Accession	GSE246060
Status	2024/3/12
Title	Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ChIP-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 GSM7854729 BATF ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Santa Cruz sc-100974 - GSM7854730 BATF ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Santa Cruz sc-100974 - GSM7854731 BATF ChIP-seq: Jiyoye Replicate 1 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Santa Cruz sc-100974 - GSM7854732 BATF ChIP-seq: Jiyoye Replicate 2 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Santa Cruz sc-100974 - GSM7854733 EBF1 ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Santa Cruz sc-137065 - GSM7854734 EBF1 ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Santa Cruz sc-137065 - GSM7854735 EBNA2 ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Abcam ab90543 - GSM7854736 EBNA2 ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Abcam ab90543 - GSM7854737 EBNA2 ChIP-seq: Jiyoye Replicate 1 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Abcam ab90543 - GSM7854738 EBNA2 ChIP-seq: Jiyoye Replicate 2 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Abcam ab90543 - GSM7854739 EBNA2 ChIP-seq: GM12878 Replicate 1 cell line:GM12878; virus type:EBV1; virus strain:B958; chip antibody:Abcam ab90543 - GSM7854740 EBNA2 ChIP-seq: GM12878 Replicate 2 cell line:GM12878; virus type:EBV1; virus strain:B958; chip antibody:Abcam ab90543 - GSM7854741 JUNB ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Active Motif 39549 - GSM7854742 JUNB ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:Active Motif 39549 - GSM7854743 JUNB ChIP-seq: JIyoye Replicate 1 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Active Motif 39549 - GSM7854744 JUNB ChIP-seq: JIyoye Replicate 2 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:Active Motif 39549 - GSM7854745 RBPJ ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:CST 5313 - GSM7854746 RBPJ ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:CST 5313 - GSM7854747 RBPJ ChIP-seq: Jiyoye Replicate 1 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:CST 5313 - GSM7854748 RBPJ ChIP-seq: Jiyoye Replicate 2 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:CST 5313 - GSM7854749 RBPJ ChIP-seq: GM12878 Replicate 1 cell line:GM12878; virus type:EBV1; virus strain:B958; chip antibody:CST 5313 - GSM7854750 RBPJ ChIP-seq: GM12878 Replicate 2 cell line:GM12878; virus type:EBV1; virus strain:B958; chip antibody:CST 5313 - GSM7854751 SPI1 ChIP-seq: AG876 Replicate 1 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:CST 2266 - GSM7854752 SPI1 ChIP-seq: AG876 Replicate 2 cell line:AG876; virus type:EBV2; virus strain:AG876; chip antibody:CST 2266 - GSM7854753 SPI1 ChIP-seq: Jiyoye Replicate 1 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:CST 2266 - GSM7854754 SPI1 ChIP-seq: Jiyoye Replicate 2 cell line:Jiyoye; virus type:EBV2; virus strain:Jiyoye; chip antibody:CST 2266 -
Platform	GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature	38475709
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