Genome-wide characterization of lncRNAs and mRNAs in muscles with differential meat quality

Meat quality is one of the most important traits in pig production. Long non-coding RNAs (lncRNAs) has been involved in diverse biological processes such as muscle development through regulating gene expression. However, studies on lncRNAs lag behind and a comparatively small number of lncRNAs have been identified in pigs. Also, effects of lncRNAs on meat quality remains to be characterized. Here, we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology. A total of 500 differentially expressed lncRNAs (DELs) and 2094 protein-coding genes (DEGs) were identified. Through KEGG analysis on DELs we first made clear that fat deposition might be the main reason resulting in differential phenotype of LT and ST, on the basis of which 41 key DELs and 50 DEGs involved in differential fat deposition were characterized. One of the key genes, cAMP-response element binding protein 1, was selected to confirm its role in porcine adipogenesis with molecular biology methods and found that it promotes the differentiation of porcine preadipocytes, consistent with its higher expression level and intramuscular fat contents in LT than that in ST muscle. Furthermore, through integrated analysis of DELs and DEGs, transcription factors important for differential fat deposition were characterized among which BCL6 have the most target DEGs while MEF2A was targeted by the most DELs. The results provide candidate genes crucial for meat quality, which will contribute to revealing the molecular mechanisms underlying meat quality we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology to identifide differentially expressed lncRNAs and mRNAs

肉品质是生猪生产中最为关键的性状之一。长链非编码RNA（long non-coding RNAs，lncRNAs）可通过调控基因表达参与肌肉发育等多种生物学过程。然而，针对lncRNAs的研究仍相对滞后，生猪中已鉴定的lncRNAs数量仍较少。此外，lncRNAs对肉品质的调控作用仍有待阐明。本研究采用RNA测序技术，对肉品质存在显著差异的背最长肌（longissimus thoracis，LT）和半腱肌（semitendinosus，ST）中的lncRNAs进行了分析。本研究共鉴定得到500个差异表达长链非编码RNA（differentially expressed lncRNAs，DELs）以及2094个差异表达蛋白编码基因（differentially expressed protein-coding genes，DEGs）。通过对DELs进行KEGG（京都基因与基因组百科全书）通路分析，本研究首次明确脂肪沉积可能是导致背最长肌与半腱肌表型差异的核心原因，并在此基础上鉴定得到41个参与脂肪沉积差异的关键DELs以及50个关键DEGs。本研究选取关键基因之一——cAMP应答元件结合蛋白1（cAMP-response element binding protein 1），采用分子生物学方法验证其在猪脂肪生成中的功能，发现其可促进猪前体脂肪细胞的分化，这与背最长肌中该基因的表达水平及肌内脂肪含量均高于半腱肌的结果相一致。此外，通过对DELs与DEGs进行整合分析，本研究鉴定得到一批与脂肪沉积差异相关的关键转录因子：其中BCL6的靶标DEGs数量最多，而MEF2A则是被最多DELs所靶向的转录因子。本研究结果可为肉品质相关关键候选基因提供重要参考，有助于揭示肉品质形成的分子机制。本研究通过RNA测序技术对肉品质存在差异的背最长肌与半腱肌进行分析，以鉴定差异表达的lncRNAs与mRNA。