Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

KINETIC AND COMPOSITIONAL ANALYSIS OF RNA POLYMERASE II IN TRYPANOSOMA BRUCEI

ABSTRACT: Genome-wide analysis of nascent RNA synthesis gives kinetic information on the transcriptional status of RNA polymerase II (Pol II). In parallel, immunoprecipitation of the largest subunit of Pol II (RPB1) provides the protein composition of the enzyme complex in the presence or absence of the transcriptional inhibitor Actinomycin D.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Trypanosoma Brucei

DISEASE(S): Trypanosomiasis

SUBMITTER: Manfred Heller

LAB HEAD: Isabel Roditi

PROVIDER: PXD039878 | Pride | 2023-05-23

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20160915_RPBI_ACT_AN_i01.raw	Raw
	20160915_RPBI_ACT_AN_i02.raw	Raw
	20160915_RPBI_ACT_AN_i03.raw	Raw
	20160915_RPBI_DMSO_AN_i01.raw	Raw
	20160915_RPBI_DMSO_AN_i02.raw	Raw

Items per page:

1 - 5 of 66

Similar Datasets

Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay

Project description:Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. This project presents the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. We additionally overlay an SFV siRNA screen to assign pro- or antiviral functions to the interactors. Among the many identified cellular interactors of SFV proteins, there was an enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD). Validating these findings, we observed a general inhibition of NMD during SFV infection and demonstrated that transient expression of the SFV capsid protein was sufficient to inhibit NMD in cells.

2021-05-07 | PXD022036 | Pride

Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

Project description:The clearance of untranslated mRNAs by Argonaute proteins is essential for embryonic development in metazoans. However, it is currently unknown whether a similar process exists in unicellular eukaryotes. The ciliate Paramecium tetraurelia harbors a vast array of Argonaute proteins of the Piwi-clade involved in various small RNA pathways, many of which have not yet been investigated. In this work, we investigated the function of a Piwi protein, Ptiwi08, whose expression is limited to a narrow time window during development, concomitant with the start of zygotic transcription. We show that Ptiwi08 acts in an endo-siRNA pathway involved in the clearance of a set of mRNAs at the post-transcriptional level. Based on their features, we hypothesized that these mRNAs may be untranslated. In this dataset, we used mass spectrometry to determine whether any protein products of these mRNAs can be found.

2023-05-10 | PXD038984 | Pride

Anti-Pol II pS5 co-immunoprecipitation in PHF3 WT, KO and ΔSPOC HEK293T cells

Project description:The analysis of differential interactome of Pol II pS5 in PHF3 WT, KO and ΔSPOC HEK293T cells using Pol II pS5 (4H8) antibody coupled to Protein G beads.

2023-10-25 | PXD039537 | Pride

ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans

Project description:ARMC5 is an armadillo domain (ARM)-containing protein. We found that Armc5 KO mice had an increased incidence of neural tube defects (NTDs). ARMC5 is the substrate recognition component of a ubiquitin ligase that targets POLR2A, the largest subunit of RNA polymerase II (Pol II). Surprisingly, the absence of ARMC5 caused the accumulation of not only POLR2A, but most of the other 11 Pol II subunits associated with POLR2A, indicating that the degradation of the whole Pol II complex is compromised. This did not lead to generalized Pol II stalling or a generalized decrease in mRNA transcription. In neural progenitor cells, ARMC5 KO only dysregulated 106 genes, some of which are known to be involved in neural tube development. FOLH1, critical for folate metabolism and vital in neural tube development, was downregulated in the KO intestine, suggesting that it is a downstream effector gene for NTD. To assess whether ARMC5 gene mutation was associated with human NTD, we conducted whole-exome sequencing of 511 patients with myelomeningocele, a severe form of NTD. Nine deleterious single nucleotide variants were discovered in the ARMC5 coding sequence. Four of them were validated in that they weakened the interaction between ARMC5 and POLR2A; consequently, POLR2A ubiquitination was decreased. This proves that our findings in mice are relevant to human NTD; it also supports the role of Pol II in mediating NTD pathogenesis. Our findings indicate that mutations in ARMC5 increase the risk of NTD and support the role of Pol II in NTD pathogenesis. Further investigation is needed to determine the cause-and-effect relationship between an enlarged Pol II pool and NTD and to validate the potential role of downregulated FOLH1 expression in NTD pathogenesis.

2023-12-06 | PXD047572 | Pride

ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans

2023-12-06 | PXD047533 | Pride

De novo heterozygous variants in POLR2A cause a neurodevelopmental syndrome with infantile-onset hypotonia

Project description: ABSTRACT POLR2A encodes RPB1, the largest subunit of the RNA polymerase II (pol II) complex, which is responsible for transcription of all ~21,000 protein-encoding genes. Here we describe the first fifteen patients harboring de novo heterozygous variants in POLR2A. The majority presents with profound infantile onset hypotonia and developmental delay. Missense variants that were expected to exert only mild structural effects, lead to malfunctioning RPB1, thereby inducing a dominant negative effect on pol II function. Intriguingly, these patients presented with a severe clinical phenotype. Conversely, variants expected to result in loss-of-function, leading to reduced availability of RPB1 were better tolerated: these patients exhibited the mildest phenotypes.

2019-09-02 | PXD011355 | Pride

Anti-Pol II pS5 co-immunoprecipitation in DIDO WT, KO and ΔSPOC HEK293T cells

Project description:The analysis of differential interactome of Pol II pS5 in DIDO WT, KO and ΔSPOC HEK293T cells using Pol II pS5 (3E8) antibody coupled to Protein G beads (no crosslinking).

2023-10-25 | PXD039567 | Pride

Mechanistic basis for selective Mediator-dependence of cell type-specifying transcription

Project description:The Mediator complex routes signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite its pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Remarkably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.

2021-09-08 | PXD017611 | Pride

Development and validation of an ELISA to measure REG3E in canine blood

Project description:Regenerating islet-derived proteins (REG) are upregulated in people with sepsis, pancreatitis, and gastrointestinal diseases. One member of the REG family, namely REG3E, was recently identified in pancreatic tissue and plasma of dogs, with high expression in pancreatitis and sepsis. Our objective was to develop and validate an ELISA to measure REG3E concentrations in canine blood. An indirect sandwich ELISA was successfully developed using recombinant canine REG3E protein and polyclonal anti-canine REG3E antibodies raised in guinea pigs and rabbits. Antibody specificity was assessed using Western blot and mass spectrometric analysis of protein purified from canine plasma using Protein A Sepharose High Performance SpinTrap columns.

2024-06-10 | PXD046936 | Pride

tRNA 3' shortening by LCCR4 as a response to stress in Trypanosoma brucei

Project description:Sensing of environmental cues is crucial for cell survival. To adapt to changes in their surroundings cells need to tightly control the repertoire of genes expressed at any time. Regulation of translation is key, especially in organisms in which transcription is hardly controlled, like Trypanosoma brucei. In this study we describe the shortening of the bulk of the cellular tRNAs during stress at the expense of the conserved 3’ CCA-tail. This tRNA shortening is specific for nutritional stress and renders tRNAs unsuitable substrates for translation. We uncovered the nuclease LCCR4 (Tb927.4.2430), a homologue of the conserved deadenylase Ccr4, as being responsible for tRNA trimming. Once optimal growth conditions are restored tRNAs are rapidly repaired by the trypanosome tRNA nucleotidyltransferase thus rendering the recycled tRNAs amenable for translation. This mechanism represents a fast and efficient way to repress translation during stress, allowing quick reactivation with a low energy input.

2021-01-13 | PXD021540 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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