ArticleScience China. Life sciences2022
Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs.
Article in Science China. Life sciences, 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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25 citing papers in PubMed, 45 citations in OpenAlex.
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- Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits.Communications biology · 2024Article
- Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens.Journal of animal science and biotechnology · 2024Article
- Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.Zoological research · 2024Article
- Single-cell profiling of the pig cecum at various developmental stages.Zoological research · 2024Article
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- KLF4 facilitates chromatin accessibility remodeling in porcine early embryos.Science China. Life sciences · 2024Article
- Trace metal elements: a bridge between host and intestinal microorganisms.Science China. Life sciences · 2023Review
- Crosstalk between trace elements and T-cell immunity during early-life health in pigs.Science China. Life sciences · 2023Review
- Selenium deficiency-induced multiple tissue damage with dysregulation of immune and redox homeostasis in broiler chicks under heat stress.Science China. Life sciences · 2023Article
- Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton.Science China. Life sciences · 2023Article
- Profiles of muscular amino acids, fatty acids, and metabolites in Shaziling pigs of different ages and relation to meat quality.Science China. Life sciences · 2023Article
- Article
- 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
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Authors and funding
14 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).
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