Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry-based characterization of SET1/COMPASS complex in Caenorhabditis elegans

ABSTRACT: Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Using co-immunopurification coupled to mass spectrometry-based proteomics, we characterized complex members and binding partners in various genetic contexts, using WDR-5 or CFP-1 proteins as baits.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive HF

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Embryo

SUBMITTER: Yohann Couté

LAB HEAD: Yohann Couté

PROVIDER: PXD029904 | Pride | 2021-12-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CFP-1_Interactome.mzid.gz	Mzid
	Ctrl.mgf	Mgf
	Ctrl.raw	Raw
	Del-set2_Ctrl.mgf	Mgf
	Del-set2_Ctrl.raw	Raw

Items per page:

1 - 5 of 19

Similar Datasets

MS-based proteomic characterization of SIN3-containing complexes in C. elegans

Project description:The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. To gain insight in the repertoire of proteins that interact with SIN-3, we performed IP-MS on mCherry::SIN-3 expressing embryos. Furthermore, we analyzed the partnership of ARID-1::GFP, ARID-1 being an already described subunit of the SIN-3L complex.

2023-10-02 | PXD039853 | Pride

Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans

Project description:The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to nonmethylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between C. elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex.

2019-09-27 | PXD015548 | Pride

Glorund IP-MS in Drosophila late stage oocyte enriched ovary

Project description:Identification of interaction partners of the sole Drosophila hnRNP F/H homolog, Glorund, during late oogenesis.

2022-06-07 | PXD033174 | Pride

Glorund corsslinked IP-MS in Drosophila late stage oocyte enriched ovary

Project description:Identification of interaction partners of the sole Drosophila hnRNP F/H homolog, Glorund, during late oogenesis.

2022-06-07 | PXD033175 | Pride

Gene expression analysis of induced renal epithelial cells

Project description:Induced renal epithelial cells were obtained by direct reprogramming of murine fibroblasts. Their expression profile was compared to control fibroblasts and primary renal tubular epithelial cells.

2016-07-01 | E-MTAB-3648 | biostudies-arrayexpress

How a tRNA modifying enzyme facilitates RNase P activity in Arabidopsis nuclei

Project description:RNase P is essential to perform the 5’ maturation of tRNA precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to understand their integration with gene expression pathways. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 makes a complex with the tRNA methyl transferases TRM1A and B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/B localize in the nucleus and find that their double knock out mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome wide tRNAseq approach, we observe that TRM1A/B are responsible for the m2,2G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/B mutants for specific tRNAs, in particular, tRNAs containing a m2,2G modification at position 26 that are strongly down-regulated in TRM1A/B mutants. Altogether, results indicate that the m2,2G adding enzymes TRM1A/B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNAs biogenesis.

2023-10-20 | PXD040022 | Pride

Identification of LEC1 target genes

Project description:The transcription factor (TF) LEAFY COTYLEDON1 (LEC1) acts as an essential regulator of Arabidopsis embryogenesis and seed development. It controls aspects of early embryogenesis such as cotyledon identity and suspensor morphology, as well as seed maturation processes such as storage compound accumulation, acquisition of desiccation tolerance and dormancy. To identify downstream components of the LEC1 regulon, dexamethasone-regulated expression of LEC1 and ChIP/chip were applied and revealed the enrichment of phytohormone- as well as elongation-related genes among LEC1 target genes. Two weeks old 35S::LEC1::GR seedlings were treated with DEX or ethanol for 24 hours before cross-linking and chromatin isolation. Four biological replicates were performed, using an ethanol-treated sample as control (LEC1_EtOH versus LEC1_DEX). After data normalization, statistical analysis and exclusion of putative false negatives, a number of 356 target promoter regions were identified.

2012-03-30 | E-GEOD-22352 | biostudies-arrayexpress

Two paralogous PHD finger proteins participate in Paramecium tetraurelia's natural genome editing

Project description:The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sexual reproduction, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique Internal Eliminated Sequences (IESs) located throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IESs excision occurs. In DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functionalities, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.

2024-08-30 | PXD046704 | Pride

Plasmodium PKG interacts with ICM1, a multi-pass membrane protein, in both asexual and sexual stages

Project description:In malaria parasites, all cGMP-dependent signalling is mediated through a single cGMP-dependent protein kinase (PKG). A major function of PKG is to control calcium signals essential for the parasite to exit red blood cells or for transmission to the mosquito vector. However, how PKG controls these signals in the absence of known second messenger-dependent calcium channels or scaffolding proteins remains a mystery. Here we identify a tightly-associated PKG partner protein in Plasmodium falciparum asexual blood stages. Named ICM1, the partner is a polytopic membrane protein with homology to transporters and calcium channels, raising the possibility of a direct functional link between PKG and calcium homeostasis

2021-02-10 | PXD020447 | Pride

SOX4 genome binding targets in glioblastoma cell line

Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle Examination of SOX4 binding profile in prostate cell LN229-SOX4 with LN229-GFP as negative control.

2014-10-20 | E-GEOD-51663 | biostudies-arrayexpress

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