Abstract
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
Highlights
These findings support the notion that many noncoding regions of DNA have important regulatory functions that affect gene expression
Following protocols established by this study, additional ATAC-seq experiments are underway to expand this assay to eight prioritized tissues for the equine Functional Annotation of Animal Genomes (FAANG) project
Just three years after starting the tissue and data collection for the equine FAANG initiative, the community has completed over 400 experiments from more than 50 tissues using a variety of assays targeting different features of the horse regulatory landscape (Table 2)
Summary
The horse reference genomes (Equcab2.0 [1] and EquCab3.0 [2]) are based on a Thoroughbred mare Twilight and remain the only high-quality genome assemblies for equids. Raudsepp et al provided a comprehensive review of major discoveries using combinations of recent technologies including genome-wide association studies (GWAS), whole-genome sequencing (WGS), and RNA-seq [3] Using these tools, successful identification of the genetic variants responsible for simple Mendelian traits have been identified, including a novel variant in glutamate metabotropic receptor 6 (GRM6) associated with congenital stationary night blindness [4] and a nonsense variant in rap guanine nucleotide exchange factor 5 (RAPGEF5) associated with equine familial isolated hypoparathyroidism [5]. Numerous studies have examined different mechanisms by which noncoding variants may affect phenotype Variants near these significantly associated SNPs have been found to create transcription factor (TF) binding sites [8], disrupt binding motifs [9], or alter TF binding affinities [10,11].
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