ArticleScientific reports2020
Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 60 citations in OpenAlex.
- 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
- ATAC-seq of low-input and cryopreserved primordial germ cells reveals functional enhancers.Development (Cambridge, England) · 2026Article
- Multi-omics dissection of the genetic regulation underlying fatty acid composition in cattle.Genome biology · 2025Article
- Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle.Genomics, proteomics & bioinformatics · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution.GigaScience · 2024Article
- Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information.BMC bioinformatics · 2023Article
- An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics.Science advances · 2023Article
- Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.Scientific reports · 2023Article
- Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines.iScience · 2023Article
- Functional annotation of the animal genomes: An integrated annotation resource for the horse.PLoS genetics · 2023Review
- Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits.Zoological research · 2023Article
- AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency.Bioinformatics (Oxford, England) · 2022Article
- A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation.Communications biology · 2022Article
- Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions.G3 (Bethesda, Md.) · 2022Article
- The early function of cortisol in liver duringFrontiers in immunology · 2022Article
- Decoding the Equine Genome: Lessons from ENCODE.Genes · 2021Review
- Pig genome functional annotation enhances the biological interpretation of complex traits and human disease.Nature communications · 2021Article
- Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.Nature communications · 2021Article
- Successful ATAC-Seq From Snap-Frozen Equine Tissues.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues.
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