Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development
Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcr...
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| Veröffentlicht in: | Scientific reports 2015-03, Vol.5 (1), p.8957-8957, Article 8957 |
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| creator | Zhao, Weimin Mu, Yulian Ma, Lei Wang, Chen Tang, Zhonglin Yang, Shulin Zhou, Rong Hu, Xiaoju Li, Meng-Hua Li, Kui |
| description | Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process. |
| doi_str_mv | 10.1038/srep08957 |
| format | Article |
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Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep08957</identifier><identifier>PMID: 25753296</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>13/106 ; 38/77 ; 38/88 ; 45/90 ; 45/91 ; 631/114 ; 631/208 ; 82/1 ; Animals ; Conserved Sequence ; Exons ; Exons - genetics ; Fetuses ; Gene Expression Regulation, Developmental ; Gene regulation ; Humanities and Social Sciences ; Isoforms ; Mice ; multidisciplinary ; Muscle Development - genetics ; Muscle, Skeletal - growth & development ; Muscle, Skeletal - metabolism ; Musculoskeletal system ; Nuclei ; Polycomb group proteins ; RNA, Long Noncoding - biosynthesis ; RNA, Long Noncoding - genetics ; RNA, Long Noncoding - isolation & purification ; Rodents ; Science ; Skeletal muscle ; Swine ; Transcription</subject><ispartof>Scientific reports, 2015-03, Vol.5 (1), p.8957-8957, Article 8957</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Mar 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited. All rights reserved 2015 Macmillan Publishers Limited. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c438t-44dc912ba48d7cb758d5360e116ca25cf06e06035286309d6b9506e510faf9293</citedby><cites>FETCH-LOGICAL-c438t-44dc912ba48d7cb758d5360e116ca25cf06e06035286309d6b9506e510faf9293</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354164/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354164/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25753296$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhao, Weimin</creatorcontrib><creatorcontrib>Mu, Yulian</creatorcontrib><creatorcontrib>Ma, Lei</creatorcontrib><creatorcontrib>Wang, Chen</creatorcontrib><creatorcontrib>Tang, Zhonglin</creatorcontrib><creatorcontrib>Yang, Shulin</creatorcontrib><creatorcontrib>Zhou, Rong</creatorcontrib><creatorcontrib>Hu, Xiaoju</creatorcontrib><creatorcontrib>Li, Meng-Hua</creatorcontrib><creatorcontrib>Li, Kui</creatorcontrib><title>Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.</description><subject>13/106</subject><subject>38/77</subject><subject>38/88</subject><subject>45/90</subject><subject>45/91</subject><subject>631/114</subject><subject>631/208</subject><subject>82/1</subject><subject>Animals</subject><subject>Conserved Sequence</subject><subject>Exons</subject><subject>Exons - genetics</subject><subject>Fetuses</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Gene regulation</subject><subject>Humanities and Social Sciences</subject><subject>Isoforms</subject><subject>Mice</subject><subject>multidisciplinary</subject><subject>Muscle Development - genetics</subject><subject>Muscle, Skeletal - growth & development</subject><subject>Muscle, Skeletal - metabolism</subject><subject>Musculoskeletal system</subject><subject>Nuclei</subject><subject>Polycomb group proteins</subject><subject>RNA, Long Noncoding - biosynthesis</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Long Noncoding - isolation & purification</subject><subject>Rodents</subject><subject>Science</subject><subject>Skeletal muscle</subject><subject>Swine</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>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>eNplkVtrFTEUhYMottQ--Ack4IsKo7mfyYtQipdCseDlOeQke05TM8mYzBTaB3-7qacejpqXJGt_WXuHhdBTSl5Twvs3tcBEei1XD9AhI0J2jDP2cO98gI5rvSJtSaYF1Y_RAZMryZlWh-jnl5s6w2jn4HDwkOYwBNduOWGbPHaXtlg3Qwm3WzEPOOa0wSE1cQOpPUs5dS770NTPn05qK-EBZhvxlIsLCXD9DvG3MC7VRcAeriHmaWzdnqBHg40Vju_3I_Tt_buvpx-784sPZ6cn550TvJ87IbzTlK2t6P3KrVey95IrApQqZ5l0A1FAFOGS9YoT7dVayyZJSgY7aKb5EXq79Z2W9QjetdbFRjOVMNpyY7IN5u9KCpdmk6-N4FJQJZrBi3uDkn8sUGczhuogRpsgL9VQpZjgVDDS0Of_oFd5Kal9z9BetwEpJ6pRL7eUK7m2DIfdMJSYu2DNLtjGPtuffkf-ibEBr7ZAbaW0gbLX8j-3X2PmrwQ</recordid><startdate>20150310</startdate><enddate>20150310</enddate><creator>Zhao, Weimin</creator><creator>Mu, Yulian</creator><creator>Ma, Lei</creator><creator>Wang, Chen</creator><creator>Tang, Zhonglin</creator><creator>Yang, Shulin</creator><creator>Zhou, Rong</creator><creator>Hu, Xiaoju</creator><creator>Li, Meng-Hua</creator><creator>Li, Kui</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>20150310</creationdate><title>Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development</title><author>Zhao, Weimin ; Mu, Yulian ; Ma, Lei ; Wang, Chen ; Tang, Zhonglin ; Yang, Shulin ; Zhou, Rong ; Hu, Xiaoju ; Li, Meng-Hua ; Li, Kui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c438t-44dc912ba48d7cb758d5360e116ca25cf06e06035286309d6b9506e510faf9293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>13/106</topic><topic>38/77</topic><topic>38/88</topic><topic>45/90</topic><topic>45/91</topic><topic>631/114</topic><topic>631/208</topic><topic>82/1</topic><topic>Animals</topic><topic>Conserved Sequence</topic><topic>Exons</topic><topic>Exons - genetics</topic><topic>Fetuses</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Gene regulation</topic><topic>Humanities and Social Sciences</topic><topic>Isoforms</topic><topic>Mice</topic><topic>multidisciplinary</topic><topic>Muscle Development - genetics</topic><topic>Muscle, Skeletal - growth & development</topic><topic>Muscle, Skeletal - metabolism</topic><topic>Musculoskeletal system</topic><topic>Nuclei</topic><topic>Polycomb group proteins</topic><topic>RNA, Long Noncoding - biosynthesis</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Long Noncoding - isolation & purification</topic><topic>Rodents</topic><topic>Science</topic><topic>Skeletal muscle</topic><topic>Swine</topic><topic>Transcription</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhao, Weimin</creatorcontrib><creatorcontrib>Mu, Yulian</creatorcontrib><creatorcontrib>Ma, Lei</creatorcontrib><creatorcontrib>Wang, Chen</creatorcontrib><creatorcontrib>Tang, Zhonglin</creatorcontrib><creatorcontrib>Yang, Shulin</creatorcontrib><creatorcontrib>Zhou, Rong</creatorcontrib><creatorcontrib>Hu, Xiaoju</creatorcontrib><creatorcontrib>Li, Meng-Hua</creatorcontrib><creatorcontrib>Li, Kui</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content 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>ProQuest Central Basic</collection><collection>MEDLINE - 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>Zhao, Weimin</au><au>Mu, Yulian</au><au>Ma, Lei</au><au>Wang, Chen</au><au>Tang, Zhonglin</au><au>Yang, Shulin</au><au>Zhou, Rong</au><au>Hu, Xiaoju</au><au>Li, Meng-Hua</au><au>Li, Kui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-03-10</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>8957</spage><epage>8957</epage><pages>8957-8957</pages><artnum>8957</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>25753296</pmid><doi>10.1038/srep08957</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 13/106 38/77 38/88 45/90 45/91 631/114 631/208 82/1 Animals Conserved Sequence Exons Exons - genetics Fetuses Gene Expression Regulation, Developmental Gene regulation Humanities and Social Sciences Isoforms Mice multidisciplinary Muscle Development - genetics Muscle, Skeletal - growth & development Muscle, Skeletal - metabolism Musculoskeletal system Nuclei Polycomb group proteins RNA, Long Noncoding - biosynthesis RNA, Long Noncoding - genetics RNA, Long Noncoding - isolation & purification Rodents Science Skeletal muscle Swine Transcription |
| title | Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development |
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