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Series GSE101666 Query DataSets for GSE101666
Status Public on Jul 01, 2019
Title 3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Epstein-Barr Virus (EBV) encoded Nuclear Antigens (EBNAs) and virus activated NF-B subunits mostly bind to enhancers in EBV transformed lymphoblastoid cells lines (LCLs). Using LCL 3D genome organization map that links EBV enhancers to promoters, we built the most comprehensive virus regulome. EBV regulome contained 1992 genes and enhancers directly linked to them. ~30% of genes essential for LCL growth were linked to EBV enhancers. CRISPR knock out of EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets including MCL1, IRF4, and EBF were identified. MYC ESEs looping to MYC TSS was dependent on EBNAs. CRISPR deletions of MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study defines the most comprehensive host-pathogen interactions on the spatial organiz ation of chromatin during infection and cancer.
 
Overall design Discarded human peripheral blood mononuclear cell from healthy anonymous platelet donors were obtained from Dana Farber Cancer Institute blood bank. Viable peripheral blood mononuclear cells were isolated using LymphoprepTM density gradient centrifugation. Resting B cells were isolated by two step immunomagnetic negative selection using EasySep B Cell Isolation Kit and RosetteSep B Cell isolation Kit (StemCell). Total RNAs were prepared and RNAs depleted for ribosomal RNA were sequenced with Illumina HiSeq 2000.
 
Contributor(s) Jiang S, Zhou H, Liang J, Gerdt C, Wang C, Ke L, Schmidt SC, Narita Y, Ma Y, Wang S, Colson T, Gewurz B, Li G, Kieff E, Zhao B
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Submission date Jul 20, 2017
Last update date Jul 25, 2021
Contact name Hufeng Zhou
E-mail(s) williamzhoubwh@gmail.com
Phone 617-525-4263
Organization name Harvard Medical School
Department Department of Microbiology and Molecular Genetics
Lab Kieff Lab
Street address 181 Longwood Ave,
City Boston
State/province M.A
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (3)
GSM2711767 Donor2 RNA-seq Rep1
GSM2711770 Donor2 RNA-seq Rep2
GSM2711773 Donor2 RNA-seq Rep3
Relations
BioProject PRJNA395150
SRA SRP113157

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE101666_RAW.tar 19.7 Mb (http)(custom) TAR (of FPKM_TRACKING, GTF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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