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Series GSE69464 Query DataSets for GSE69464
Status Public on Jul 03, 2015
Title SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Genome stability relies on epigenetic mechanisms that enforce repression of endogenous retroviruses (ERVs). Current evidence suggests that distinct chromatin-based mechanisms repress ERVs in cells of embryonic origin (histone methylation-dominant) versus more differentiated cells (DNA methylation-dominant). However, the latter aspect of this model has not been tested. Remarkably, and in contrast to the prevailing model, we find that repressive histone methylation catalyzed by the enzyme SETDB1 is critical for suppression of specific ERV families and exogenous retroviruses in committed B-lineage cells from adult mice. The profile of ERV activation in SETDB1-deficient B cells is distinct from that observed in corresponding embryonic tissues, despite the loss of repressive chromatin modifications at all ERVs. We provide evidence that, upon loss of SETDB1, ERVs are activated in a lineage-specific manner depending on the set of transcription factors available to target proviral regulatory elements. These findings have important implications for genome stability in somatic cells, as well as the interface between epigenetic repression and viral latency.
 
Overall design Expression profiling and bisulfite PCR sequencing in Setdb1 C/C and Setdb1 D/D pro-B cells
 
Contributor(s) Collins PL, Kyle K, Egawa T, Shinkai Y, Oltz EM
Citation(s) 26100872
Submission date Jun 02, 2015
Last update date May 15, 2019
Contact name Patrick Collins
E-mail(s) patlennycollins@yahoo.com
Organization name Washington University
Department Pathology and Immunology
Lab Oltz
Street address 1217 Oakleaf dr
City Saint Louis
State/province MO
ZIP/Postal code 63119
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (2)
GSM1701537 Setdb1_C/C_RNA-seq
GSM1701538 Setdb1_Δ/Δ_RNA-seq
This SubSeries is part of SuperSeries:
GSE69504 SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes
Relations
BioProject PRJNA285753
SRA SRP059027

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Supplementary file Size Download File type/resource
GSE69464_RAW.tar 474.3 Mb (http)(custom) TAR (of BW)
GSE69464_all.genes_RPKM.txt.gz 749.2 Kb (ftp)(http) TXT
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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