Back to Search Start Over

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

Authors :
Jianping Quan
Ming Yang
Xingwang Wang
Gengyuan Cai
Rongrong Ding
Zhanwei Zhuang
Shenping Zhou
Suxu Tan
Donglin Ruan
Jiajin Wu
Enqin Zheng
Zebin Zhang
Langqing Liu
Fanming Meng
Jie Wu
Cineng Xu
Yibin Qiu
Shiyuan Wang
Meng Lin
Shaoyun Li
Yong Ye
Fuchen Zhou
Danyang Lin
Xuehua Li
Shaoxiong Deng
Yuling Zhang
Zekai Yao
Xin Gao
Yingshan Yang
Yiyi Liu
Yuexin Zhan
Zhihong Liu
Jiaming Zhang
Fucai Ma
Jifei Yang
Qiaoer Chen
Jisheng Yang
Jian Ye
Linsong Dong
Ting Gu
Sixiu Huang
Zheng Xu
Zicong Li
Jie Yang
Wen Huang
Zhenfang Wu
Source :
Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)
Publication Year :
2024
Publisher :
Nature Portfolio, 2024.

Abstract

Abstract Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.

Subjects

Subjects :
Science

Details

Language :
English
ISSN :
20411723
Volume :
15
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Nature Communications
Publication Type :
Academic Journal
Accession number :
edsdoj.90f889317bfe466e807967daa4a618ad
Document Type :
article
Full Text :
https://doi.org/10.1038/s41467-024-49923-5