Functional annotation of putative cis-regulatory elements in the genomes of two Thoroughbred stallions

The Functional Annotation of Animal Genomes (FAANG) consortium aims to functionally annotate animal genomes, and work in the horse has substantially contributed to that goal. Within 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. Chromatin preparation and sequencing was performed in a comparable manner to previously published work in two mares. 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, moderate to strong correlations amongst usable reads, total peak number, and unique peak number will need to be addressed to parse technical differences from biological differences amongst tissues and allow for future comparisons of the stallion dataset with ChIP-seq data previously reported for two Thoroughbred mares. These new publicly available data expand a growing resource available for identifying the function of regions within the equine genome, within and between sexes, and they serve as a reference for the activation state of genes across healthy tissues.