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| 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
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| 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.
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| Overall design |
Each EBNA3 was tagged individually in recombinant viruses and ChIP-seq was performed to determine global localization of each EBNA3.
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| Contributor(s) |
Paschos K, Allday M |
| Citation(s) |
27903901 |
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| Submission date |
Oct 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Allday |
| Organization name |
Imperial College London
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| Department |
Medicine
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| Lab |
Allday
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| Street address |
Norfolk Place
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| City |
London |
| State/province |
London |
| ZIP/Postal code |
W2 1PG |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA348375 |
| SRA |
SRP091520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE88729_RAW.tar |
360.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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