Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq

Abstract

Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.

Characterization of Accessible Chromatin Regions in Cattle Rumen Epithelial Tissue during Weaning

“…The ENCODE guidelines for ATAC-seq projects recommend 50 million reads for paired-end sequencing for each replicate ( , accessed on 6 September 2021). Recent studies in cattle identified accessible chromatin regions in different tissues, including muscle, bronchial lymph nodes, liver, lung, hypothalamus, brain, adipose, and spleen [ 12 , 13 , 14 , 39 ]; however, none of them evaluated rumen tissue. This study aimed to identify accessible chromatin regions and genomic regulatory elements that may control rumen epithelial development changes during weaning in calves.…”

“…The use of ATAC-seq for rumen epithelial tissue to generate a comprehensive landscape of chromatin events will advance our knowledge of the regulatory element mechanisms in play during rumen development. Few studies have used ATAC-seq in cattle [ 12 , 13 , 14 ]. Recent studies using ATAC-seq reported open chromatin regions for bronchial lymph nodes of dairy calves [ 12 ]; liver, muscle, and hypothalamus of indicine cattle [ 13 ]; and muscle tissue in adults and embryos from Qinchuan cattle [ 14 ]; however, none of them evaluated rumen, especially in the critical weaning period.…”

“…Few studies have used ATAC-seq in cattle [ 12 , 13 , 14 ]. Recent studies using ATAC-seq reported open chromatin regions for bronchial lymph nodes of dairy calves [ 12 ]; liver, muscle, and hypothalamus of indicine cattle [ 13 ]; and muscle tissue in adults and embryos from Qinchuan cattle [ 14 ]; however, none of them evaluated rumen, especially in the critical weaning period. The main objectives of this study were to identify and characterize regions of accessible chromatin in pre- and post-weaning calves from rumen epithelial tissue and to identify differentially accessible chromatin regions (DARs) using the ATAC-seq approach to elucidate genetic regulatory elements during the weaning in cattle.…”

Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation

“…However, particularly in bovine models, previous studies in the context of skeletal muscle chromatin accessibility have mainly focused on comparative analysis across distant species to identify tissue‐specific regulatory elements 20–22 . Recently, Cao et al described comparative analysis of enhancers between adult and embryo bovine muscle using chromatin accessibility 23 . Despite the foetal stage is critical for skeletal muscle development, only limited evidence of foetal muscle growth and development was available from prior studies, and these findings may ignore that skeletal muscle development is a dynamic process comprised of multiple developmental stages.…”

“…[20][21][22] Recently, Cao et al described comparative analysis of enhancers between adult and embryo bovine muscle using chromatin accessibility. 23 Despite the foetal stage is critical for skeletal muscle development, only limited evidence of foetal muscle growth and development was available from prior studies, and these findings may ignore that skeletal muscle development is a dynamic process comprised of multiple developmental stages. In our study, we reconstructed the course of myogenic differentiation in vitro, providing an ideal model to define when and how these regulatory changes occur during skeletal muscle development.…”