GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE58245 Query DataSets for GSE58245
Status Public on Mar 18, 2015
Title Genomic-scale identification of host genes regulated by EBV during lytic cycle [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy 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 Surface IgG on Akata cells was cross-linked by application of anti-IgG and 48 hours later chromatin was prepared from 1 x 10^8 cells. An additional sample was treated with acyclovir to halt viral replication prior to EBV genome replication. Chromatin was fixed, extracted and sheared and precipitated with an antibody to Zta (BZLF1). Sequencing of the precipitated DNA was undertaken and aligned to the EBV and human genomes.
Contributor(s) Sinclair A, Ramasubramanyan S, Patel H, Osborn K, Zuo J, Peters G, Al-Mohammed R, Rowe M, Jenner R
Citation(s) 25779048
Submission date Jun 05, 2014
Last update date Sep 15, 2021
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)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (4)
GSM1404652 input
GSM1404653 input plus acyclovir
GSM1404654 Zta chip
This SubSeries is part of SuperSeries:
GSE58246 Genomic-scale identification of host genes regulated by EBV during the lytic cycle
Reanalyzed by GSE83354
BioProject PRJNA251726
SRA SRP042971

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
GSE58245_20110121_EBV_ChIP_Hs_Akata_combined_Zta_10-7_peaks.bed.gz 71.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap