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Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates trancription termination

ABSTRACT: Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates trancription termination

PROVIDER: PRJNA436595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6796430.fastq.gz	Fastqsanger.gz
	SRR6796440_1.fastq.gz	Fastqsanger.gz
	SRR6796440_2.fastq.gz	Fastqsanger.gz
	SRR6796450.fastq.gz	Fastqsanger.gz
	SRR6796460.fastq.gz	Fastqsanger.gz

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Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates trancription termination

Project description:Termination of RNA polymerase II (Pol II) transcription is a key step, that is important for 3’end formation of functional mRNA, mRNA release and Pol II recycling. Even so, this underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 interacts with Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 de-phosphorylation by the conserved PP1 phosphatase Dis2, which also de-phosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and de-phosphorylation of Pol II C-terminal domain.

2018-12-26 | GSE111326 | GEO

PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA pol II transcription termination

Project description:The restrictor, ZC3H4/WDR82, terminates antisense transcription from bidirectional promoters, but its mechanism is poorly understood. We report that ZC3H4/WDR82 immunoprecipitate with PP1 phosphatase and its nuclear targeting subunit, PNUTS, which binds to WDR82. AlphaFold predicts a complex of PP1/PNUTS with restrictor where both PNUTS and ZC3H4 contact WDR82. A substrate trap, PP1H66K-PNUTS, comprising inactive PP1 fused to the PNUTS C-terminus antagonizes restrictor mediated termination whereas PP1WT-PNUTS has less effect suggesting that phosphatase activity is required for termination. One PP1/PNUTS substrate implicated in termination by restrictor is pol II CTD Ser5-P. PP1H66K-PNUTS induces Ser5-P hyperphosphorylation at 5’ ends presumably by inhibiting dephosphorylation. NET-seq analysis suggests that CTD Ser5 dephosphorylation would promote termination by increasing pol II pausing. Both inhibition of termination and CTD hyperphosphorylation require the WDR82 binding domain of PP1H66K-PNUTS that mediates restrictor binding. In summary, the PP1/PNUTS phosphatase associated with restrictor via WDR82 promotes efficient transcription termination.

2025-04-06 | PXD061598 | Pride

Control of RNA pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism

Project description: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.

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Knockout of PP1 in Leishmania major reveals a critical role for protein phosphatase 1 during RNA polymerase II transcription termination

Project description:Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously identified a complex in Leishmania major and T. brucei composed of PNUTS, PP1, Wdr82 and a J-binding protein (JBP3). We show that deletion of PP1 in L. major leads to readthrough transcription and expression of downstream genes.

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PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [eNET-seq]

Project description:The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. A chimera comprising inactive PP1H66K fused to the C-terminal PNUTS sequences including its WDR82 binding domain binds to restrictor and acts as a dominant negative inhibitor of antisense termination and CTD Ser5 dephosphorylation. The PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We speculate that the elevated elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4 is coupled to termination of antisense transcription.

2025-04-05 | GSE269358 | GEO

PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [ChIP-seq]

2025-04-05 | GSE269359 | GEO

PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [nascent RNA-seq]

Project description:The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. A chimera comprising inactive PP1H66K fused to C-terminal PNUTS sequences is a dominant-negative inhibitor of antisense termination and CTD Ser5 dephosphorylation and both activities require the PNUTS WDR82 binding domain. PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We propose that the elevated elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4 is coupled to termination of antisense transcription.

2025-04-05 | GSE269357 | GEO

Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination.

Project description:Termination of RNA polymerase II (Pol II) transcription is a key step that is important for 3' end formation of functional mRNA, mRNA release, and Pol II recycling. Even so, the underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 is found on Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 dephosphorylation by the conserved PP1 phosphatase Dis2, which also dephosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and dephosphorylation of Pol II C-terminal domain.

| S-EPMC6180485 | biostudies-literature

Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes.

Project description:Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously found that base J functions to prevent readthrough transcription within gene clusters via the PJW/PP1 complex. Analysis of the complex in T. brucei faild to identify the catalytic PP1 component. We now show the RNAi ablation of PP1-1 in T. brucei leads to readthrough transcription and expression of downstream genes.

2024-07-17 | GSE244975 | GEO

Protein phosphatase PP1-NIPP1 activates mesenchymal genes in HeLa cells

Project description:The deletion of the protein phosphatase-1 (PP1) regulator NIPP1 is embryonic lethal during gastrulation, hinting at a key role of PP1-NIPP1 in lineage specification. Consistent with this notion we show here that a mild, stable overexpression of NIPP1 in HeLa cells caused a massive induction of genes of the mesenchymal lineage, in particular smooth/cardiac-muscle and matrix markers. This reprogramming was associated with the formation of actin-based stress fibers and retracting filopodia, and a reduced proliferation potential. The NIPP1-induced mesenchymal transition required functional substrate and PP1-binding domains, suggesting that it involves the selective dephosphorylation of substrates of PP1-NIPP1.

2015-04-04 | GSE67558 | GEO

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