Depot-specific gene expression during differentiation of Hanwoo muscular satellite cells

Abstract

<p>The Korean Hanwoo cattle is highly regarded for its high marbling ability (intramuscular fat) and this trait is the key drive of profitability for the industry. The study of muscle development and differentiation in Hanwoo is important to improve understanding of the genes and pathways that regulate these processes and to identify markers for genomic selection. In this study, we performed a culture cell experiment using bovine muscle satellite cells combined with a time-series RNA-seq analysis to measure the transcriptome expression levels during the development of satellite cells from <i>Longissimus dorsi</i> (LD) and <i>Semimembranosus</i> (SM) muscle. RNA-seq data was collected on days 0, 1, 2, 4, 7 and 14 after differentiation treatment with an average of 35,727,746 cleaned reads per sample. Between 77% and 85% of the reads were mapped to the reference genome (<i>Bos taurus</i> UMD3.1 from Ensembl). The genes Hoxc11, Sim2, Hoxc8, Hoxb9, Zic2, Zic4, Tbx4 and Hoxb4 were differentially expressed between LD and SM across time, suggesting that they could drive specific characterization of each muscle. The levels of expression vary vastly between time points according to the stage of muscle differentiation and development. At the beginning of the experiment, the genes involved in proliferation were enriched while their expression reduced drastically after day 2. However, at day 4 and until day 14 there was an enrichment in the genes involved in actin cytoskeleton, muscle cell differentiation and structural constituents of muscle.</p>