Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Abstract

Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

Transcriptional, chromatin, and metabolic landscapes of LDHA inhibitor–resistant pancreatic ductal adenocarcinoma

“…Furthermore, ATAC-seq analysis and its integration with the RNA-seq analysis revealed that only a small subset of mRNAs (1% to 12%) associated with differential expression were associated with changes in chromatin accessibility within promoter regions. These results are consistent with those of other studies, which also reported an approximately 10% overlap between RNA-seq and ATAC-seq data ( 36 ). Furthermore, the usefulness of integrated analyses was highlighted by the ability of integrated RNA-seq and ATAC-seq data to identify changes in chromatin accessibility associated with consequent changes in mRNA expression, which allowed for the identification of potential transcriptional regulators associated with changes in mRNA expression.…”

An updatedC. elegansnuclear body muscle transcriptome for studies in muscle formation and function

“…We also performed a motif enrichment analysis in these core promoters and identified several novel cis -acting elements ( Supplemental Figure S4 Panel B and Supplemental Table S2 ). We mapped 12 members of the human Krueppel-like transcription factors family (KLF), which are important regulators of gene expression in vertebrate development and are involved in muscle health and disease (Prosdocimo et al 2015), Myogenin (MYOG), a muscle-specific basic-helix-loop-helix (bHLH) transcription factor involved in muscle development, myogenesis, and repair (Nabeshima et al 1993), and NHLH1, a helix-loop-helix transcription factor that is involved in growth and development of a wide variety of tissues and species (Cogliati et al 2002) and has been linked to muscle growth and development (Miao et al 2021). The complete list is shown in Supplemental Table S2 .…”

The chromatin accessibility landscape in the dental pulp of mouse molars and incisors

“…Chromatin accessibility deduced from ATAC-seq is often used with RNA sequencing (RNA-seq) to correlate cis-acting regulatory regions such as enhancers and promoters with gene expression (Nair et al, 2021). Both approaches have become increasingly powerful for investigating distinct differences in the regulatory wirings among closely related cell types or tissues (Miao et al, 2021). For example, using ATAC-seq and RNA-seq, Arenas-Mena and others reported evidence for the existence of a gene regulatory hierarchy during sea urchin embryogenesis (Arenas-Mena et al, 2021).…”