ArticleBMC genomics2022
Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 39 citations in OpenAlex.
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- H3K4me3 CUT&Tag and Transcriptome Analysis Reveal the Epigenetic Regulatory Landscape in Mammary Gland Tissues of Yili Horses at Different Lactation Stages.Animals : an open access journal from MDPI · 2026Article
- Article
- An Increase in Male Recombination Rate With Age in Dairy Cattle Is Heritable and Polygenic.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Pharmacoepigenomics in Personalized Medicine: A Hypothesis-Generating Approach to Introduce CpG-PGx SNPs as New Candidates for a Systematic Insight into Genomic-Epigenomic-Phenomic-Pharmacogenomics (G-E-Ph-PGx) Axis.Journal of personalized medicine · 2025Article
- A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.BMC biology · 2025Article
- An integrative approach to prioritize candidate causal genes for complex traits in cattle.PLoS genetics · 2025Article
- Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP.Genetics, selection, evolution : GSE · 2025Article
- Mammary gland multi-omics data reveals new genetic insights into milk production traits in dairy cattle.PLoS genetics · 2025Article
- Sequence-based GWAS in 180,000 German Holstein cattle reveals new candidate variants for milk production traits.Genetics, selection, evolution : GSE · 2025Article
- Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle.Frontiers in genetics · 2025Article
- Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases.Computational and structural biotechnology journal · 2024Article
- Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations.Genetics, selection, evolution : GSE · 2024Article
- Using expression data to fine map QTL associated with fertility in dairy cattle.Genetics, selection, evolution : GSE · 2024Article
- A common regulatory haplotype doubles lactoferrin concentration in milk.Genetics, selection, evolution : GSE · 2024Article
- Variation in histone configurations correlates with gene expression across nine inbred strains of mice.Genome research · 2023Article
- Using QTL to Identify Genes and Pathways Underlying the Regulation and Production of Milk Components in Cattle.Animals : an open access journal from MDPI · 2023Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCausal variants for complex traits, such as eQTL are often found in non-coding regions of the genome, where they are hypothesised to influence phenotypes by regulating gene expression. Many regulatory regions are marked by histone modifications, which can be assayed by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Sequence reads from ChIP-seq form peaks at putative regulatory regions, which may reflect the amount of regulatory activity at this region. Therefore, eQTL which are also associated with differences in histone modifications are excellent candidate causal variants.
resultsWe assayed the histone modifications H3K4Me3, H3K4Me1 and H3K27ac and mRNA in the mammary gland of up to 400 animals. We identified QTL for peak height (histone QTL), exon expression (eeQTL), allele specific expression (aseQTL) and allele specific binding (asbQTL). By intersecting these results, we identify variants which may influence gene expression by altering regulatory regions of the genome, and may be causal variants for other traits. Lastly, we find that these variants are found in putative transcription factor binding sites, identifying a mechanism for the effect of many eQTL.
conclusionsWe find that allele specific and traditional QTL analysis often identify the same genetic variants and provide evidence that many eQTL are regulatory variants which alter activity at regulatory regions of the bovine genome. Our work provides methodological and biological updates on how regulatory mechanisms interplay at multi-omics levels.
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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 Socratic graph.