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Series GSE102590 Query DataSets for GSE102590
Status Public on Jun 07, 2018
Title A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
Organism Schizosaccharomyces pombe
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to ensure proper mRNA maturation and prevent interference between neighboring genes. Pol II slowing downstream of the cleavage and polyadenylation signal (CPS) leads to recruitment of cleavage and polyadenylation factors and termination, but how this chain of events is initiated remains unclear. In a chemical-genetic screen we identified protein phosphatase 1 (PP1) isoforms as substrates of human positive transcription elongation factor b (P-TEFb), the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 complex. Here we show that Cdk9 and PP1 govern phosphorylation of the conserved transcription factor Spt5 in the fission yeast Schizosaccharomyces pombe. Cdk9 phosphorylates both Spt5 and a negative regulatory site on the PP1 isoform Dis2. Sites phosphorylated by Cdk9 in the Spt5 carboxy-terminal domain (CTD) are dephosphorylated by Dis2 in vitro, and Cdk9 inhibition in vivo leads to rapid Spt5 dephosphorylation that is retarded by concurrent Dis2 inactivation. Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis indicates that Spt5 is dephosphorylated as transcription complexes traverse the CPS, prior to or concomitant with Pol II pausing. A Dis2-inactivating mutation stabilizes Spt5 phosphorylation (pSpt5) on chromatin, promotes transcription beyond the normal termination zone detected by precision run-on transcription and sequencing (PRO-seq), and is suppressed by ablation of Cdk9 target sites in Spt5. These results support a model whereby the transition of Pol II from elongation to termination is regulated by opposing activities of Cdk9 and Dis2 towards their common substrate Spt5—a bistable switch analogous to a Cdk1-PP1 module that controls exit from mitosis.
 
Overall design PRO-seq: Data represent 20 different treatments of various S. pombe strains performed in biological replicates. There are processed files for both replicates and combined replicate data for each experiment.
ChIP-seq: Data represent 6 different ChIP-seq experiments in S. pombe, performed in biological replicates. There are raw and processed files for all biological replicates.
ChIP-seq: Data represent 16 different ChIP-seq experiments in S. pombe, performed in biological replicates. There are raw and processed files for all biological replicates.
PRO-seq: Experiment was done in five different S. pombe strains as biological duplicates. There are processed files for both replicates and combined replicate data for each sample.
 
Contributor(s) Parua PK, Booth GT, Sanso M, Tanny J
Citation(s) 29899453, 32496538
Submission date Aug 11, 2017
Last update date Jul 25, 2021
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 (52)
GSM2741479 18C_Cdk9as_DMSO_rep1
GSM2741480 18C_Cdk9as_DMSO_rep2
GSM2741481 18C_Cdk9as_3MBPP1_rep1
Relations
BioProject PRJNA398083
SRA SRP115327

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
GSE102590_7772_7157_43149_HVLYCBGXY_pombe_18C_Cdk9as_DMSO_COMBINED_GGCTAC_R1_pombe_SpikeNormed_minus.bw 9.3 Mb (ftp)(http) BW
GSE102590_7772_7157_43149_HVLYCBGXY_pombe_18C_Cdk9as_DMSO_COMBINED_GGCTAC_R1_pombe_SpikeNormed_plus.bw 9.1 Mb (ftp)(http) BW
GSE102590_7772_7157_43150_HVLYCBGXY_pombe_18C_Cdk9as_3MBPP1_COMBINED_CTTGTA_R1_pombe_SpikeNormed_minus.bw 8.2 Mb (ftp)(http) BW
GSE102590_7772_7157_43150_HVLYCBGXY_pombe_18C_Cdk9as_3MBPP1_COMBINED_CTTGTA_R1_pombe_SpikeNormed_plus.bw 8.2 Mb (ftp)(http) BW
GSE102590_7772_7157_43151_HVLYCBGXY_pombe_18C_dis2ts_DMSO_COMBINED_ATTCCT_R1_pombe_SpikeNormed_minus.bw 5.7 Mb (ftp)(http) BW
GSE102590_7772_7157_43151_HVLYCBGXY_pombe_18C_dis2ts_DMSO_COMBINED_ATTCCT_R1_pombe_SpikeNormed_plus.bw 5.6 Mb (ftp)(http) BW
GSE102590_7772_7157_43152_HVLYCBGXY_pombe_18C_dis2ts_3MBPP1_COMBINED_CAAAAG_R1_pombe_SpikeNormed_minus.bw 5.4 Mb (ftp)(http) BW
GSE102590_7772_7157_43152_HVLYCBGXY_pombe_18C_dis2ts_3MBPP1_COMBINED_CAAAAG_R1_pombe_SpikeNormed_plus.bw 5.3 Mb (ftp)(http) BW
GSE102590_7772_7157_43153_HVLYCBGXY_pombe_30C_dis2ts_DMSO_COMBINED_CAACTA_R1_pombe_SpikeNormed_minus.bw 6.6 Mb (ftp)(http) BW
GSE102590_7772_7157_43153_HVLYCBGXY_pombe_30C_dis2ts_DMSO_COMBINED_CAACTA_R1_pombe_SpikeNormed_plus.bw 6.5 Mb (ftp)(http) BW
GSE102590_7772_7157_43154_HVLYCBGXY_pombe_30C_dis2ts_3MBPP1_COMBINED_CACCGG_R1_pombe_SpikeNormed_minus.bw 5.5 Mb (ftp)(http) BW
GSE102590_7772_7157_43154_HVLYCBGXY_pombe_30C_dis2ts_3MBPP1_COMBINED_CACCGG_R1_pombe_SpikeNormed_plus.bw 5.4 Mb (ftp)(http) BW
GSE102590_7772_7157_43155_HVLYCBGXY_pombe_18C_Cdk9as_dis2ts_DMSO_COMBINED_CACGAT_R1_pombe_SpikeNormed_minus.bw 5.7 Mb (ftp)(http) BW
GSE102590_7772_7157_43155_HVLYCBGXY_pombe_18C_Cdk9as_dis2ts_DMSO_COMBINED_CACGAT_R1_pombe_SpikeNormed_plus.bw 5.6 Mb (ftp)(http) BW
GSE102590_7772_7157_43156_HVLYCBGXY_pombe_18C_Cdk9as_dis2ts_3MBPP1_COMBINED_CACTCA_R1_pombe_SpikeNormed_minus.bw 6.5 Mb (ftp)(http) BW
GSE102590_7772_7157_43156_HVLYCBGXY_pombe_18C_Cdk9as_dis2ts_3MBPP1_COMBINED_CACTCA_R1_pombe_SpikeNormed_plus.bw 6.5 Mb (ftp)(http) BW
GSE102590_7772_7157_43157_HVLYCBGXY_pombe_30C_Cdk9as_dis2ts_DMSO_COMBINED_CAGGCG_R1_pombe_SpikeNormed_minus.bw 5.5 Mb (ftp)(http) BW
GSE102590_7772_7157_43157_HVLYCBGXY_pombe_30C_Cdk9as_dis2ts_DMSO_COMBINED_CAGGCG_R1_pombe_SpikeNormed_plus.bw 5.4 Mb (ftp)(http) BW
GSE102590_7772_7157_43158_HVLYCBGXY_pombe_30C_Cdk9as_dis2ts_3MBPP1_COMBINED_CATGGC_R1_pombe_SpikeNormed_minus.bw 5.4 Mb (ftp)(http) BW
GSE102590_7772_7157_43158_HVLYCBGXY_pombe_30C_Cdk9as_dis2ts_3MBPP1_COMBINED_CATGGC_R1_pombe_SpikeNormed_plus.bw 5.3 Mb (ftp)(http) BW
GSE102590_ChIPSeq_Spt5_Myc_Combined.bedgraph.gz 93.3 Mb (ftp)(http) BEDGRAPH
GSE102590_ChIPSeq_pSpt5_Combined.bedgraph.gz 109.8 Mb (ftp)(http) BEDGRAPH
GSE102590_Concatenate_pp_chipseq_MACS2_dis2cs_IgG.bigwig 42.0 Mb (ftp)(http) BIGWIG
GSE102590_Concatenate_pp_chipseq_MACS2_dis2cs_myc.bigwig 78.4 Mb (ftp)(http) BIGWIG
GSE102590_Concatenate_pp_chipseq_MACS2_dis2cs_pSpt5.bigwig 85.9 Mb (ftp)(http) BIGWIG
GSE102590_Concatenate_pp_chipseq_MACS2_wt_IgG.bigwig 42.6 Mb (ftp)(http) BIGWIG
GSE102590_Concatenate_pp_chipseq_MACS2_wt_myc.bigwig 80.4 Mb (ftp)(http) BIGWIG
GSE102590_Concatenate_pp_chipseq_MACS2_wt_pSpt5.bigwig 84.7 Mb (ftp)(http) BIGWIG
GSE102590_RAW.tar 1.1 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG, BW)
GSE102590_ePROseq_Pombe_Fisher_WT_COMBINED_pombe_spikeNormed_minus.bw 2.8 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_WT_COMBINED_pombe_spikeNormed_plus.bw 2.8 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2Del_COMBINED_pombe_spikeNormed_minus.bw 3.0 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2Del_COMBINED_pombe_spikeNormed_plus.bw 2.9 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_11_COMBINED_pombe_spikeNormed_minus.bw 4.7 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_11_COMBINED_pombe_spikeNormed_plus.bw 4.7 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_T316A_COMBINED_pombe_spikeNormed_minus.bw 4.2 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_T316A_COMBINED_pombe_spikeNormed_plus.bw 4.1 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_T316D_COMBINED_pombe_spikeNormed_minus.bw 4.6 Mb (ftp)(http) BW
GSE102590_ePROseq_Pombe_Fisher_dis2_T316D_COMBINED_pombe_spikeNormed_plus.bw 4.5 Mb (ftp)(http) BW
GSE102590_pp_chipseq_IgGSubtracted_dis2cs_myc.bigwig 7.8 Mb (ftp)(http) BIGWIG
GSE102590_pp_chipseq_IgGSubtracted_dis2cs_pSpt5.bigwig 7.9 Mb (ftp)(http) BIGWIG
GSE102590_pp_chipseq_IgGSubtracted_wt_myc.bigwig 7.9 Mb (ftp)(http) BIGWIG
GSE102590_pp_chipseq_IgGSubtracted_wt_pSpt5.bigwig 7.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file

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