Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Base J binding protein (JBP3) is a Component of a Novel Trypanosomatid PNUTS-PP1 Phosphatase Complex involved in RNA Pol II Transcription Termination

ABSTRACT: Base J is a modified DNA base that is enriched at RNA polymerase II termination sites and telomeres. We previously found that base J functions to prevent readthrough transcription within gene clusters in T. brucei. We now identify a complex in Leishmania and T. brucei composed of PNUTS, PP1, Wdr82 and a J-binding protein (JBP3). We show the RNAi ablation of PNUTS in T. brucei leads to readthrough transcription and expression of downstream genes.

ORGANISM(S): Trypanosoma brucei

PROVIDER: GSE135708 | GEO | 2020/01/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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.

2022-10-01 | GSE200788 | GEO

The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [eCLIP]

Project description:Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-protein phosphatase 1 (PP1) complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion also enhances global KSHV gene expression and overall viral replication. Reflecting its host gene activities, PNUTS binds viral RNAs downstream of polyadenylation sites, restricts transcription readthrough of viral genes, and requires PP1 interaction. Surprisingly, PNUTS represses the KSHV reporter by decreasing productive elongation at the 5´-end of the gene. From these data, we conclude that PNUTS' activity forms an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.

2022-11-19 | GSE201045 | GEO

The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [CRISPR]

2022-11-19 | GSE200991 | GEO

The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [RNA-seq]

2022-11-19 | GSE201000 | GEO

The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [ChIP-seq]

2022-11-19 | GSE200992 | GEO

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.

2019-10-30 | GSE134198 | GEO

Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression [PNUTS]

Project description:Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and homeostasis. Here, we determined the role of PNUTS in endothelial cell aging. We confirmed that PNUTS is repressed in senescent endothelial cells (ECs). Moreover, PNUTS silencing elicits several of the hallmarks of endothelial aging: senescence, reduced angiogenesis and loss of barrier function. To validate our findings in vivo, we generated an endothelial-specific inducible PNUTS-deficient mouse line (Cdh5-CreERT2;PNUTSfl/fl), termed PNUTSEC-KO. Two weeks after PNUTS deletion, PNUTSEC-KO mice presented severe multiorgan failure and vascular leakage. Transcriptomic analysis of PNUTS-silenced HUVECs and lungs of PNUTSEC-KO mice revealed that the PNUTS-PP1 axis tightly regulates the expression of semaphorin 3B (SEMA3B). Indeed, silencing of SEMA3B completely restored barrier function after PNUTS loss-of-function. These results reveal a pivotal role for PNUTS in endothelial homeostasis through a SEMA3B downstream pathway that provides a potential target against the effects of aging in ECs.

2024-04-15 | GSE263742 | GEO

Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [RNA]

Project description:Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs. polyA-mRNAs or 4sU-labeled RNAs from BMDMs, either untreated or treated for with lipopolysaccharide (LPS) for the indicated time. Experiments were carried out in cells containing either a short hairpin targeting either of these: 1) Wdr82; 2) Set1a+Set1b; 3) Pnuts; or the empty vector (LMP) or a scrambled as a control. When specified, cells were pre-treated with 5,6-Dichloro-1-Î²-D-ribofuranosylbenzimidazole (DRB) in order to prevent RNA polymerase II elongation.

2015-11-09 | E-GEOD-66953 | biostudies-arrayexpress

Aging-regulated PNUTS maintains endothelial barrier function via SEMA3B suppression

2024-04-14 | GSE263531 | GEO

Base J binding protein (JBP3) is a Component of a Novel Trypanosomatid PNUTS-PP1 Phosphatase Complex involved in RNA Pol II Transcription Termination

Project description:Base J binding protein (JBP3) is a Component of a Novel Trypanosomatid PNUTS-PP1 Phosphatase Complex involved in RNA Pol II Transcription Termination

| PRJNA559811 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data