ArticleFrontiers in nutrition2021
Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs.
Article in Frontiers in nutrition, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 60 citations in OpenAlex.
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- Identification of differentially expressed lncRNAs in different daily weight gains of Jiangquan black pigs and functional analysis of LOC100518120.BMC genomics · 2026Article
- Integrative ATAC-Seq and RNA-Seq analysis identifies key genes for intramuscular fat content in Laiwu pigs.BMC genomics · 2026Article
- Novel Insights into G0S2 as a Central Regulator of Lipid Metabolism and Its Implications for Meat Quality.Animals : an open access journal from MDPI · 2026Review
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- Integrating transcriptome and proteome profiles to compare carcass and meat quality traits between Songliao and Songlei black pigs.Frontiers in nutrition · 2026Article
- Deciphering skeletal muscle development: cellular heterogeneity and molecular regulatory networks from single-cell and spatial transcriptomic perspectives.Frontiers in cell and developmental biology · 2026Review
- Complementary structure of statistical significance and predictive relevance in explainable machine learning-based transcriptomic tissue classification of Hanwoo cattle.Frontiers in genetics · 2026Article
- An Integrated Multi-Omics Study of Mammalian Skeletal, Cardiac, and Smooth Muscles.International journal of molecular sciences · 2025Article
- Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs.Genetics, selection, evolution : GSE · 2025Article
- Cortisol-Induced Chromatin Remodeling and Gene Expression in Skeletal Muscle of Rainbow Trout: Integrative ATAC-Seq and RNA-Seq Analysis.International journal of molecular sciences · 2025Article
- Echinocandin Adaptation inJournal of fungi (Basel, Switzerland) · 2025Article
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- Integrating metabolomics and transcriptomics to analyze differences in muscle mass and flavor formation inFrontiers in veterinary science · 2025Article
- Integrative genetic and epigenetic control of skeletal muscle fiber traits in agricultural animals.Frontiers in genetics · 2025Review
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- Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds.Animals : an open access journal from MDPI · 2024Article
- Integration of ATAC-Seq and RNA-Seq Reveals VDR-SELENBP1 Axis Promotes Adipogenesis of Porcine Intramuscular Preadipocytes.International journal of molecular sciences · 2024Article
- Deciphering Mechanisms of Adipocyte Differentiation in Abdominal Fat of Broilers.Journal of agricultural and food chemistry · 2024Article
- Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs.BMC genomics · 2024Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 (
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