ArticleBMC genomics2020
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 83 citations in OpenAlex.
- Molecular Genetics and Epigenetics Regulatory Role of miRNAs on Adipogenesis and Intramuscular Fat Development in Beef Cattle: In the Context of Meat Quality.Molecular biotechnology · 2026Review
- Pretraining improves prediction of genomic datasets across species.Bioinformatics (Oxford, England) · 2026Article
- Ensembl 2026.Nucleic acids research · 2026Article
- A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.BMC genomics · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.Nature communications · 2024Article
- Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development.Epigenetics & chromatin · 2024Article
- Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats.Molecular biology and evolution · 2024Article
- An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.Genome research · 2023Article
- Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.G3 (Bethesda, Md.) · 2023Article
- Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages.International journal of molecular sciences · 2023Article
- Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes.Animals : an open access journal from MDPI · 2023Article
- Profiling the immune epigenome across global cattle breeds.Genome biology · 2023Article
- Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.Science (New York, N.Y.) · 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
- A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment.Frontiers in bioengineering and biotechnology · 2023Review
- Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation.Frontiers in genome editing · 2023Article
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundAlthough considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues.
resultsOverall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions.
conclusionsThe lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
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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.