Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions.
Abstract: The Functional Annotation of Animal Genomes (FAANG) consortium aims to annotate animal genomes across species, and work in the horse has substantially contributed to that goal. As part of this initiative, chromatin immunoprecipitation with sequencing (ChIP-seq) was performed to identify histone modifications corresponding to enhancers (H3K4me1), promoters (H3K4me3), activators (H3K27ac), and repressors (H3K27me3) in eight tissues from two Thoroughbred stallions: adipose, parietal cortex, heart, lamina, liver, lung, skeletal muscle, and testis. The average genome coverage of peaks identified by MACS2 for H3K4me1, H3K4me3, and H3K27ac was 6.2%, 2.2%, and 4.1%, respectively. Peaks were called for H3K27me3, a broad mark, using both MACS2 and SICERpy, with MACS2 identifying a greater average number of peaks (158K; 10.4% genome coverage) than SICERpy (32K; 24.3% genome coverage). Tissue-unique peaks were identified with BEDTools, and 1%-47% of peaks were unique to a tissue for a given histone modification. However, correlations among usable reads, total peak number, and unique peak number ranged from 0.01 to 0.92, indicating additional data collection is necessary to parse technical from true biological differences. These publicly available data expand a growing resource available for identifying regulatory regions within the equine genome, and they serve as a reference for genome regulation across healthy tissues of the adult Thoroughbred stallion.
Copyright © 2025 Barber, Kingsley, Peng, Giulotto, Bellone, Finno, Kalbfleisch and Petersen.
Publication Date: 2025-02-27 PubMed ID: 40084169PubMed Central: PMC11903428DOI: 10.3389/fgene.2025.1534461Google Scholar: Lookup
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Summary
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This research article is about the detailed genomic investigation of two Thoroughbred stallions, contributing to the goal of annotating animal genomes under the auspices of the Functional Annotation of Animal Genomes (FAANG) consortium.
FAANG Consortium and Histone Modifications
- The Functional Annotation of Animal Genomes (FAANG) consortium is an international collaboration aimed at generating comprehensive maps of functional elements in the genomes of domesticated animal species. The main objective is to enable a better understanding of biology, selective breeding for genetic improvement, and prediction of traits associated with genetic sequences.
- In the context of this study, histone modifications were examined to characterize and understand their role in gene regulation. Histones are proteins around which DNA is wound, impacting how genes are expressed. Changes in the modifications of these histones can affect this expression.
ChIP-seq Analysis and Results
- As part of the research, the team performed Chromatin Immunoprecipitation with sequencing (ChIP-seq), a technique that identifies the binding sites of DNA-associated proteins and analyzes protein-DNA interactions. It was used to identify histone modifications related to gene regulators such as enhancers, promoters, activators, and repressors in eight different tissues from two Thoroughbred stallions.
- The genome coverage of the identified peaks for each histone modification was reported in terms of percentages.
- Interestingly, the average genome coverage differed based on the histone modification identified, which could suggest different levels of gene activity or regulation associated with these histone marks.
Correlation and Future Work
- The statistical analysis performed indicated correlations among usable reads, total peak number, and unique peak number ranging from 0.01 to 0.92. This variability suggests that further data collection will be required to differentiate between true biological differences and those resulting from technical aspects of the data generation process.
- This research adds value to the growing resources that help identify regulatory regions in the equine (horse) genome. It can also serve as a reference for better understanding genome regulation across healthy tissues in adult Thoroughbred stallions.
Cite This Article
APA
Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL.
(2025).
Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions.
Front Genet, 16, 1534461.
https://doi.org/10.3389/fgene.2025.1534461 Publication
Researcher Affiliations
- University of Nebraska Medical Center, Eppley Institute for Research in Cancer and Allied Diseases, Omaha, NE, United States.
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, United States.
- Department of Veterinary Science, University of Kentucky, Lexington, KY, United States.
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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