AUTHOR=Liu Yi-Fan , Zhang Ming , Shan Yan-Ju , Pang Li-Chuan , Ji Gai-Ge , Ju Xiao-Jun , Tu Yun-Jie , Shi Shi-Ying , Bai Hao , Zou Jian-Min , Shu Jing-Ting 

TITLE=Transcriptome sequencing analysis of the role of miR-499-5p and SOX6 in chicken skeletal myofiber specification

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1008649

DOI=10.3389/fgene.2022.1008649

ISSN=1664-8021

ABSTRACT=<p>MicroRNAs (miRNAs) might play critical roles in skeletal myofiber specification. In a previous study, we found that chicken miR-499-5p is specifically expressed in slow-twitch muscle and that its potential target gene is <italic>SOX6</italic>. In this study, we performed RNA sequencing to investigate the effects of <italic>SOX6</italic> and miR-499-5p on the modulation and regulation of chicken muscle fiber type and its regulatory mechanism. The expression levels of miR-499-5p and <italic>SOX6</italic> demonstrated opposing trends in different skeletal muscles and were associated with muscle fiber type composition. Differential expression analysis revealed that miR-499-5p overexpression led to significant changes in the expression of 297 genes in chicken primary myoblasts (CPMs). Myofiber type-related genes, including <italic>MYH7B</italic> and <italic>CSRP3</italic>, showed expression patterns similar to those in slow-twitch muscle. According to functional enrichment analysis, differentially expressed genes were mostly associated with muscle development and muscle fiber-related processes. <italic>SOX6</italic> was identified as the target gene of miR-499-5p in CPM using target gene mining and luciferase reporter assays. <italic>SOX6</italic> knockdown resulted in upregulation of the slow myosin genes and downregulation of fast myosin genes. Furthermore, protein-protein interaction network analysis revealed that <italic>MYH7B</italic> and <italic>RUNX2</italic> may be the direct targets of <italic>SOX6</italic>. These results indicated that chicken miR-499-5p may promote slow-twitch muscle fiber formation by repressing <italic>SOX6</italic> expression. Our study provides a dataset that can be used as a reference for animal meat quality and human muscle disease studies.</p>