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Series GSE57732 Query DataSets for GSE57732
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
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.
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.
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
Organization name University of Sussex
Department School of Life Sciences
Lab Biochemistry and Bioscience
Street address University of Sussex
City Brighton
State/province E. Sussex
ZIP/Postal code BN1 9QG
Country United Kingdom
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1387801 Control B cell RNASeq biological replicate 1
GSM1387802 Control B cell RNASeq biological replicate 2
GSM1387803 BZLF1 B cell RNASeq biological replicate 1
This SubSeries is part of SuperSeries:
GSE58246 Genomic-scale identification of host genes regulated by EBV during the lytic cycle
BioProject PRJNA247968
SRA SRP042043

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Supplementary file Size Download File type/resource
GSE57732_CONTROLvsBZLF1.RNASeq.edgeR.DE_results.tsv.gz 631.2 Kb (ftp)(http) TSV
GSE57732_CONTROLvsBZLF1.RNASeq.genes.counts.tsv.gz 299.2 Kb (ftp)(http) TSV
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