GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE34785 Query DataSets for GSE34785
Status Public on Mar 09, 2012
Title Genome-wide assay of Vezf1 and RNA Polymerase II binding
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The protein Vezf1 plays multiple roles important for embryonic development. In Vezf1-/- mouse embryonic stem (MES) cells our earlier data showed widespread changes in gene expression profiles, including decreased expression of the full length active isoform of Dnmt3b methyltransferase and concomitant genome wide reduction in DNA methylation. Here we show that, in HeLaS3 cells, there is a strong genome-wide correlation between Vezf1 binding and peaks of elongating Ser2-P Pol ll, reflecting Vezf1 dependent slowing of elongation. In Wt MES cells the elongating form of RNA polymerase II accumulates near Vezf1 binding sites within the dnmt3b gene and at several other Vezf1 sites, and this accumulation is significantly reduced at these sites in Vezf1-/- MES cells. Depending upon genomic location, Vezf1 mediated Pol II pausing can have different regulatory roles in transcription and splicing. We find examples of genes in which Vezf1 binding sites are located near cassette exons, and in which loss of Vezf1 leads to a change in the relative abundance of alternatively spliced messages. We further show that Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 tri-methylation, consistent with the role of histone modifications at alternatively spliced sites.
Overall design Comparison of Vezf1 and RNA Pol II binding in mouse and human cells.
Contributor(s) Gowher H, Brick K, Felsenfeld G
Citation(s) 22308494
Submission date Dec 29, 2011
Last update date May 15, 2019
Contact name Kevin Brick
Organization name NIDDK
Department GBB
Street address 5/205 Memorial Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (9)
GSM866196 HA-flag-Vezf1 ChIP-Seq Sample 1
GSM866197 HA-flag-Vezf1 ChIP-Seq Sample 2
GSM866198 RNA Polymerase 2 ChIP-Seq HELA
SRA SRP010580
BioProject PRJNA151057

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
GSE34785_Input_HELA_Pool_w1000s100.wig.gz 77.5 Mb (ftp)(http) WIG
GSE34785_Input_mm9ES_Vezf1ko_w1000s100.wig.gz 37.4 Mb (ftp)(http) WIG
GSE34785_Input_mm9ES_wt_w1000s100.wig.gz 39.5 Mb (ftp)(http) WIG
GSE34785_Ser2Pol2_HELA_w1000s100.wig.gz 64.7 Mb (ftp)(http) WIG
GSE34785_Ser2Pol2_mm9ES_Vezf1ko_w1000s100.wig.gz 28.7 Mb (ftp)(http) WIG
GSE34785_Ser2Pol2_mm9ES_wt_w1000s100.wig.gz 28.9 Mb (ftp)(http) WIG
GSE34785_Vezf1_HELA_Pool_w1000s100.wig.gz 85.0 Mb (ftp)(http) WIG
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