ArticleG3 (Bethesda, Md.)2022
Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 28 citations in OpenAlex.
- Dynamic changes in chromatin accessibility and gene expression involved in fetal myogenesis of Min pigs.Animal bioscience · 2025Article
- Tissue-Specific Chromatin Accessibility Regions and Transcription Factor Binding Sites in Pig Brain and Endocrine Tissues.Molecular neurobiology · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Effects of foetal size, sex and developmental stage on adaptive transcriptional responses of skeletal muscle to intrauterine growth restriction in pigs.Scientific reports · 2024Article
- ROCCO: a robust method for detection of open chromatin via convex optimization.Bioinformatics (Oxford, England) · 2023Article
- An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits.Animals : an open access journal from MDPI · 2023Article
- An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs.International journal of molecular sciences · 2023Article
- Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages.International journal of molecular sciences · 2023Article
- A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines.Genetics, selection, evolution : GSE · 2023Article
- The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs.International journal of molecular sciences · 2023Article
- Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs.Animals : an open access journal from MDPI · 2022Article
- Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions.G3 (Bethesda, Md.) · 2022Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 3 countries.
Funding
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Registered trials
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.