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Series GSE97827 Query DataSets for GSE97827
Status Public on May 24, 2017
Title RNA pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD phosphorylation and transcriptional direction
Organisms Saccharomyces cerevisiae; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Using pol II mutants in human cells we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; H3K36me3 shifted within genes toward 5’ ends and H3K4me2 extended further upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5’ ends of genes that is conserved in yeast. We propose a “dwell-time in the target zone” model to explain the effects of transcriptional dynamics on establishment of co-transcriptionally deposited protein modifications. Promoter-proximal Ser2 phosphorylation is associated with longer pol II dwell time at start sites and reduced transcriptional polarity due to strongly enhanced divergent antisense transcription at promoters.
 
Overall design The effect of transcription elongation rate on histone H3K36me3, H3K4me2 and pol II CTD phosphorylation was analyzed by ChIP-seq in isogenic human HEK293 cell lines that inducibly express a-amanitin resistant mutants of the RNA polymerase II large subunit with slow elongation rates. Anti-pol II total nascent RNA sequencing (tNET-seq) was developed to assay transcription by WT and slow pol II. Slow pol II mutants in S. cerevisiae were also assayed for pol II CTD Ser2 phosphorylation.
 
Contributor(s) Bentley D, Erickson B
Citation(s) 28506463
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM058613 Coupling of transcription with pre-mRNA metabolism UNIVERSITY OF COLORADO DENVER DAVID Leonard BENTLEY
R35 GM118051 Coupling of transcription with nascent pre-mRNA metabolism UNIVERSITY OF COLORADO DENVER DAVID Leonard BENTLEY
Submission date Apr 14, 2017
Last update date Jul 25, 2021
Contact name David L. Bentley
E-mail(s) david.bentley@ucdenver.edu
Organization name U. Colorado School of Medicine
Department Biochemistry and Mol. Genetics
Street address 12801 E. 17th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (4)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (53)
GSM2579051 ChIP-seq H3K36me3 WT pol II Rep1
GSM2579052 ChIP-seq H3K36me3 WT pol II Rep2
GSM2579053 ChIP-seq H3K36me3 R749H pol II Rep1
Relations
BioProject PRJNA382974
SRA SRP103940

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
GSE97827_H1108Y_tNetSeq_merge_negative_bedgraph.tdf 35.0 Mb (ftp)(http) TDF
GSE97827_H1108Y_tNetSeq_merge_positive_bedgraph.tdf 34.5 Mb (ftp)(http) TDF
GSE97827_R749H_Ser2p_tNetSeq_negative_bedgraph.tdf 15.5 Mb (ftp)(http) TDF
GSE97827_R749H_Ser2p_tNetSeq_postive_bedgraph.tdf 15.2 Mb (ftp)(http) TDF
GSE97827_R749H_tNetSeq_merge_negative_bedgraph.tdf 78.0 Mb (ftp)(http) TDF
GSE97827_R749H_tNetSeq_merge_positive_bedgraph.tdf 75.4 Mb (ftp)(http) TDF
GSE97827_RAW.tar 3.3 Gb (http)(custom) TAR (of BW)
GSE97827_WT_Ser2p_negative.bedgraph.tdf 26.1 Mb (ftp)(http) TDF
GSE97827_WT_Ser2p_positive.bedgraph.tdf 25.3 Mb (ftp)(http) TDF
GSE97827_WT_tNetSeq_merge_negative.bedgraph.tdf 89.3 Mb (ftp)(http) TDF
GSE97827_WT_tNetSeq_merge_positive.bedgraph.tdf 85.5 Mb (ftp)(http) TDF
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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