ArticleJournal of animal science and biotechnology2022
Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs.
Article in Journal of animal science and biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation.Animals : an open access journal from MDPI · 2026Review
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks.bioRxiv : the preprint server for biology · 2026Article
- Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.International journal of molecular sciences · 2026Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Muscle growth differences in Lijiang pigs revealed by ATAC-seq multi-omics.Frontiers in veterinary science · 2024Article
- Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species.Molecular biology and evolution · 2023Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Profiling of N6-methyladenosine methylation in porcine longissimus dorsi muscle and unravelling the hub gene ADIPOQ promotes adipogenesis in an mJournal of animal science and biotechnology · 2023Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.
resultsHere we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle.
conclusionsOur data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs.
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