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Series GSE88729 Query DataSets for GSE88729
Status Public on Nov 12, 2016
Title Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIP-seq performed on lymphoblastoid cell lines (LCLs), expressing epitope-tagged EBNA3A, EBNA3B or EBNA3C from EBV-recombinants, revealed important principles of EBNA3 binding to chromatin. When combined with global chromatin looping data, EBNA3-bound loci were found to have a singular character, each directly associating with either EBNA3-repressed or EBNA3-activated genes, but not with both. EBNA3A and EBNA3C showed significant association with repressed and activated genes. Significant direct association for EBNA3B loci could only be shown with EBNA3B-repressed genes. A comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 revealed substantial co-localization of EBNA3s with RUNX3 – a protein induced by EBV during B cell transformation. The beta-subunit of core binding factor (CBFβ), that heterodimerizes with RUNX3, could co-immunoprecipitate robustly EBNA3B and EBNA3C, but only weakly EBNA3A. Depletion of either RUNX3 or CBFβ with lentivirus-delivered shRNA impaired epitope-tagged EBNA3B and EBNA3C binding at multiple regulated gene loci, indicating a requirement for CBF heterodimers in EBNA3 recruitment during target-gene regulation. ShRNA-mediated depletion of CBFβ in an EBNA3C-conditional LCL confirmed the role of CBF in the regulation of EBNA3C-induced and -repressed genes. These results reveal an important role for RUNX3/CBF during B cell transformation and EBV latency that was hitherto unexplored.
 
Overall design Each EBNA3 was tagged individually in recombinant viruses and ChIP-seq was performed to determine global localization of each EBNA3.
 
Contributor(s) Paschos K, Allday M
Citation(s) 27903901
Submission date Oct 13, 2016
Last update date Mar 20, 2019
Contact name Martin Allday
Organization name Imperial College London
Department Medicine
Lab Allday
Street address Norfolk Place
City London
State/province London
ZIP/Postal code W2 1PG
Country United Kingdom
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (7)
GSM2344873 WT-D11
GSM2344874 3A-TAP-D11
GSM2344875 TAP-3B-D11
Relations
BioProject PRJNA348375
SRA SRP091520

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
GSE88729_RAW.tar 360.0 Kb (http)(custom) TAR (of TXT)
Raw data are available in SRA
Processed data provided as supplementary file

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