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Series GSE38411 Query DataSets for GSE38411
Status Public on Jun 02, 2012
Title Cohesins Repress KSHV Immediate Early Gene Transcription During Latency
Organisms Homo sapiens; Human gammaherpesvirus 8
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin-organizing factors, like CTCF and cohesins, have been implicated in the control of complex viral regulatory programs. We investigated the role of CTCF and cohesin in the control of the latent to lytic switch for Kaposi's Sarcoma-Associated Herpesvirus (KSHV). We found that cohesin subunits, but not CTCF, were required for the repression of KSHV immediate early gene transcription. Depletion of cohesin subunits Rad21, SMC1, or SMC3 resulted in lytic cycle gene transcription and viral DNA replication. In contrast, depletion of CTCF failed to induce lytic transcription or DNA replication. ChiP-Seq analysis revealed that cohesins and CTCF bound to several sites within the immediate early control regions for ORF50 and more distal 5' sites that also regulate the divergently transcribed ORF45-46-47 gene cluster. Rad21 depletion led to a robust increase in ORF45 and ORF47 transcripts, with similar kinetics to that observed with chemical induction by sodium butyrate. During latency, the chromatin between the ORF45 and ORF50 transcription start sites was enriched in histone H3K4me3 with elevated H3K9ac at the ORF45 promoter and elevated H3K27me3 at the ORF50 promoter. A paused form of RNA pol II was loosely associated with the ORF45 promoter region during latency, but was converted to an active elongating form upon reactivation induced by Rad21 depletion. Butyrate-induced transcription of ORF45 and ORF47 was resistant to cyclohexamide, suggesting that these genes have immediate early features similar to ORF50. Butyrate-treatment caused the rapid dissociation of cohesins and loss of CTCF binding at the immediate early gene locus, suggesting that cohesins may be a direct target of butyrate-mediated lytic induction. Our findings implicate cohesins as a major repressor of KSHV lytic gene activation, and function coordinately with CTCF to regulate the switch between latent and lytic gene activity.
Overall design Study of chromatin-organizing factors, like CTCF and cohesins.
Contributor(s) Chen HS, Wikramasinghe P, Showe L, Lieberman PM
Citation(s) 22740398
Submission date Jun 01, 2012
Last update date May 15, 2019
Contact name Priyankara J Wickramasinghe
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL15642 Illumina Genome Analyzer II (Human herpesvirus 8)
Samples (5)
GSM941710 CTCF_ChIPSeq
GSM941711 SMC1_ChIPSeq
BioProject PRJNA167828
SRA SRP013484

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38411_RAW.tar 650.0 Kb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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