ArticleFrontiers in genetics2021
Characterizing Genetic Regulatory Elements in Ovine Tissues.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- Unravelling viral identity: avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses.Virus evolution · 2026Article
- A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep.Genomics, proteomics & bioinformatics · 2025Article
- Regulatory element map of sheep reproductive tissues: functional annotation of tissue-specific strong active enhancers.Frontiers in veterinary science · 2025Article
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- Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep.Genomics, proteomics & bioinformatics · 2024Article
- Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats.BMC genomic data · 2023Article
- Recent advances in the genomic resources for sheep.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
- Epigenetic regulation of functional candidate genes for milk production traits in dairy sheep subjected to protein restriction in the prepubertal stage.BMC genomics · 2023Article
- Article
- Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning.International journal of molecular sciences · 2022Article
- A high-density genome-wide association with absolute blood monocyte count in domestic sheep identifies novel loci.PloS one · 2022Article
- Examining the extent of environmental contributions toward DNA methylation and phenotypic variation.Animal frontiers : the review magazine of animal agriculture · 2021Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole-genome bisulfite sequencing (WGBS) was performed to determine the complement of whole-genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues, and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in the spleen and cerebellum and CTCF in the liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in the liver and spleen, and promoters in the cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Furthermore, the liver and spleen displayed in common the greatest percent of active promoter (65%) and active enhancer (81%) states, and the liver and cerebellum displayed in common the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%). In addition, both known and
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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.