Screening Of Key Transcription Factors Affecting Muscle Growth In Lijiang Pigs Based On ATAC-seq

Lijiang pig is an excellent local breed unique to Yunnan Province,which lean and fatty meat are both available.Under the same rearing and management conditions,it can be naturally separated into larger and smaller subgroups according to body size.In order to reveal the underlying molecular regulation mechanism of this phenomenon,the larger Lijiang pigs and the smaller Lijiang pigs were used as experimental materials,and then ATAC-seq was performed on the longest dorsal muscle tissue at 6 months of age.Further,comparative analysis was performed in combination with transcriptome results,aimed at screening key transcription factors affecting muscle growth in Lijiang pigs.The main results of this study are as follows:(1)10,032 and 9,766 open chromatin regions(OCRs)were detected in the longest dorsal muscle tissues of smaller Lijiang pigs(LJS)and larger Lijiang pigs(LJL),respectively;among them,there were 2,895 and 2,629 OCRs unique to LJS and LJL,respectively,and7,137 OCRs shared between the two groups.(2)The genomic feature distribution of OCRs unique to each group was highly similar,and the chromatin accessibility of Promoter,Intron and Distal intergenic was the highest;2,566 genes that may be regulated by LJS-unique OCRs are mainly enriched in cortical actin cytoskeleton organization,calcium signaling pathway,thyroid hormone signaling pathway,etc.2,360 genes that may be regulated by LJL-unique OCRs were mainly enriched in actin cytoskeleton organization,insulin signaling pathway,Fox O signaling pathway,and m TOR signaling pathway etc.(3)389 and 387 known transcription factors were enriched in LJS-unique OCRs and LJL-unique OCRs,respectively,of which 355 were shared in both groups;MEF2 and KLF/SP transcription factors are more likely to be combined with these OCRs.(4)The integrated analysis of ATAC-seq and RNA-seq yielded 112 and 113 differentially expressed genes(DEGs)that may be regulated by LJS-unique OCRs and LJL-unique OCRs,respectively,and there is a high enrichment of transcription factor motifs such as MEF2 A,MEF2C,CTCF and PATZ1 on the OCRs of these DEGs;transcription factor footprint analysis verified the binding activity of MEF2 A and MEF2 C,and further transcription factor-target gene regulatory network analysis predicted 41 potential target genes of MEF2 A and MEF2 C,including PLEKHM3,JUNB,USP2,IER5,DGKζ,etc.In conclusion,with the help of ATAC-seq sequencing technology,the genome-wide chromatin accessibility landscape of larger and smaller Lijiang pig skeletal muscle tissues was obtained for the first time,and the key transcription factors affecting Lijiang pig muscle growth were preliminarily screened,and the results provided a new theoretical basis for Lijiang pig breeding based on molecular genetic means.