Identification Of Conserved Non-coding Elements In Yak Genome Using ATAC-seq

Conserved non-coding elements(CNEs)are non-coding sequences that do not encode proteins and do not encode rRNA or tRNA in the genome,but are extremely conserved during evolution.CNEs are universal in the genome and tend to cluster in the vicinity of genes with regulatory roles in multicellular development.In the genome,CNEs are possible as regulatory elements directly or indirectly in the regulation of gene expression,play an important role in the development,phenotype and adaptive evolution of different species.The yak is the domestic animal of the bovidae that can thrive in the Qinghai-Tibet plateau(QTP)has formed a unique morphology and physiological mechanism to adapt to high altitude environment.Recently,multi-omics research has studied the high altitude adaptation mechanism of yak from different levels such as genome,transcriptome,re-sequencing and microRNA profiles.Although numerous genes have been identified as being related to high-altitude adaptation,there are still few systematic research the adaptation to high-altitude of regulatory elements and regulation mechanisms.We identified CNEs of yaks by comparative genomics and performed ATAC-seq of yak heart tissue to reveal sequences with regulatory activity in the whole genome.Study identifies CNEs associated with plateau adaptation in the yak genome,providing new candidate elements and new perspectives for understanding the plateau adaptation mechanism in yaks.First,the comparative genomics method was used to perform multiple alignment sequence of genomic sequences from seven species: bison,wisent,yak,cattle,indicus,buffalo and gayal.Based on PhastCons software,3,653 candidate CNEs with regulatory functions were identified.GO enrichment analysis of CNEs-related genes revealed the presence of functions related to germline angiogenesis,embryonic cardiovascular development,and vascular endothelial growth factor,which are associated with the adaptation of yaks to plateau environments.Further functional annotation of these CNEs-related genes revealed 33 genes associated with plateau adaptation,including reported genes related to hypoxia-inducible pathway ARNT,genes related to vascular endothelial growth ANGPTL4,VAV3,and genes related to cardiac regulation CAMK2 D.These CNEs may participate in the regulation of the above genes,thereby playing an important role in yak adaptation to the plateau environment.Second,chromatin accessibility landscape of three yak heart tissues was performed using ATAC-seq technology.A total of 28 G raw data was generated,with an average output of 216,178,322 raw reads.After quality control and comparison,a total of 332,265 regulatory peaks were obtained in the genome,of which more than 60% of the peaks fell in the intergenic region and more than 20% in the intron region,indicating high data quality and functionalities in chromatin open regions which we identified.Finally,the results of the CNEs and ATAC-seq were integrated to obtain 252 CNEs with regulatory functions.These CNEs are the most conserved sequences elements in the yak genome and are supported by yak heart ATAC-seq,and may have important functions.GO enrichment analysis of the genes in the vicinity of these CNEs revealed they were mainly related to functions such as oxygen activity response,monooxygenase activity regulation,nitric oxide synthase activity regulation,cardiac contractility regulation,and angiotensin receptor activity,indicating that CNEs are highly likely to be involved in the regulatory expression of target genes as important functional elements in the yak adaptation plateau.In this study,we identified CNEs in the yak genome by comparative genomics,constructed the chromatin accessibility landscape of yak heart by ATAC-seq,and found CNEs with regulatory functions related to the adaptation of yaks in high altitude adaptation.This study explores the plateau adaptive regulatory mechanism from the perspective of regulatory elements,which not only provides new genetic data for the study of plateau adaptive regulatory elements,but also provides new insights for understanding the yak plateau adaptive mechanism.