Abstract
One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in eight prioritized tissues collected as part of the FAANG equine biobank from two thoroughbred mares. Data were generated according to optimized experimental parameters developed during quality control testing. To ensure that we obtained sufficient ChIP and successful peak-calling, data and peak-calls were assessed using six quality metrics, replicate comparisons, and site-specific evaluations. Tissue specificity was explored by identifying binding motifs within unique active regions, and motifs were further characterized by gene ontology (GO) and protein–protein interaction analyses. The histone marks identified in this study represent some of the first resources for tissue-specific regulation within the equine genome. As such, these publicly available annotation data can be used to advance equine studies investigating health, performance, reproduction, and other traits of economic interest in the horse.
Highlights
In 1992, researchers discovered the first disease mutation in horses, conferring hyperkalemic periodic paralysis (HYPP) in Quarter Horses [1], yet identification of additional equine genetic diseases progressed slowly, with only nine disease-associated variants discovered prior to 2007 [2,3]
A super-enhancer that significantly contributes to the risk of type II diabetes in humans was identified by combining a genome-wide association study (GWAS) with locations of regulatory elements and other functional regions across the genome [11]
Jensen–Shannon distance is a common statistic used to compare two distributions that can be applied to chromatin immunoprecipitation (ChIP) datasets using deepTools version 2.4.3 [28], and a threshold was determined by agreement among Functional Annotation of ANimal Genomes (FAANG) collaborators
Summary
In 1992, researchers discovered the first disease mutation in horses, conferring hyperkalemic periodic paralysis (HYPP) in Quarter Horses [1], yet identification of additional equine genetic diseases progressed slowly, with only nine disease-associated variants discovered prior to 2007 [2,3]. While the majority of characterized equine disease variants are located within coding regions, an increasing amount of research in humans and other animal species suggests that a large number of disease mutations are harbored within regulatory elements and other functional. Current genomic annotations for the horse have limited information about the functions of these non-coding regions, making it difficult to identify variants that alter gene regulation. With the increasing focus on the importance of regulatory elements in the pathogenesis of many diseases, it is clear that annotations of the equine genome need to encompass both coding and non-coding functional elements in order to understand complex genetic diseases and other traits affecting horses and the equine industry
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