Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

Abstract

Cattle-yak is a hybrid F1 generation of cattle and yak, which has a history of more than 3000 years and has shown better production performance and higher economic benefits than those of yaks. However, up to now, there has been no study on the transcriptome-wide m6A methylation profile of bovine skeletal muscle and its potential biological function during muscle development. Here, we observed significant changes in the expression levels of muscle-related marker genes and methylation-related enzymes during the development of cattle-yak, and the overall m6A content in the Longissimus dorsi muscle of 18-month-old cattle-yak decreased significantly. A total of 36,602 peaks, 11,223 genes and 8388 lncRNAs were identified in the two groups, including 2989 differential peaks (427 up-regulated peaks and 2562 down-regulated peaks), 1457 differentially expressed genes (833 up-regulated genes and 624 down-regulated genes) and 857 differentially expressed lncRNAs (293 up-regulated lncRNAs and 564 down-regulated lncRNAs). GO and KEGG analysis revealed that they were significantly enriched in some muscle-related pathways (Wnt signaling pathway and MAPK signaling pathway) and high-altitude adaptation-related pathway (HIF-1 signaling pathway). Moreover, m6A abundance was positively correlated with gene expression levels, while it was negatively correlated with lncRNA expression levels. This indicates that m6A modification played an important role in the Longissimus dorsi muscle development of cattle-yak; however, the regulation mechanism of m6A-modified mRNA and lncRNA may be different. This study was the first report of transcriptome-wide m6A-modified mRNAs and lncRNAs atlas in the Longissimus dorsi muscle development of cattle-yak, one which will provide new perspectives for genetic improvement in bovines.

Comprehensive analysis of LncRNAs modified by m6A methylation in sheep skin

“…M 6 A methylation of lncRNAs in skeletal muscles of pig and Cattle-Yak has been excavated to find new candidate lncRNAs of muscle-fiber-type conversion and muscle development [32,33]. The change of m 6 A methylation of lncRNAs in IPEC-J2 cells induced by Clostridium perfringens beta2 toxin has been described [34].…”

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak

“…Therefore, elucidating the molecular mechanisms underlying the regulation of skeletal muscle growth and development is a crucial prerequisite for expediting genetic breeding and enhancement of Gannan yak, thereby optimizing economic benefits for herders. In recent years, research efforts have primarily focused on the transcriptional regulation and m6 A methylation of yak and cattle-yak [15,30], but few…”

“…Therefore, elucidating the molecular mechanisms underlying the regulation of skeletal muscle growth and development is a crucial prerequisite for expediting genetic breeding and enhancement of Gannan yak, thereby optimizing economic benefits for herders. In recent years, research efforts have primarily focused on the transcriptional regulation and m6 A methylation of yak and cattle–yak [ 15 , 30 ], but few studies have been conducted from the perspective of chromatin opening. To this end, we employed the ATAC-seq analysis method to elucidate the disparities in muscle growth and development between Gannan yak and Jeryak by investigating chromatin accessibility.…”

“…Furthermore, the regulation of epigenetic mechanisms also plays a crucial role in the complex process of muscle development [ 13 , 14 ]. For example, m6 A modification positively regulates the expression levels of genes related to skeletal muscle growth and development at different developmental stages in Jeryaks, whereas it is negatively correlated with the expression levels of lncRNAs [ 15 ]. However, studies on skeletal muscle development in Gannan yaks and Jeryaks have mainly focused on phenotypic and transcriptional aspects, with limited analysis from an epigenetic regulatory perspective.…”

Proteomic Analysis Reveals the Effects of Different Dietary Protein Levels on Growth and Development of Jersey-Yak

“…Jersey-yak is a hybrid offspring of Jersey cattle and yak (a hybrid offspring of female yaks artificially inseminated with high-quality frozen semen of Jersey cattle). The production performance of the hybrid progeny has shown obvious heterosis [5]. Hybridization improves the growth performance of yak, making it adaptable to a plain environment [6].…”