Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle
Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi musc...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311920632610 |
| _version_ | 1829479206801637376 |
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| author | Cen-cen LI Shu-long YU Hai-feng REN Wei WU Ya-ling WANG Qiu HAN Hai-xia XU Yong-jie XU Peng-peng ZHANG |
| author_facet | Cen-cen LI Shu-long YU Hai-feng REN Wei WU Ya-ling WANG Qiu HAN Hai-xia XU Yong-jie XU Peng-peng ZHANG |
| author_sort | Cen-cen LI |
| collection | DOAJ |
| description | Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle (LDM) during embryonic development. We identified a total of 739 lincRNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, lincRNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of lincRNAs in five embryonic development stages were analyzed and 45 differentially expressed lincRNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the lincRNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate lincRNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of lincRNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions. |
| first_indexed | 2024-12-14T17:32:25Z |
| format | Article |
| id | doaj.art-46b8ddf0aeda4f88a06867adca69f098 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-14T17:32:25Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-46b8ddf0aeda4f88a06867adca69f0982022-12-21T22:53:04ZengElsevierJournal of Integrative Agriculture2095-31192021-01-01201201211Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscleCen-cen LI0Shu-long YU1Hai-feng REN2Wei WU3Ya-ling WANG4Qiu HAN5Hai-xia XU6Yong-jie XU7Peng-peng ZHANG8College of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCollege of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaCorrespondence ZHANG Peng-peng, Tel: +86-376-6391380; College of Life Sciences, Xinyang Normal University, Xinyang 464000, P.R.ChinaPigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle (LDM) during embryonic development. We identified a total of 739 lincRNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, lincRNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of lincRNAs in five embryonic development stages were analyzed and 45 differentially expressed lincRNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the lincRNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate lincRNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of lincRNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.http://www.sciencedirect.com/science/article/pii/S2095311920632610lincRNAspigskeletal muscleembryopotential target genes |
| spellingShingle | Cen-cen LI Shu-long YU Hai-feng REN Wei WU Ya-ling WANG Qiu HAN Hai-xia XU Yong-jie XU Peng-peng ZHANG Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle Journal of Integrative Agriculture lincRNAs pig skeletal muscle embryo potential target genes |
| title | Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| title_full | Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| title_fullStr | Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| title_full_unstemmed | Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| title_short | Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle |
| title_sort | identification and functional prediction of long intergenic noncoding rnas in fetal porcine longissimus dorsi muscle |
| topic | lincRNAs pig skeletal muscle embryo potential target genes |
| url | http://www.sciencedirect.com/science/article/pii/S2095311920632610 |
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