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Series GSE115682 Query DataSets for GSE115682
Status Public on May 21, 2020
Title Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both are enriched in coding regions, and H2Bub1 levels are directly proportional to those of phospho-Spt5. Cdk9-dependence of antisense suppression correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Combined reduction of Cdk9 activity and loss of H2Bub1 prevent recruitment of the histone deacetylase Clr6-CII to transcribed genes, and lead to decreased histone occupancy and increased histone acetylation within gene coding regions. These results uncover new pathways linking regulators of RNAPII transcription elongation to suppression of aberrant antisense transcription, and demonstrate novel interactions between co-transcriptional histone modification pathways.
 
Overall design ChIP-seq: Data represent eighteen different ChIP-seq experiments in S. pombe, performed in biological replicates. There are raw sequencing files for all biological replicates and processed files after combining the replicates.

Please note that the *Combined.bigwig processed data was generated from both rep1 and rep2 data combined and is available as Series supplementary files.
 
Contributor(s) Parua PK, Sansó M, Tanny JC
Citation(s) 32496538
Submission date Jun 12, 2018
Last update date Jul 27, 2020
Contact name Robert P Fisher
E-mail(s) robert.fisher@mssm.edu
Phone 2126598677
Organization name Icahn School of Medicine at Mount Sinai
Department Oncological Sciences
Lab 15-76
Street address One Gustave L. Levy Place, Box 1130, L15-76
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platforms (2)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
GPL20584 Illumina NextSeq 500 (Schizosaccharomyces pombe)
Samples (24)
GSM3187616 Input_rep1
GSM3187617 Input_rep2
GSM3187618 H2B_rep1
Relations
BioProject PRJNA475759
SRA SRP150346

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
GSE115682_RAW.tar 194.8 Mb (http)(custom) TAR (of BIGWIG)
GSE115682_cdk9as_3mb_myc.bigwig 42.0 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_3mb_pol2.bigwig 3.9 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_dmso_myc.bigwig 3.8 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_dmso_pol2.bigwig 3.9 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_htb1kr_3mb_myc.bigwig 3.8 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_htb1kr_3mb_pol2.bigwig 3.9 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_htb1kr_dmso_myc.bigwig 3.8 Mb (ftp)(http) BIGWIG
GSE115682_cdk9as_htb1kr_dmso_pol2.bigwig 3.9 Mb (ftp)(http) BIGWIG
GSE115682_chipseq_H2B_Combined.bigwig 100.5 Mb (ftp)(http) BIGWIG
GSE115682_chipseq_H2Bub1_Combined.bigwig 94.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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