Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development

Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRN...

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Autores principales:	Wenjuan Zhao, Zijing Li, Quan Liu, Su Xie, Mengxun Li, Yuan Wang, Changchun Li
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/37da08a1768d48528ad9d981b1a2b286
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spelling	oai:doaj.org-article:37da08a1768d48528ad9d981b1a2b2862021-12-02T16:31:48ZAnalysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development10.1038/s41598-021-94014-w2045-2322https://doaj.org/article/37da08a1768d48528ad9d981b1a2b2862021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94014-whttps://doaj.org/toc/2045-2322Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.Wenjuan ZhaoZijing LiQuan LiuSu XieMengxun LiYuan WangChangchun LiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenjuan Zhao Zijing Li Quan Liu Su Xie Mengxun Li Yuan Wang Changchun Li Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
description	Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.
format	article
author	Wenjuan Zhao Zijing Li Quan Liu Su Xie Mengxun Li Yuan Wang Changchun Li
author_facet	Wenjuan Zhao Zijing Li Quan Liu Su Xie Mengxun Li Yuan Wang Changchun Li
author_sort	Wenjuan Zhao
title	Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
title_short	Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
title_full	Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
title_fullStr	Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
title_full_unstemmed	Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development
title_sort	analysis of long intergenic non-coding rnas transcriptomic profiling in skeletal muscle growth during porcine embryonic development
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/37da08a1768d48528ad9d981b1a2b286
work_keys_str_mv	AT wenjuanzhao analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT zijingli analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT quanliu analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT suxie analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT mengxunli analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT yuanwang analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment AT changchunli analysisoflongintergenicnoncodingrnastranscriptomicprofilinginskeletalmusclegrowthduringporcineembryonicdevelopment
_version_	1718383863904862208

Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development

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