The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

Journal of Animal Science and Biotechnology

Xinhua Hou¹  Ligang Wang¹  Tianyu Deng¹  Lixian Wang¹  Fuping Zhao¹  Liangyu Shi¹  Longchao Zhang²  Jianfei Gong²  Hongmei Gao²  Hua Yan²  Jingwei Yue²  Xin Liu²  Lijun Shi² 

[1] Institute of Animal Science, Chinese Academy of Agricultural Sciences;Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture;

关键词: Chromatin accessibility;    Embryo;    Pig;    Skeletal muscle;    Transcriptome;   

DOI  :  10.1186/s40104-021-00577-z

来源: DOAJ

【 摘 要 】

Abstract Background The 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). Results In 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. Conclusions This 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.

【 授权许可】

Unknown