Abstract
As DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development of life. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and layers revealed that lower methylation in broilers might contribute to the muscle development. Differential methylated region analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development related terms at E13 and E19. Furthermore, by constructing the network of the lncRNA, we identified a lncRNA named MYH1-AS that potentially regulated muscle development. These findings depicted an integrative landscape of late period of embryonic myogenesis in chicken and gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in the skeletal muscle development. In addition, our study provided a reliable epigenetic resource for further muscle studies.