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Profiling RNA editing in human tissues: towards the inosinome Atlas
Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly pervasive in humans with respect to other mammals and is implicated in a number of diverse...
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Published in: | Scientific reports 2015-10, Vol.5 (1), p.14941-14941, Article 14941 |
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description | Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly pervasive in humans with respect to other mammals and is implicated in a number of diverse human pathologies. Here we present the first human inosinome atlas comprising 3,041,422 A-to-I events identified in six tissues from three healthy individuals. Matched directional total-RNA-Seq and whole genome sequence datasets were generated and analysed within a dedicated computational framework, also capable of detecting hyper-edited reads. Inosinome profiles are tissue specific and edited gene sets consistently show enrichment of genes involved in neurological disorders and cancer. Overall frequency of editing also varies, but is strongly correlated with ADAR expression levels. The inosinome database is available at:
http://srv00.recas.ba.infn.it/editing
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http://srv00.recas.ba.infn.it/editing
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http://srv00.recas.ba.infn.it/editing
.</description><subject>45/23</subject><subject>45/91</subject><subject>49/23</subject><subject>49/91</subject><subject>631/337</subject><subject>631/337/2019</subject><subject>Adenine</subject><subject>Adenine - metabolism</subject><subject>Adenosine Deaminase - genetics</subject><subject>Adenosine Deaminase - metabolism</subject><subject>Base Sequence</subject><subject>Binding Sites - genetics</subject><subject>Biological effects</subject><subject>Brain - metabolism</subject><subject>Cancer</subject><subject>Cell Line</subject><subject>Computational neuroscience</subject><subject>Databases, Genetic</subject><subject>Double-stranded RNA</subject><subject>Editing</subject><subject>Enzymes</subject><subject>Genome, Human - genetics</subject><subject>Genomes</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Inosine - metabolism</subject><subject>Internet</subject><subject>Kidney - metabolism</subject><subject>Liver - metabolism</subject><subject>Lung - metabolism</subject><subject>multidisciplinary</subject><subject>Muscles - metabolism</subject><subject>Myocardium - metabolism</subject><subject>Neurological diseases</subject><subject>Nucleotide sequence</subject><subject>Organ Specificity - genetics</subject><subject>Post-transcription</subject><subject>RNA - genetics</subject><subject>RNA - metabolism</subject><subject>RNA Editing</subject><subject>Science</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Transcription</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNplkV1LwzAYhYMobsxd-Aek4I0K03y1abwQxvALREX0OqRtumW0yUxSxX9vxuaYGgh54TycvIcDwCGC5wiS_MI7tUCUU7QD-hjSdIQJxrtbcw8MvZ_DeFIcMb4PejijlGOI-2Dy7GytG22mycvjOFGVDstZm2TWtdIkQXvfKX-ZBPspXeWTMFNRtT7eViXj0Eh_APZq2Xg1XL8D8HZz_Tq5Gz083d5Pxg-jMoU0jErOWQWLkmPOM5ThUhKYyawmhOecMq4qzPI0l6hCGKG0KDjjsOasoJAoFLEBuFr5LrqiVVWpTHCyEQunW-m-hJVa_FaMnomp_RA05XmOWTQ4WRs4-x5TBdFqX6qmkUbZzgvEMCIZRCSN6PEfdG47Z2I8gfIYJGc8o5E6XVGlsz4WUW-WQVAs2xGbdiJ7tL39hvzpIgJnK8BHyUyV2_ryn9s3YWSXfA</recordid><startdate>20151009</startdate><enddate>20151009</enddate><creator>Picardi, Ernesto</creator><creator>Manzari, Caterina</creator><creator>Mastropasqua, Francesca</creator><creator>Aiello, Italia</creator><creator>D’Erchia, Anna Maria</creator><creator>Pesole, Graziano</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>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20151009</creationdate><title>Profiling RNA editing in human tissues: towards the inosinome Atlas</title><author>Picardi, Ernesto ; Manzari, Caterina ; Mastropasqua, Francesca ; Aiello, Italia ; D’Erchia, Anna Maria ; Pesole, Graziano</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c504t-c997d0bc92996162ca306a6f33989479ed27858a1d12115bb9790f97b403e1f33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>45/23</topic><topic>45/91</topic><topic>49/23</topic><topic>49/91</topic><topic>631/337</topic><topic>631/337/2019</topic><topic>Adenine</topic><topic>Adenine - metabolism</topic><topic>Adenosine Deaminase - genetics</topic><topic>Adenosine Deaminase - metabolism</topic><topic>Base Sequence</topic><topic>Binding Sites - genetics</topic><topic>Biological effects</topic><topic>Brain - metabolism</topic><topic>Cancer</topic><topic>Cell Line</topic><topic>Computational neuroscience</topic><topic>Databases, Genetic</topic><topic>Double-stranded RNA</topic><topic>Editing</topic><topic>Enzymes</topic><topic>Genome, Human - genetics</topic><topic>Genomes</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Inosine - metabolism</topic><topic>Internet</topic><topic>Kidney - metabolism</topic><topic>Liver - metabolism</topic><topic>Lung - metabolism</topic><topic>multidisciplinary</topic><topic>Muscles - metabolism</topic><topic>Myocardium - metabolism</topic><topic>Neurological diseases</topic><topic>Nucleotide sequence</topic><topic>Organ Specificity - genetics</topic><topic>Post-transcription</topic><topic>RNA - genetics</topic><topic>RNA - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Picardi, Ernesto</au><au>Manzari, Caterina</au><au>Mastropasqua, Francesca</au><au>Aiello, Italia</au><au>D’Erchia, Anna Maria</au><au>Pesole, Graziano</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Profiling RNA editing in human tissues: towards the inosinome Atlas</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-10-09</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>14941</spage><epage>14941</epage><pages>14941-14941</pages><artnum>14941</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly pervasive in humans with respect to other mammals and is implicated in a number of diverse human pathologies. Here we present the first human inosinome atlas comprising 3,041,422 A-to-I events identified in six tissues from three healthy individuals. Matched directional total-RNA-Seq and whole genome sequence datasets were generated and analysed within a dedicated computational framework, also capable of detecting hyper-edited reads. Inosinome profiles are tissue specific and edited gene sets consistently show enrichment of genes involved in neurological disorders and cancer. Overall frequency of editing also varies, but is strongly correlated with ADAR expression levels. The inosinome database is available at:
http://srv00.recas.ba.infn.it/editing
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subjects | 45/23 45/91 49/23 49/91 631/337 631/337/2019 Adenine Adenine - metabolism Adenosine Deaminase - genetics Adenosine Deaminase - metabolism Base Sequence Binding Sites - genetics Biological effects Brain - metabolism Cancer Cell Line Computational neuroscience Databases, Genetic Double-stranded RNA Editing Enzymes Genome, Human - genetics Genomes Humanities and Social Sciences Humans Inosine - metabolism Internet Kidney - metabolism Liver - metabolism Lung - metabolism multidisciplinary Muscles - metabolism Myocardium - metabolism Neurological diseases Nucleotide sequence Organ Specificity - genetics Post-transcription RNA - genetics RNA - metabolism RNA Editing Science Sequence Analysis, DNA - methods Transcription |
title | Profiling RNA editing in human tissues: towards the inosinome Atlas |
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