A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

Huanhuan Zhou,Jianhai Chen,Yu Luan,Yunxia Zhao,Saixian Zhang,Xiaolong Qi,Shuhong Zhao,Zhangxu Wang,Yuhua Fu,Jingjin Li,Ye Hou,Daoyuan Wang,Yueyuan Xu,Jianlin Han,Xinyun Li,Mingyang Hu

doi:10.1038/s41467-021-22448-x

Abstract

Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.

Highlights

Major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model
We identified the genomic localization of histone H3 lysine 4 trimethylation (H3K4me3) and H3 lysine 27 acetylation (H3K27ac) by ChIP-seq and characterized open chromatin regions using ATAC-seq methods (Supplementary Tables 1–3 and Supplementary Data 1–2)
In addition to the values of cross-correlation, the fraction of reads in peaks (FRiP), transcription start site (TSS) enrichment analyses, and Principal Component Analysis (PCA), showed that our ChIP-seq and ATAC-seq data were of sufficient quality for further analyses (Supplementary Fig. 1d–i, Supplementary Tables 2–3, and Supplementary Data 2)

Summary

Introduction

Major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. We systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. We follow the guidelines of the previous ENCODE and Roadmap Epigenomics projects[1,5,6] and design RNA sequencing (RNA-seq), chromatin immunoprecipitation followed by sequencing (ChIP-seq), an assay for transposase-accessible chromatin using sequencing (ATAC-seq), and high-throughput chromosome conformation capture (Hi-C) methodologies to identify and characterize the function of cis-regulatory elements in the pig genome. Our study fundamentally enriches cisregulatory element annotation in the pig genome, which lays a foundation for pig and human biology studies and, especially, extends ENCODE and Roadmap Epigenomics projects in the research field of large animals

Methods

Results

Conclusion