Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions.

IF 2.8 3区 生物学 Q2 GENETICS & HEREDITY Frontiers in Genetics Pub Date : 2025-02-27 eCollection Date: 2025-01-01 DOI:10.3389/fgene.2025.1534461
Alexa M Barber, Nicole B Kingsley, Sichong Peng, Elena Giulotto, Rebecca R Bellone, Carrie J Finno, Ted Kalbfleisch, Jessica L Petersen
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引用次数: 0

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.

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来源期刊
Frontiers in Genetics
Frontiers in Genetics Biochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
5.50
自引率
8.10%
发文量
3491
审稿时长
14 weeks
期刊介绍: Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public. The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.
期刊最新文献
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