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Series GSE98498 Query DataSets for GSE98498
Status Public on Nov 13, 2017
Title The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [DNA-seq]
Organisms Homo sapiens; human gammaherpesvirus 4
Experiment type Other
Summary Using chromatin conformation capture methods, we learned that the latent episome of the human Epstein-Barr virus (EBV) displays preferential chromosome association that correlates with gene density. The episome avoids gene-rich chromosomes and favors gene-poor chromosomes. Kaposi’s sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not, suggesting limited evolutionary conservation of this strategy. Moreover, the strongest contacts we detected between the human genome and EBV episome localized to OriP, the latent origin of replication. This genetic element, and the EBNA1 protein that binds there, are sufficient to reconstitute chromosome association preferences of the entire episome. Upon reactivation from latency, however, these preferences are lost. Detailed mapping of changes in interchromosomal contacts reveal that the episome moves away from repressive heterochromatin and toward activating euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during the genetic switch from EBV latency to reactivation. The involvement of only a myriad of interchromosomal contacts also argues for a possible role of this type of long-range association in gene regulation.
Overall design DNA-seq examination of viral DNA in latent LGNFR- and reactivated LGNFR+ Akata-ZTA cells pre-treated with acyclovir and induced with doxycycline.

Please note that the wig files are a slightly modified format in that they display a viral genome not available as a chromosome on the UCSC genome browser. The wig files are readable by the IGV browser (as described in the associated publication).
Contributor(s) Moquin SA, Miranda JL
Citation(s) 29142137
Submission date May 03, 2017
Last update date Jul 25, 2021
Contact name JJ Miranda
Organization name Barnard College, Columbia University
Street address 3009 Broadway
City New York
ZIP/Postal code 10027
Country USA
Platforms (1)
GPL23362 Illumina HiSeq 4000 (Homo sapiens; Human gammaherpesvirus 4)
Samples (10)
GSM2597432 ATZ LGNFR+ DNA seq rep 1
GSM2597433 ATZ LGNFR- DNA seq rep 1
GSM2597434 ATZ LGNFR+ DNA seq rep 2
This SubSeries is part of SuperSeries:
GSE98123 The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation
BioProject PRJNA385273
SRA SRP106325

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
GSE98498_RAW.tar 8.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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