A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Michelle M Halstead,Huaijun Zhou,Ganrea Chanthavixay,Ian Korf,Juan F Medrano,Perot Saelao,Alison L Van Eenennaam,Ying Wang,Catherine W Ernst,Christopher K Tuggle,Pablo J Ross,Colin Kern

doi:10.1186/s12864-020-07078-9

Michelle M Halstead, Huaijun Zhou + Show 10 more

Open Access

https://doi.org/10.1186/s12864-020-07078-9

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Abstract

BackgroundAlthough considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues.ResultsOverall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions.ConclusionsThe lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.

Highlights

Considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized
ATAC-seq library quality control and preprocessing Using a modified ATAC-seq protocol, genome-wide chromatin accessibility was profiled in eight tissues derived from two adult male Hereford cattle and two adult male Yorkshire pigs: three brain tissues, liver, lung, spleen, subcutaneous adipose, and skeletal muscle (Fig. 1a)
With the exception of one cattle cerebellum sample, which was lost during processing, ATAC-seq data were generated for two biological replicates per tissue (Table S1)

Summary

Introduction

Considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. Despite considerable progress to annotate protein-coding genes in livestock species, the vast majority of these genomes is noncoding and remains poorly characterized. Epigenomics techniques, such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing (DNase-seq), have been extensively employed to catalog functional elements in humans [1] and classical model organisms [2,3,4,5,6]. ATAC-seq quickly became one of the leading methods for identification of open chromatin, largely due to the simplicity of the technique and low input requirements, which made it possible to study chromatin structure in rare samples

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