The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers generates insight into embryonic muscle development in chicken

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. 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 laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) 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 lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.