Evidence of microRNA Regulation of Intramuscular Fat Deposition in Beef Cattle

This study aims to identify known and novel microRNAs expressed in Bos indicus muscle, as well as changes of the expression level of these molecules, in order to investigate the influence on regulatory pathways for intramuscular fat (IMF) deposition in Nelore cattle. Total RNA was extracted from 30 animals divided into High (H) and Low (L) IMF content groups, based on extreme genomic estimated values (GEBV) for this trait. MicroRNA libraries were constructed and sequenced using NGS technology (Miseq-Illumina) generating 1 million reads/sample. MicroRNAs were filtered by FastX, annotated by miRDeep2 and differentially expressed (DE) microRNAs were identified by DESeq2 package. Twenty-six novel and 463 known microRNAs were identified and six of them were DE (FDR <0.1), which bta-let-7f, bta-let-7a-5p and bta-miR-423 were downregulated; bta-miR-100, bta-miR-143 and bta-miR-146b were upregulated in the L group. MicroRNAs target genes were identified by TargetScan program and filtered by muscle RNA-seq data obtained in previous studies, creating a list with 2,579 target genes. The regulatory pathways associated with the miRNA target gene list were identified and analyzed by IPA® software. The most important pathway related with lipid metabolism herein identified was PPAR-RXR signaling, with 44 target genes involved. This pathway showed to be downregulated for adipogenesis and upregulated for fatty acid oxidation in the L group, through regulating gene expressions of PPARa and PKA by let-7a and let-7f; ADIPOR2 by miR-423; STAT5b by miR-100. These results agree with our hypothesis that microRNA expression can modulate lipid metabolism and fat deposition, although in vitro analyzes are required to complement this research.