Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs

Abstract

Intramuscular fat (IMF) content is an important trait that can affect pork quality. Previous studies have identified many genes that can regulate IMF. Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in various biological processes. However, lincRNAs related to IMF in pig are largely unknown, and the mechanisms by which they regulate IMF are yet to be elucidated. Here we reconstructed 105,687 transcripts and identified 1,032 lincRNAs in pig longissimus dorsi muscle (LDM) of four stages with different IMF contents based on published RNA-seq. These lincRNAs show typical characteristics such as shorter length and lower expression compared with protein-coding genes. Combined with methylation data, we found that both the promoter and genebody methylation of lincRNAs can negatively regulate lincRNA expression. We found that lincRNAs exhibit high correlation with their protein-coding neighbors in expression. Co-expression network analysis resulted in eight stage-specific modules, gene ontology and pathway analysis of them suggested that some lincRNAs were involved in IMF-related processes, such as fatty acid metabolism and peroxisome proliferator-activated receptor signaling pathway. Furthermore, we identified hub lincRNAs and found six of them may play important roles in IMF development. This work detailed some lincRNAs which may affect of IMF development in pig, and facilitated future research on these lincRNAs and molecular assisted breeding for pig.

Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

“…By contrast, lincRNAs had shorter transcript length, longer exon length, fewer exon number, and lower expression level than protein-coding transcripts. These results are consistent with previous reports [19,20].…”

“…We used the following steps according to the laboratory's previous studies to identify lincRNAs from the nonredundant transcriptome [19], and the main steps are shown as follows ( Figure 1A):…”

Transcriptome analysis of in vitro fertilization and parthenogenesis activation during early embryonic development in pigs

“…Finally, we obtained 15,070 putative lincRNA transcripts produced by 7,185 loci, which were distributed in all chromosomes, except the Y chromosome (Figure 3B), and 6,113 of these 15,070 lincRNA transcripts had no overlap with currently annotated transcripts. Moreover, based on the comparison of the basic characterization between lincRNAs and protein-coding genes, such as average transcript length, mean exon length, exon number, and average expression, lincRNAs have shorter transcript length, longer exon length, and smaller exon number (SupplementaryFigure S3 A-D), which are consistent with previous reports(Zou et al, 2018). In addition, we perform differential expression analysis of linRNAs in adjacent stages.DELs had a similar trend with protein-coding genes in which a large number of DEGs and DELs both occurred at the same stage (SupplementaryFigure S3 E-F), indicating that the function of DELs is similar to that of DEGs.…”

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12

“…Coexpression network analysis resulted in 8 stagespecific modules. Moreover, highly connected central genes (hubs) were identified within each module and 6 (TCONS_00007267, TCONS_00039827, TCONS_00049066, TCONS_00049068, TCONS_00062080, and TCONS_00062081) of them were highly expressed in the muscle or fat and may play vital roles in IMF development (Zou et al, 2018).…”