ArticleZoological research2023
Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits.
Article in Zoological research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Chromatin accessibility of the jejunum in two high-yielding laying hen strains under divergent mineral phosphorus supply during the transition to egg laying.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2026Article
- Bayesian fine-mapping pinpoints candidate genes and pleiotropic loci of production traits from a chicken backcrossing scheme.BMC genomics · 2026Article
- Integrated RNA-seq and ATAC-seq analyses reveal muscle development differences between european meat pigeon and shiqi pigeon during embryonic to post-hatching stages.Frontiers in cell and developmental biology · 2026Article
- A Functional Regulatory Variant ofAnimals : an open access journal from MDPI · 2025Article
- Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line.Nature communications · 2025Article
- Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.Evolutionary applications · 2025Article
- Article
- Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.GigaScience · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Article
- Application of GWAS and mGWAS in Livestock and Poultry Breeding.Animals : an open access journal from MDPI · 2024Review
- Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken.Communications biology · 2024Article
- Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens.Frontiers in genetics · 2024Article
- Article
- Research Note: Identification of core promoter region of the polyunsaturated fatty acid synthesis-related gene family in chicken.Poultry science · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose
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