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Series GSE134198 Query DataSets for GSE134198
Status Public on Oct 30, 2019
Title Control of RNA pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Control of transcription speed, which influences many co-transcriptional processes, is poorly understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA pol II elongation rate. The PNUTS W401A mutation, which disrupts PP1 binding, causes genome-wide acceleration of transcription associated with hyper-phosphorylation of the Spt5 elongation factor. Immediately downstream of poly(A) sites, pol II decelerates from >2kb/min to <1 kb/min, which correlates with Spt5 dephosphorylation. Pol II deceleration and Spt5 dephosphorylation require poly(A) site recognition and the PNUTS-PP1 complex, which is in turn necessary for transcription termination. These results lead to a new model for termination, the “sitting duck torpedo” mechanism, where poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert pol II into a viable target for the Xrn2 terminator exonuclease. Spt5 and its bacterial homologue NusG therefore have related functions controlling kinetic competition between RNA polymerases and the termination factors that pursue them.
Overall design Transcription elongation rates were determined within gene bodies and dwonstream of termination sites by mapping pol II positions after release of a DRB block or after inhibiting initiation with triptolide. Elongation rates were estimated under conditions where termination was inhibited by a dominant negative mutants of the exonuclease Xrn2 or the PP! nuclear targeting subunit, PNUTS. In addition Spt5 phosphorylation was measured by ChIP and found to correlate closely with chages in elongation rate.
Contributor(s) Bentley D, Erickson B
Citation(s) 31677974
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 GM118051 Coupling of transcription with nascent pre-mRNA metabolism UNIVERSITY OF COLORADO DENVER DAVID Leonard BENTLEY
Submission date Jul 12, 2019
Last update date Feb 03, 2020
Contact name David Bentley
Phone 3037243237
Organization name UCD AMC
Department BMG
Lab Bentley
Street address 12801 E. 17th Ave, RC1 So. RM 10401D
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (84)
GSM3938680 293FlpIN_pcDNA5_Xrn2_WT_DRB_PolII
GSM3938681 293FlpIN_pcDNA5_Xrn2_WT_DRB_WashOut_T5_PolII
GSM3938682 293FlpIN_pcDNA5_Xrn2_WT_DRB_WashOut_T10_PolII
BioProject PRJNA554298
SRA SRP214452

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Supplementary file Size Download File type/resource
GSE134198_RAW.tar 15.2 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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