COPI transport complexes bind to specific RNAs in neuronal cells
Our fundamental understanding of how several thousand diverse RNAs are recognized in the soma, sorted, packaged, transported and localized within the cell is fragmentary. The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and repr...
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| Veröffentlicht in: | Human molecular genetics 2013-02, Vol.22 (4), p.729-736 |
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| container_title | Human molecular genetics |
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| creator | Todd, Adrian G Lin, Hai Ebert, Allison D Liu, Yunlong Androphy, Elliot J |
| description | Our fundamental understanding of how several thousand diverse RNAs are recognized in the soma, sorted, packaged, transported and localized within the cell is fragmentary. The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and represent a candidate RNA sorting and transport system. To determine the RNA-binding profile of Golgi-derived COPI in neuronal cells, we performed formaldehyde-linked RNA immunoprecipitation, followed by high-throughput sequencing, a process we term FLRIP-Seq (FLRIP, formaldehyde-cross-linked immunoprecipitation). We demonstrate that COPa co-immunoprecipitates a specific set of RNAs that are enriched in G-quadruplex motifs and fragile X mental retardation protein-associated RNAs and that encode factors that predominantly localize to the plasma membrane and cytoskeleton and function within signaling pathways. These data support the novel function of COPI in inter-compartmental trafficking of RNA. |
| doi_str_mv | 10.1093/hmg/dds480 |
| format | Article |
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The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and represent a candidate RNA sorting and transport system. To determine the RNA-binding profile of Golgi-derived COPI in neuronal cells, we performed formaldehyde-linked RNA immunoprecipitation, followed by high-throughput sequencing, a process we term FLRIP-Seq (FLRIP, formaldehyde-cross-linked immunoprecipitation). We demonstrate that COPa co-immunoprecipitates a specific set of RNAs that are enriched in G-quadruplex motifs and fragile X mental retardation protein-associated RNAs and that encode factors that predominantly localize to the plasma membrane and cytoskeleton and function within signaling pathways. These data support the novel function of COPI in inter-compartmental trafficking of RNA.</description><identifier>ISSN: 0964-6906</identifier><identifier>EISSN: 1460-2083</identifier><identifier>DOI: 10.1093/hmg/dds480</identifier><identifier>PMID: 23175440</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>3' Untranslated Regions ; Animals ; Antigens, Neoplasm - metabolism ; Base Sequence ; Cell Line, Tumor ; Cell Membrane - metabolism ; Coat Protein Complex I - metabolism ; Coatomer Protein - metabolism ; Consensus Sequence ; Cytoskeleton - metabolism ; Fragile X Mental Retardation Protein - metabolism ; Mice ; Nerve Tissue Proteins - metabolism ; Neurites - metabolism ; Protein Binding ; Protein Subunits - metabolism ; Protein Transport ; RNA Transport ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; RNA-Binding Proteins - metabolism ; Sequence Analysis, RNA ; Transcriptome</subject><ispartof>Human molecular genetics, 2013-02, Vol.22 (4), p.729-736</ispartof><rights>The Author 2012. 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For Permissions, please email: journals.permissions@oup.com 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23175440$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Todd, Adrian G</creatorcontrib><creatorcontrib>Lin, Hai</creatorcontrib><creatorcontrib>Ebert, Allison D</creatorcontrib><creatorcontrib>Liu, Yunlong</creatorcontrib><creatorcontrib>Androphy, Elliot J</creatorcontrib><title>COPI transport complexes bind to specific RNAs in neuronal cells</title><title>Human molecular genetics</title><addtitle>Hum Mol Genet</addtitle><description>Our fundamental understanding of how several thousand diverse RNAs are recognized in the soma, sorted, packaged, transported and localized within the cell is fragmentary. The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and represent a candidate RNA sorting and transport system. To determine the RNA-binding profile of Golgi-derived COPI in neuronal cells, we performed formaldehyde-linked RNA immunoprecipitation, followed by high-throughput sequencing, a process we term FLRIP-Seq (FLRIP, formaldehyde-cross-linked immunoprecipitation). We demonstrate that COPa co-immunoprecipitates a specific set of RNAs that are enriched in G-quadruplex motifs and fragile X mental retardation protein-associated RNAs and that encode factors that predominantly localize to the plasma membrane and cytoskeleton and function within signaling pathways. These data support the novel function of COPI in inter-compartmental trafficking of RNA.</description><subject>3' Untranslated Regions</subject><subject>Animals</subject><subject>Antigens, Neoplasm - metabolism</subject><subject>Base Sequence</subject><subject>Cell Line, Tumor</subject><subject>Cell Membrane - metabolism</subject><subject>Coat Protein Complex I - metabolism</subject><subject>Coatomer Protein - metabolism</subject><subject>Consensus Sequence</subject><subject>Cytoskeleton - metabolism</subject><subject>Fragile X Mental Retardation Protein - metabolism</subject><subject>Mice</subject><subject>Nerve Tissue Proteins - metabolism</subject><subject>Neurites - metabolism</subject><subject>Protein Binding</subject><subject>Protein Subunits - metabolism</subject><subject>Protein Transport</subject><subject>RNA Transport</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>RNA-Binding Proteins - metabolism</subject><subject>Sequence Analysis, RNA</subject><subject>Transcriptome</subject><issn>0964-6906</issn><issn>1460-2083</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkMtOwzAQRS0EoqWw4QOQl2xC7cTPDaKqeFSqKEKwjhxn3AYldogTBH9PEQXB6i7m6pyZQeiUkgtKdDbdNOtpWUamyB4aUyZIkhKV7aMx0YIlQhMxQkcxvhBCBcvkIRqlGZWcMTJGV_PVwwL3nfGxDV2PbWjaGt4h4qLyJe4Dji3YylUWP97PIq489jB0wZsaW6jreIwOnKkjnOxygp5vrp_md8lydbuYz5ZJS7XoE8GZY1amZaEVo6oUtADBDSMCpOQcrONACTgLxjFGSeqk5WkBTlJlqWPZBF1-c9uhaKC04LdL13nbVY3pPvJgqvz_xFebfB3e8kwrxaTaAs53gC68DhD7vKni1wnGQxhiTjOqhOZK82317K_rV_LztuwTFHNv2g</recordid><startdate>20130215</startdate><enddate>20130215</enddate><creator>Todd, Adrian G</creator><creator>Lin, Hai</creator><creator>Ebert, Allison D</creator><creator>Liu, Yunlong</creator><creator>Androphy, Elliot J</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20130215</creationdate><title>COPI transport complexes bind to specific RNAs in neuronal cells</title><author>Todd, Adrian G ; Lin, Hai ; Ebert, Allison D ; Liu, Yunlong ; Androphy, Elliot J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p196t-654f4c72db98418d61be65a406e7755ecf5e10efceaf44102f7c52bef718c1f43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>3' Untranslated Regions</topic><topic>Animals</topic><topic>Antigens, Neoplasm - metabolism</topic><topic>Base Sequence</topic><topic>Cell Line, Tumor</topic><topic>Cell Membrane - metabolism</topic><topic>Coat Protein Complex I - metabolism</topic><topic>Coatomer Protein - metabolism</topic><topic>Consensus Sequence</topic><topic>Cytoskeleton - metabolism</topic><topic>Fragile X Mental Retardation Protein - metabolism</topic><topic>Mice</topic><topic>Nerve Tissue Proteins - metabolism</topic><topic>Neurites - metabolism</topic><topic>Protein Binding</topic><topic>Protein Subunits - metabolism</topic><topic>Protein Transport</topic><topic>RNA Transport</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>RNA-Binding Proteins - metabolism</topic><topic>Sequence Analysis, RNA</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Todd, Adrian G</creatorcontrib><creatorcontrib>Lin, Hai</creatorcontrib><creatorcontrib>Ebert, Allison D</creatorcontrib><creatorcontrib>Liu, Yunlong</creatorcontrib><creatorcontrib>Androphy, Elliot J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Human molecular genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Todd, Adrian G</au><au>Lin, Hai</au><au>Ebert, Allison D</au><au>Liu, Yunlong</au><au>Androphy, Elliot J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>COPI transport complexes bind to specific RNAs in neuronal cells</atitle><jtitle>Human molecular genetics</jtitle><addtitle>Hum Mol Genet</addtitle><date>2013-02-15</date><risdate>2013</risdate><volume>22</volume><issue>4</issue><spage>729</spage><epage>736</epage><pages>729-736</pages><issn>0964-6906</issn><eissn>1460-2083</eissn><abstract>Our fundamental understanding of how several thousand diverse RNAs are recognized in the soma, sorted, packaged, transported and localized within the cell is fragmentary. The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and represent a candidate RNA sorting and transport system. To determine the RNA-binding profile of Golgi-derived COPI in neuronal cells, we performed formaldehyde-linked RNA immunoprecipitation, followed by high-throughput sequencing, a process we term FLRIP-Seq (FLRIP, formaldehyde-cross-linked immunoprecipitation). We demonstrate that COPa co-immunoprecipitates a specific set of RNAs that are enriched in G-quadruplex motifs and fragile X mental retardation protein-associated RNAs and that encode factors that predominantly localize to the plasma membrane and cytoskeleton and function within signaling pathways. 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| issn | 0964-6906 1460-2083 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | 3' Untranslated Regions Animals Antigens, Neoplasm - metabolism Base Sequence Cell Line, Tumor Cell Membrane - metabolism Coat Protein Complex I - metabolism Coatomer Protein - metabolism Consensus Sequence Cytoskeleton - metabolism Fragile X Mental Retardation Protein - metabolism Mice Nerve Tissue Proteins - metabolism Neurites - metabolism Protein Binding Protein Subunits - metabolism Protein Transport RNA Transport RNA, Messenger - genetics RNA, Messenger - metabolism RNA-Binding Proteins - metabolism Sequence Analysis, RNA Transcriptome |
| title | COPI transport complexes bind to specific RNAs in neuronal cells |
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