomaz ; Anders, Simon ; Schwarzl, Thomas ; Alleaume, Anne-Marie ; Sieber, Jana ; Hollerer, Ina ; Bhuvanagiri, Madhuri ; Huber, Wolfgang ; Hentze, Matthias W. ; Kulozik, Andreas E.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c508t-e84f1bff4351bb7df51f7ad9dec0a4fd5829c05d8fa66f9958f7eb4b38df0d383</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/1647/48</topic><topic>631/337</topic><topic>631/45/612/1230</topic><topic>96</topic><topic>Binding Sites</topic><topic>Crosslinking</topic><topic>Fragmentation</topic><topic>Fragments</topic><topic>Gene sequencing</topic><topic>HeLa Cells</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Immunoprecipitation</topic><topic>multidisciplinary</topic><topic>Next-generation sequencing</topic><topic>Nucleic Acid Amplification Techniques</topic><topic>Peptide mapping</topic><topic>Protein Binding</topic><topic>Protein interaction</topic><topic>Proteins</topic><topic>Reverse transcription</topic><topic>Ribonucleic acid</topic><topic>Ribonucleoproteins - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hauer, Christian</au><au>Curk, Tomaz</au><au>Anders, Simon</au><au>Schwarzl, Thomas</au><au>Alleaume, Anne-Marie</au><au>Sieber, Jana</au><au>Hollerer, Ina</au><au>Bhuvanagiri, Madhuri</au><au>Huber, Wolfgang</au><au>Hentze, Matthias W.</au><au>Kulozik, Andreas E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP</atitle><jtitle>Nature communications</jtitle><stitle>Nat Commun</stitle><addtitle>Nat Commun</addtitle><date>2015-08-11</date><risdate>2015</risdate><volume>6</volume><issue>1</issue><spage>7921</spage><epage>7921</epage><pages>7921-7921</pages><artnum>7921</artnum><issn>2041-1723</issn><eissn>2041-1723</eissn><abstract>Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.
Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) can map RNA binding sites of RNA-binding proteins (RBPs). Here, the authors report an analysis tool that improves the binding site assignment for some RBPs that have length-dependent broader distribution for their iCLIP fragments.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26260686</pmid><doi>10.1038/ncomms8921</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-4868-1805</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 631/1647/48 631/337 631/45/612/1230 96 Binding Sites Crosslinking Fragmentation Fragments Gene sequencing HeLa Cells Humanities and Social Sciences Humans Immunoprecipitation multidisciplinary Next-generation sequencing Nucleic Acid Amplification Techniques Peptide mapping Protein Binding Protein interaction Proteins Reverse transcription Ribonucleic acid Ribonucleoproteins - chemistry Ribonucleoproteins - metabolism RNA RNA - metabolism RNA-binding protein RNA-Binding Proteins - chemistry RNA-Binding Proteins - metabolism RNA-protein interactions Science Science (multidisciplinary) Ultraviolet radiation |
| title | Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP |
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