Accession	GSE246059
Status	2024/3/12
Title	Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ATAC-Seq)
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	There are two major types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) like RBPJ, EBF1, and SPI1, type 2 EBNA2 shares only ~50% amino acid identity and may have distinct effects on the genome. In this study, we examined EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Our analyses revealed that both types 1 and 2 EBNA2 strongly bind to SPI1 and AP-1 motifs (BATF and JUNB). However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 with RBPJ. These differences in b hTF co-occupancy revealed type-specific gene expression of known EBNA2 targets. Both type 1 and 2 EBNA2 binding events were highly enriched at systemic lupus erythematosus (SLE) and showed type-specific enrichment at the risk loci of multiple sclerosis (type 1) and primary biliary cholangitis (type 2). Collectively, this study reveals extensive type-specific EBNA2 interactions with the human genome, genotype-dependent binding, and distinct associations with autoimmune disorders. Our results highlight the importance of considering EBV type in disease-related investigations.
Samples	GSM ID Sample info Characteristics Description GSM7854721 ATAC-seq: AG876 Replicate 1 cell line: AG876;virus type: EBV2;virus strain: AG876 - GSM7854722 ATAC-seq: AG876 Replicate 2 cell line: AG876;virus type: EBV2;virus strain: AG876 - GSM7854723 ATAC-seq: Jiyoye Replicate 1 cell line: Jiyoye;virus type: EBV2;virus strain: Jiyoye - GSM7854724 ATAC-seq: Jiyoye Replicate 2 cell line: Jiyoye;virus type: EBV2;virus strain: Jiyoye - GSM7854725 ATAC-seq: GM12878 Replicate 1 cell line: GM12878;virus type: EBV1;virus strain: B958 - GSM7854726 ATAC-seq: GM12878 Replicate 2 cell line: GM12878;virus type: EBV1;virus strain: B958 - GSM7854727 ATAC-seq: MutuIII Replicate 1 cell line: MutuIII;virus type: EBV1;virus strain: Mutu - GSM7854728 ATAC-seq: MutuIII Replicate 2 cell line: MutuIII;virus type: EBV1;virus strain: Mutu -
Platform	GPL18573  GPL24676  : Illumina NextSeq 500 (Homo sapiens);Illumina NovaSeq 6000 (Homo sapiens)
Literature	38475709
Download	Download Genome Binding/Occupancy Profiling Analysis Data