Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of small RNA biogenesis and turnover in the absence of the PRC2 associated protein Ded2p

ABSTRACT: Investigation of small RNA biogenesis and turnover in the absence of the PRC2 associated protein Ded2p

PROVIDER: PRJNA786623 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17145393.fastq.gz	Fastqsanger.gz
	SRR17145394.fastq.gz	Fastqsanger.gz
	SRR17145395.fastq.gz	Fastqsanger.gz
	SRR17145396.fastq.gz	Fastqsanger.gz
	SRR17145397.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Investigation of small RNA biogenesis and turnover in the absence of the PRC2 associated protein Ded2p

Project description:Heterochromatic histone H3 methylation at lysine 9 (H3K9me2/3) and lysine 27 (H3K27me3) is generally catalyzed by SUV39 and EZH family methyltransferases, respectively, and has distinct functions in most eukaryotes. In contrast, the ciliated protozoan Tetrahymena lacks the SUV39 enzyme, and the EZH enzyme Ezl1p is responsible for the deposition of both H3K9me3 and H3K27me3 during Piwi-directed DNA elimination. Understanding how both modifications are catalyzed by the EZH enzyme should shed light on the mechanism and the evolution of the division of labor between the two heterochromatic histone methyltransferase families in eukaryotes. Here, we show that loss of the novel protein Ded2p abolishes the accumulation of H3K9me3 but not H3K27me3 in Tetrahymena. The phenotypes of DED2 KO cells revealed that H3K27me3 is sufficient for promoting secondary small RNA biogenesis but not for suppressing TEs, assembling heterochromatin bodies and completing DNA elimination. Ded2p associates with Ezl1p through Rnf2p, a component of Tetrahymena Polycomb Repressive Complex 2 (PRC2) to promote the accumulation of H3K9me3. Our results indicate that there are functional distinctions between H3K9me3 and H3K27me3 in different steps of the DNA elimination process and the specificity of the methyltransferase activity of PRC2 can be modulated by its associated factor to catalyze H3K9me3.

2023-04-01 | GSE190308 | GEO

upregulation of transcripts in the absence of prc2 repressory complex-Dissecting the role of the polycomb repressor

Project description:rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out 6 dye-swap - CATMA arrays

2010-12-01 | E-GEOD-19851 | biostudies-arrayexpress

upregulation of transcripts in the absence of prc2 repressory complex-Dissecting the role of the polycomb repressor

2010-12-01 | GSE19851 | GEO

Pooled CRISPR/Cas9 screen for genes that contribute to ribosome biogenesis and turnover

Project description:Pooled CRISPR/Cas9 screen for genes that contribute to ribosome biogenesis and turnover

| PRJNA809653 | ENA

Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling

Project description:Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we hypothesize that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We exemplify how the turnover data may facilitate insights into unknown functions of PTMs and provide a web-tool for the scientific community that allows interrogation and visualisation of all turnover data. Since the methodology is applicable to many cell types and modifications, it has substantial potential to prioritize PTMs for functional investigation in the future.

2022-03-14 | PXD023234 | panorama

PRC2

Project description:PRC2

| PRJNA761389 | ENA

Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling

Project description:Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we hypothesize that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We exemplify how the turnover data may facilitate insights into unknown functions of PTMs and provide a web-tool for the scientific community that allows interrogation and visualisation of all turnover data. Since the methodology is applicable to many cell types and modifications, it has substantial potential to prioritize PTMs for functional investigation in the future.

2021-11-10 | PXD023218 | Pride

Small molecule RBI2 disrupts ribosome biogenesis through pre-rRNA depletion

Project description:In all domains of life, the rate of protein synthesis is directly linked to the rates of cell growth and proliferation. Consequently, highly proliferative cancer cells are especially sensitive to perturbations in ribosome biogenesis. While ribosome synthesis and cancer have a well-established relationship, only recently has ribosome biogenesis drawn interest as a cancer therapeutic target. Here, we have exploited the relationship between ribosome biogenesis and cancer cell proliferation by using a potent ribosome biogenesis inhibitor: RBI2 (Ribosome Biogenesis Inhibitor 2) to perturb cancer cell growth and viability. We demonstrate that RBI2 significantly decreases cell viability in malignant melanoma cells and breast cancer cell lines. Treatment with RBI2 dramatically and rapidly decreases ribosomal RNA (rRNA) synthesis, without affecting the occupancy of RNA polymerase I (Pol I) on the ribosomal DNA template. Next-generation RNA sequencing (RNA-seq) reveals that RBI2 and previously described ribosome biogenesis inhibitor CX-5461 induce distinct changes in the transcriptome. Investigation of the content of the pre-rRNAs through RT-qPCR reveals an increase in polyadenylation of cellular rRNA after treatment with RBI2, a known pathway by which rRNA degradation occurs. Northern blotting revealed that RBI2 does not appear to impair or alter rRNA processing. Collectively, these data suggest that RBI2 inhibits rRNA synthesis distinctly from other previously described ribosome biogenesis inhibitors, potentially through a novel pathway that upregulates turnover of premature rRNAs.

2021-11-08 | GSE188262 | GEO

Investigation of the transcriptional profile of stimulated HUMAN CRISPR/Cas9 MOCK and A2ARKO α-lewisY CAR T cells in the presence/absence of NECA

Project description:Investigation of the transcriptional profile of sorted and stimulated CD8 and CD4 murine CRISPR/Cas9 MOCK and A2ARKO α-her2 CAR T cells in the presence/absence of NECA

2021-03-29 | GSE166807 | GEO

Identification of JARID2/PRC2 interactome in human embryonic stem cells

Project description:JARID2 is an integral subunit of the chromatin modifier PRC2 (Polycomb Repressive Complex 2). PRC2 methylates lysine 27 in histone H3 and is required for human development. Mutaitons of PRC2 subunits have been frequently found in a variety of adult and pediatric cancer, suggesting that PRC2 critically regulates normal and cancer development. The goal of this project is to identify new regulator or co-factors of PRC2 and study their molecular interactions and activities in order to better understand function and regulation of PRC2 in normal and cancer development.

2020-08-04 | PXD015670 | 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