The vast, conserved mammalian lincRNome
We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimen...
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| Veröffentlicht in: | PLoS computational biology 2013-02, Vol.9 (2), p.e1002917-e1002917 |
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| creator | Managadze, David Lobkovsky, Alexander E Wolf, Yuri I Shabalina, Svetlana A Rogozin, Igor B Koonin, Eugene V |
| description | We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized. |
| doi_str_mv | 10.1371/journal.pcbi.1002917 |
| format | Article |
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Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1002917</identifier><identifier>PMID: 23468607</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Biology ; Confidence intervals ; Databases, Genetic ; Estimates ; Experiments ; Gene expression ; Genetics ; Genome ; Genome Size ; Genomes ; Genomics ; Humans ; Mice ; Molecular genetics ; RNA sequencing ; RNA, Long Noncoding - genetics ; Studies</subject><ispartof>PLoS computational biology, 2013-02, Vol.9 (2), p.e1002917-e1002917</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Citation: Managadze D, Lobkovsky AE, Wolf YI, Shabalina SA, Rogozin IB, et al. (2013) The Vast, Conserved Mammalian lincRNome. PLoS Comput Biol 9(2): e1002917. doi:10.1371/journal.pcbi.1002917</rights><rights>2013</rights><rights>2013 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Citation: Managadze D, Lobkovsky AE, Wolf YI, Shabalina SA, Rogozin IB, et al. (2013) The Vast, Conserved Mammalian lincRNome. 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Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized.</description><subject>Animals</subject><subject>Biology</subject><subject>Confidence intervals</subject><subject>Databases, Genetic</subject><subject>Estimates</subject><subject>Experiments</subject><subject>Gene expression</subject><subject>Genetics</subject><subject>Genome</subject><subject>Genome Size</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Mice</subject><subject>Molecular genetics</subject><subject>RNA sequencing</subject><subject>RNA, Long Noncoding - genetics</subject><subject>Studies</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqVUk1vEzEQXSEQLYV_gCASB0AiwfbYu94LUlXxEakqUilna-Idp45216m9ieDf4zTbqkFckA8ejd-8mfc8RfGSsxmHin9chU3ssZ2t7cLPOGOi5tWj4pgrBdMKlH78ID4qnqW0YiyHdfm0OBIgS12y6rh4e3VNky2m4cPEhj5R3FIz6bDrsPXYT1rf28uL0NHz4onDNtGL8T4pfn75fHX2bXr-_ev87PR8akuAYdrY3JIEEFYC3EJBjawEh6VUUtZUsUWpa1s7JYVwSqBUzjopUPMKSFkHJ8XrPe-6DcmMGpPhwCVIqGSZEfM9ogm4MuvoO4y_TUBvbhMhLg3GwduWTKm4ZkxaZoGkzNq1FhKrbJVWjVMsc30au20WHTWW-iFie0B6-NL7a7MMW5ONVKAhE7wbCWK42VAaTOeTpbbFnsLmdm5VguKw6_XmL-i_1c32qCVmAb53Ife1-TTU-fxD5HzOn4IQUnNe81zw_qAgYwb6NSxxk5KZ_7j8D-zFIVbusTaGlCK5e1c4M7sFvBvf7BbQjAuYy149dPS-6G7j4A9tW9OO</recordid><startdate>20130201</startdate><enddate>20130201</enddate><creator>Managadze, David</creator><creator>Lobkovsky, Alexander E</creator><creator>Wolf, Yuri I</creator><creator>Shabalina, Svetlana A</creator><creator>Rogozin, Igor B</creator><creator>Koonin, Eugene V</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>ISN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</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>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0N</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>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130201</creationdate><title>The vast, conserved mammalian lincRNome</title><author>Managadze, David ; Lobkovsky, Alexander E ; Wolf, Yuri I ; Shabalina, Svetlana A ; Rogozin, Igor B ; Koonin, Eugene V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c633t-dc553e23ea723fb539a063fa645449e70b689c9f5422f52a45fcf42a8173e5cf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Biology</topic><topic>Confidence intervals</topic><topic>Databases, Genetic</topic><topic>Estimates</topic><topic>Experiments</topic><topic>Gene expression</topic><topic>Genetics</topic><topic>Genome</topic><topic>Genome Size</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Humans</topic><topic>Mice</topic><topic>Molecular genetics</topic><topic>RNA sequencing</topic><topic>RNA, Long Noncoding - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Managadze, David</au><au>Lobkovsky, Alexander E</au><au>Wolf, Yuri I</au><au>Shabalina, Svetlana A</au><au>Rogozin, Igor B</au><au>Koonin, Eugene V</au><au>Markel, Scott</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The vast, conserved mammalian lincRNome</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2013-02-01</date><risdate>2013</risdate><volume>9</volume><issue>2</issue><spage>e1002917</spage><epage>e1002917</epage><pages>e1002917-e1002917</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimentally validated lincRNAs are random samples of the lincRNomes of the corresponding species, we estimate the total lincRNome size at approximately 40,000 to 50,000 species, at least twice the number of protein-coding genes. We further estimate that the fraction of the human and mouse euchromatic genomes encoding lincRNAs is more than twofold greater than the fraction of protein-coding sequences. Although the sequences of most lincRNAs are much less strongly conserved than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, with 60 to 70% of the lincRNA genes shared between human and mouse. The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23468607</pmid><doi>10.1371/journal.pcbi.1002917</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Biology Confidence intervals Databases, Genetic Estimates Experiments Gene expression Genetics Genome Genome Size Genomes Genomics Humans Mice Molecular genetics RNA sequencing RNA, Long Noncoding - genetics Studies |
| title | The vast, conserved mammalian lincRNome |
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