Abstract
BackgroundThe development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc).ResultsIn total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within − 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.ConclusionsThis work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
Highlights
The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility
Genome-wide identification of Accessible chromatin regions (ACR) during pig embryonic development To examine the genome-wide ACRs involved in muscle development, we profiled the accessibility of chromatin at 45, 70 and 100 days during pig embryonic development by ATAC-seq
Detailed information on the high-quality libraries derived from each individual can be found in Additional file 2: Fig. S1 and Additional file 2: Fig. S2, which show that all the libraries exhibited the expected fragment length, contained abundant nucleosome-free and mononucleosomal spanning fragments (Additional file 2: Fig. S1), and exhibited the highest peak signal across the whole gene body in the Transcription start sites (TSS) (Additional file 2: Fig. S2)
Summary
The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. How chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). Previous research has shown that the development of skeletal muscle is a complex process that includes the formation of embryonic muscle fibers, the expansion of postnatal muscle fibers, and the regeneration of adult muscles [2]. Research on the genetic mechanisms affecting muscle development, during embryonic stages, will be beneficial for improving pork production methods and for expanding pig breeding strategies. Pigs are more closely related to humans in terms of their size, anatomy, genome, and physiology than other non-primate species (e.g., traditional rodent models); pigs are more suitable than other species for research on human health [5, 6]
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