表观遗传学
表观基因组
生物
遗传学
表观遗传学
基因组
染色质
染色质免疫沉淀
表达数量性状基因座
国际人类基因组单体型图计划
计算生物学
基因
人类基因组
DNA甲基化
基因表达
单核苷酸多态性
发起人
基因型
作者
Cristian Groza,X Chen,Alain Pacis,Simon Maguire,Albéna Pramatarova,Katherine A. Aracena,Tomi Pastinen,Luis B. Barreiro,Guillaume Bourque
出处
期刊:Cell genomics
[Elsevier]
日期:2023-05-01
卷期号:3 (5): 100294-100294
被引量:2
标识
DOI:10.1016/j.xgen.2023.100294
摘要
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
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