Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs  

作　　者：Tao Jiang Ziqi Ling Zhimin Zhou Xiaoyun Chen Liqing Chen Sha Liu Yingchun Sun Jiawen Yang Bin Yang Jianzhen Huang Lusheng Huang 

机构地区：[1]State Key Laboratory of Pig Genetic Improvement and Production Technology,Jiangxi Agricultural University,Nanchang 330045,China

出　　处：《Journal of Animal Science and Biotechnology》2023年第2期529-545,共17页畜牧与生物技术杂志（英文版）

基　　金：supported by National Key Research and Development Program of China(2021YFF1000601).

摘　　要：Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

关 键 词：Chromatin accessibility Pig Tissue specific TRANSCRIPTOME Transposable elements 

分 类 号：S828[农业科学—畜牧学]