A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.

IF 4.4 1区 生物学 Q1 BIOLOGY
Jiaqi Li, Lei Xu, Xiaoyun Liang, Letian Li, Frederic Farnir, Xixia Huang, Qiuming Chen
{"title":"A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.","authors":"Jiaqi Li, Lei Xu, Xiaoyun Liang, Letian Li, Frederic Farnir, Xixia Huang, Qiuming Chen","doi":"10.1186/s12915-025-02257-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Allele-specific expression (ASE) analysis is a crucial tool for validating expression quantitative trait loci (eQTLs), identifying causal variants associated with complex traits, and investigating the genetic mechanisms underlying heterosis. In this study, we characterized ASE variants across 35 tissues using 7532 publicly available RNA-seq datasets. Additionally, we explored the mechanisms driving ASE through integration with epigenomic data and examined the relationship between ASE and dominance effects on gene expression and milk-related traits in Holstein cattle.</p><p><strong>Results: </strong>ASE variants exhibited stronger tissue specificity and lower reproducibility compared to eQTLs. Interestingly, variants with opposite directional effects demonstrated greater resilience across diverse environments. Functional annotation revealed that ASE variants were enriched in both enhancer and promoter regions during transcription and implicated in post-transcriptional and translational processes, including mutations that affect mRNA splicing and trigger nonsense-mediated decay. Analysis of eQTLs, splicing QTLs (sQTLs), and validated QTLs associated with milk-related traits in Holstein cattle, coupled with enrichment analysis in QTL databases and effect size evaluation, indicated that ASE variants were more closely aligned with dominant effects than additive effects, particularly in reproductive and immune-related tissues/traits, which exhibited higher levels of heterosis.</p><p><strong>Conclusions: </strong>Our findings not only enhance our understanding of the genetic mechanisms underlying heterosis and ASE formation but also provide a valuable resource of regulatory variants that can be leveraged to improve economic traits through molecular breeding or the strategic exploitation of heterosis.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"148"},"PeriodicalIF":4.4000,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12915-025-02257-0","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Background: Allele-specific expression (ASE) analysis is a crucial tool for validating expression quantitative trait loci (eQTLs), identifying causal variants associated with complex traits, and investigating the genetic mechanisms underlying heterosis. In this study, we characterized ASE variants across 35 tissues using 7532 publicly available RNA-seq datasets. Additionally, we explored the mechanisms driving ASE through integration with epigenomic data and examined the relationship between ASE and dominance effects on gene expression and milk-related traits in Holstein cattle.

Results: ASE variants exhibited stronger tissue specificity and lower reproducibility compared to eQTLs. Interestingly, variants with opposite directional effects demonstrated greater resilience across diverse environments. Functional annotation revealed that ASE variants were enriched in both enhancer and promoter regions during transcription and implicated in post-transcriptional and translational processes, including mutations that affect mRNA splicing and trigger nonsense-mediated decay. Analysis of eQTLs, splicing QTLs (sQTLs), and validated QTLs associated with milk-related traits in Holstein cattle, coupled with enrichment analysis in QTL databases and effect size evaluation, indicated that ASE variants were more closely aligned with dominant effects than additive effects, particularly in reproductive and immune-related tissues/traits, which exhibited higher levels of heterosis.

Conclusions: Our findings not only enhance our understanding of the genetic mechanisms underlying heterosis and ASE formation but also provide a valuable resource of regulatory variants that can be leveraged to improve economic traits through molecular breeding or the strategic exploitation of heterosis.

等位基因特异性表达的多组织图谱揭示了牛中等位基因特异性表达的特征、机制及其与显性效应的关系。
背景:等位基因特异性表达(ASE)分析是验证表达数量性状位点(eqtl)、鉴定与复杂性状相关的因果变异以及研究杂种优势遗传机制的重要工具。在这项研究中,我们使用7532个公开的RNA-seq数据集对35个组织中的ASE变异进行了表征。此外,我们通过整合表观基因组数据探索了ASE的驱动机制,并研究了ASE与优势效应对荷斯坦牛基因表达和牛奶相关性状的关系。结果:与eqtl相比,ASE变异具有更强的组织特异性和更低的重复性。有趣的是,具有相反方向效应的变异在不同的环境中表现出更大的弹性。功能注释显示,在转录过程中,ASE变体在增强子和启动子区域都富集,并涉及转录后和翻译过程,包括影响mRNA剪接和触发无义介导的衰变的突变。对荷斯坦牛产奶性状相关的eqtl、splicing QTL (sqtl)和验证QTL的分析,结合QTL数据库的富集分析和效应大小评估,表明ASE变异与显性效应的关系比加性效应更紧密,特别是在生殖和免疫相关组织/性状中,表现出更高的杂种优势水平。结论:本研究结果不仅提高了我们对杂种优势和ASE形成的遗传机制的理解,而且为通过分子育种或战略性利用杂种优势来改善经济性状提供了有价值的调控变异资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
BMC Biology
BMC Biology 生物-生物学
CiteScore
7.80
自引率
1.90%
发文量
260
审稿时长
3 months
期刊介绍: BMC Biology is a broad scope journal covering all areas of biology. Our content includes research articles, new methods and tools. BMC Biology also publishes reviews, Q&A, and commentaries.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信