Genome-wide DNA Methylation Profiles and Their Relationships with mRNA and the microRNA Transcriptome in Bovine Muscle Tissue (Bos taurine)

Abstract

DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.

Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles

“…There was a negative correlation between methylation levels in the promoters of miRNAs and the miRNA expression levels ( r  = −2.19, P  = 5.32 × 10 −17 ; Supplementary Fig. S7), in agreement with previous studies on bovine muscle tissue56. However, between LDM and PMM, there were only five miRNAs that exhibited different methylation levels in their promoter regions, including miR-378, miR-181c, miR-181d, miR-139 and miR-216 (Supplementary Table S5).…”

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture

“…For our data, the DNA methylation pattern was found to be clearly distinct around TSS for expressed and nonexpressed genes. As expected (Huang et al, ), we observed extremely low methylation levels for expressed and complete methylation for nonexpressed genes (Supporting Information Figure 6). Consistent with previous reports (Kundaje et al, ; Sharp et al, ), the methylation level is noticeably lower around TSS for genes also bearing active promoter marks for both coding and noncoding transcribed regions (Supporting Information Figure 6b).…”

“…Various genome‐wide studies have established the role of DNA methylation in control of gene expression, according to the location within the transcriptional unit. Demethylated promoters and methylated gene body have been reported to promote active transcription (Huang et al, ; Jones, ), although after nucleosome assembly, transcription cannot be initiated for genes with methylated CpGs around the TSS (Hashimshony, Zhang, Keshet, Bustin, & Cedar, ; Jones, ; Kass, Landsberger, & Wolffe, ). For our data, the DNA methylation pattern was found to be clearly distinct around TSS for expressed and nonexpressed genes.…”

The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells

“…This was e.g. shown in bovine muscle tissue (Huang et al, 2014). For multiple species a genome-wide negative correlation between promoter methylation and gene expression was described, whereas genebody methylation has been reported to be positively correlated with gene expression (Deaton and Bird, 2011;Jjingo et al, 2012).…”