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.
Highlights
Pigs are a major protein source and important biomedical models for human metabolic diseases, such as obesity, type II diabetes, and cardiovascular diseases, because their body size and physiological/anatomical features are similar to those of humans (Robich et al, 2010)
We used RNA-seq data from published study including four groups, which had different Intramuscular fat (IMF) contents (Wang et al, 2017), to identify lincRNAs in longissimus dorsi muscle (LDM) related to IMF development
We found that genes in the four modules remarkably participated in IMF-related biological processes or pathways, such as fatty acid metabolism and cholesterol metabolic and adipocytokine signaling pathways (Figures 7A,D–F and Supplementary Table S6).This finding suggested that lincRNAs in these modules may play vital roles in IMF development
Summary
Pigs are a major protein source and important biomedical models for human metabolic diseases, such as obesity, type II diabetes, and cardiovascular diseases, because their body size and physiological/anatomical features are similar to those of humans (Robich et al, 2010). IMF content, which refers to the amount of fats, including phospholipids, triglycerides, and cholesterol within muscles (Hocquette et al, 2010), is one of the important factors that affect meat quality, such as flavor and drip loss (Fernandez et al, 1999; Fiedler et al, 2003). Previous studies have discovered some key regulators in IMF development, such as fibroblast growth factor 21 (Wang et al, 2015), miRNA196a/b (Liu L. et al, 2017), miR-130a (Wei et al, 2017), PU. antisense lncRNA (Wei et al, 2015), and protein tyrosine phosphatase non-receptor type 1 (Won et al, 2017), these studies mainly focused on protein-coding genes and microRNAs, researches about the roles of lincRNAs on IMF development are scarce
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