Accession	GSE225704
Status	2023/2/21
Title	Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [ATAC-seq]
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. We tested this in a dataset obtained by sequencing the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after Influenza virus infection, which also allowed us to investigate the potential role of MEIs in immunity. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that 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.
Samples	GSM ID Sample info Characteristics Description GSM7054476 GM12878, ATAC biol rep 1 cell line:GM12878; cell type:lymphoblastoid cell line; infection:influenza - GSM7054477 GM12878, ATAC biol rep 2 cell line:GM12878; cell type:lymphoblastoid cell line; infection:influenza - GSM7054478 GM12878, ATAC biol rep 3 cell line:GM12878; cell type:lymphoblastoid cell line; infection:influenza -
Platform	GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature	37228750
Download	Download Genome Binding/Occupancy Profiling Analysis Data