ArticleBMC biology2022
Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome.
Article in BMC biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 55 citations in OpenAlex.
- Multi-Layer Transcriptomic Comparison Across Human, Pig, and Mouse Informs Tissue- and Trait-Specific Animal Model Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comparative Analysis of Gut Microbiome, Metabolome and Meat Quality Among Chinese Steppe Red Cattle, Simmental Hybrid Cattle and Yanhuang Cattle.Animals : an open access journal from MDPI · 2026Article
- Multi-Omics Insights Into the Mechanisms of Early Muscle Fiber Difference and Transformation Between Lean-Type and Chinese Indigenous Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Understanding super enhancers in genome architecture and their roles in livestock breeding.BMC genomics · 2026Review
- Sequence-Based Models for RNA-Protein Interactions Imputation Might Be Insufficient for Novel Signal Prediction in eCLIP Data.International journal of molecular sciences · 2026Article
- Integrative Multi-Omics Analysis Unveils Candidate Genes and Functional Variants for Growth and Reproductive Traits in Duroc Pigs.Animals : an open access journal from MDPI · 2025Article
- Single-nucleus transcriptome profiling of skeletal muscle in Diqing Tibetan pigs with distinct body sizes.BMC genomics · 2025Article
- The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.Genetics, selection, evolution : GSE · 2025Article
- Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs.BMC biology · 2025Article
- Integrative Genomic, Transcriptomic and Epigenomic Analysis Reveals cis-regulatory Contributions to High-altitude Adaptation in Tibetan Pigs.Molecular biology and evolution · 2025Article
- A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.BMC genomics · 2025Article
- Comprehensive analysis of RNA-chromatin, RNA-, and DNA-protein interactions.NAR genomics and bioinformatics · 2025Article
- Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.Genome research · 2024Article
- Article
- Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens.Nature communications · 2024Article
- Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens.Journal of animal science and biotechnology · 2024Article
- Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken.Communications biology · 2024Article
- Article
- Lipid Droplet-Mitochondria Contacts in Health and Disease.International journal of molecular sciences · 2024Review
- Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.Genetics, selection, evolution : GSE · 2024Article
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Authors and funding
14 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene expression programs are intimately linked to the interplay of active cis regulatory elements mediated by chromatin contacts and associated RNAs. Genome-wide association studies (GWAS) have identified many variants in these regulatory elements that can contribute to phenotypic diversity. However, the functional interpretation of these variants remains nontrivial due to the lack of chromatin contact information or limited contact resolution. Furthermore, the distribution and role of chromatin-associated RNAs in gene expression and chromatin conformation remain poorly understood. To address this, we first present a comprehensive interaction map of nuclear dynamics of 3D chromatin-chromatin interactions (H3K27ac BL-HiChIP) and RNA-chromatin interactions (GRID-seq) to reveal genomic variants that contribute to complex skeletal muscle traits.
resultsIn a genome-wide scan, we provide systematic fine mapping and gene prioritization from GWAS leading signals that underlie phenotypic variability of growth rate, meat quality, and carcass performance. A set of candidate functional variants and 54 target genes previously not detected were identified, with 71% of these candidate functional variants choosing to skip over their nearest gene to regulate the target gene in a long-range manner. The effects of three functional variants regulating KLF6 (related to days to 100 kg), MXRA8 (related to lean meat percentage), and TAF11 (related to loin muscle depth) were observed in two pig populations. Moreover, we find that this multi-omics interaction map consists of functional communities that are enriched in specific biological functions, and GWAS target genes can serve as core genes for exploring peripheral trait-relevant genes.
conclusionsOur results provide a valuable resource of candidate functional variants for complex skeletal muscle-related traits and establish an integrated approach to complement existing 3D genomics by exploiting RNA-chromatin and chromatin-chromatin interactions for future association studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.