Skeletal muscle lncRNA profile associated with fatty acids in beef cattle

Abstract

Abstract This study aimed to identify differentially expressed (DE) long non-coding RNAs (lncRNAs) in muscle tissue of Nellore cattle clustered by their fatty acid profile. Longissimus thoracis muscle samples from 48 young bulls were used to quantify fatty acid (FA) (myristic, palmitic, stearic, oleic, linoleic, conjugated linoleic (CLA), α-linolenic and the groups of saturated fatty acids (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), ω3, ω6, PUFA/SFA ratio and ω6/ω3) and to generate RNA-Sequencing data for transcriptomic analyses. The K-means analysis was used to classify the 48 animals into three clusters based on their FA patterns. The C1 had significantly (p ≤ 0.05) higher PUFA, ω3, ω6, linoleic and α-linolenic content than C2 and C3. The proportion of MUFA, CLA and oleic in the C2 and C3 were significantly (p ≤ 0.05) higher in relation to C1, while C3 had significantly (p ≤ 0.05) higher proportions of ω6/ω3, SFA, myristic, palmitic and stearic proportion than C1 and C2. DE analyses were performed on three different comparisons, C1 vs. C2, C1 vs. C3 and C2 vs. C3, and 25, 28 and 22 DE lncRNAs (fold change > | 2 |, p-value < 0.01 and false discovery rate (FDR) < 0.05) were found, respectively. For C1 vs. C2 comparison, a new transcript “lncRNA_16456.3” was found and was interacted with the genes FAM126A (Family with sequence similarity 126 member A) and IL6 (Interleukin-6). These genes were enriched by GO biological function terms related to cellular response to lipid pathway. For the C1 vs. C3 comparison, the lncRNA "lncRNA_13894.1" interacting with the BNIP3 gene (BCL2/Adenovirus E1B 19 kDa protein-interacting protein 3) was enriched by GO biological function terms related to fat cell differentiation. For the C2 vs. C3 comparison, a new transcript “lncRNA_16618.6” interacted with genes involved in G protein-coupled receptors (GPCRs). Those genes play a crucial role in regulating lipolysis mediated by the cAMP signaling pathway and may be contributing to a higher PUFA fatty acid content in beef. For the three comparisons: C1 vs. C2, C1 vs. C3, and C2 vs. C3, the identified lncRNAs, including genic and intergenic (lincRNA were associated with genes affecting immune response, energy metabolism, lipid and FA metabolism, whose seem to play an essential role in the physiological processes related to meat quality. These findings provide new insights to better understand the biological mechanisms involved in gene regulation of FA composition in beef. This could be valuable for further investigation regarding interaction between lncRNAs and mRNAs and how these interactions may affect meat quality.