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| Status |
Public on Mar 18, 2015 |
| Title |
Genomic-scale identification of host genes regulated by EBV during lytic cycle [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Infection of resting primary B-lymphocytes by Epstein Barr virus (EBV) generates a population of cells that are effectively immortal. This represents the first step in the establishment of life-long viral latency in vivo and generates precursors that can develop into the lymphoid malignancies. However, virus spread requires a switch from latency to the lytic replication cycle, a process orchestrated by the virally encoded protein Zta, an AP1-like transcription factor that interacts with a 7 base-pair DNA sequence element. As Zta has the potential to reprogram the patterns of gene expression in the host cell, we undertook global transcriptome analyses (RNA sequencing) in a BurkittÂ’s lymphoma derived cell line in which the Zta is expressed from an inducible promoter, mimicking the switch from latency to lytic cycle. We identified 2,263 host genes whose expression levels were altered. In parallel, we performed chromatin precipitation and next-generation DNA sequencing (ChIP-Seq) to identify genes that are direct targets of Zta. Integrating these data sets revealed 277 host genes that appear to be directly regulated by Zta. Surprisingly, the frequency and distribution of the Zta binding peaks suggests that Zta regulates host genes through long-range enhancers, with a median distance of 25.8kb from the transcriptional start site, rather than equivalents of the promoter elements through which Zta regulates viral genes.
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| Overall design |
Akata cells transduced with a plasmid encoding Zta, NGFR and GFP from a doxycycline regulated promoter, and control cells in which the Zta sequences were in the opposite orientation, were treated with 500 ng/ml doxycycline for 24h. The NGFR-expressing cells were isolated with anti-NGFR antibodies coupled to paramagnetic beads. RNA was prepared from two independent populations of control and Zta-expressing cells and the poly A-selected transcripts were analyzed by direct sequencing.
ZTA: also referred to as BZLF1.
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| Contributor(s) |
Ramasubramanyan S, Osborn K, Zou J, Al-Mohammad R, Patel H, Peters G, Rowe M, Jenner RG, Sinclair AJ |
| Citation(s) |
25779048 |
| Submission date |
May 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alison Jane Sinclair |
| E-mail(s) |
a.j.sinclair@sussex.ac.uk
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| Organization name |
University of Sussex
|
| Department |
School of Life Sciences
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| Lab |
Biochemistry and Bioscience
|
| Street address |
University of Sussex
|
| City |
Brighton |
| State/province |
E. Sussex |
| ZIP/Postal code |
BN1 9QG |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (4)
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| GSM1387801 |
Control B cell RNASeq biological replicate 1 |
| GSM1387802 |
Control B cell RNASeq biological replicate 2 |
| GSM1387803 |
BZLF1 B cell RNASeq biological replicate 1 |
| GSM1387804 |
BZLF1 B cell RNASeq biological replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE58246 |
Genomic-scale identification of host genes regulated by EBV during the lytic cycle |
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| Relations |
| BioProject |
PRJNA247968 |
| SRA |
SRP042043 |
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