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.
Highlights
Some gene ontology (GO) terms were significantly associated with muscle development and energy metabolism, such as skeletal muscle tissue development, muscle contraction, cell proliferation, protein catabolic process, insulin receptor signaling pathway and regulation of glucose transport (Fig. 5A; Fig. 5C)
Muscle development related pathways corresponding to 13 DE lincRNAs, we found that SHH targeted by lincRNA MSTRG.[27] and MSTRG.[388] played an important role in myogenesis (Fig. 6C), and SHH had an essential inductive function in the early activation of the myogenic regulatory factors Myf‐5 and M yoD27,28
We investigated Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis of potential target genes of DE lincRNAs, and found that skeletal muscle organ and tissue development processes, muscle contraction, striated muscle cell development were some of significantly enriched GO terms
Summary
Skeletal muscle growth and development are a complex process, which directly determine the meat production and quality in the pig industry. We identified many target genes of DE lincRNAs that play critical roles in skeletal muscle development. According to these results, we observed that numerous target genes significantly related to DE lincRNAs were involved in the biological processes of skeletal muscle development, such as ACTC1, FOXP1, IGF2BP3, MYOG, MYOZ1, MEF2A, SP1, TGFB2. We investigated Gene Ontology and KEGG pathways analysis of potential target genes of DE lincRNAs, and found that skeletal muscle organ and tissue development processes, muscle contraction, striated muscle cell development were some of significantly enriched GO terms. Some cardiac diseases, such as viral myocarditis, dilated cardiomyopathy, and hypertrophic cardiomyopathy, were significantly enriched, these results suggest that DE lincRNAs may have an important effect on myocardial development
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