Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap, Zeste, Psq, and Adf1 associated proteins

ABSTRACT: Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap, Zeste, Psq, and Adf1 associated proteins

PROVIDER: PRJNA823688 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18645005.fastq.gz	Fastqsanger.gz
	SRR18645005_1.fastq.gz	Fastqsanger.gz
	SRR18645005_2.fastq.gz	Fastqsanger.gz
	SRR18645006.fastq.gz	Fastqsanger.gz
	SRR18645006_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap, Zeste, Psq, and Adf1 associated proteins

Project description:To gain an insight into the PRE DNA-binding protein regulatory network, here, using immunoaffinity purification coupled to the high throughput mass spectrometry, we isolated factors associated with the Combgap, Psq, Zeste and Adf1 PRE DNA-binding proteins. We show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.

2022-06-10 | GSE200213 | GEO

Comparative analysis of PRE DNA-binding factors interactomes: purification of Combgap, Zeste, Psq and Adf1 associated proteins

Project description:The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling silenced and active states of genes in multicellular organisms, respectively. In Drosophila PcG/TrxG proteins are recruited to chromatin via binding to specialized DNA-elements termed Polycomb Response Elements (PREs). While precise mechanisms of PcG/TrxG proteins recruitment remains unknown, the important role is suggested to belong to sequence specific DNA-binding factors. Here, using affinity purification coupled with high throughput mass spectrometry (IP/MS), we isolated factors associated with Combgap, Psq, Zeste and Adf1 PRE DNA-binding Drosophila proteins. As a control we used unspecific IgG. For affinity purification the nuclear extract from Drosophila S2 cells and polyclonal antibodies against Combgap, Psq, Zeste and Adf1 were used.

2024-05-22 | PXD029459 | Pride

Defining the RNA Interactome by Total RNA-Associated Protein Purification

Project description:Defining the RNA Interactome by Total RNA-Associated Protein Purification

| PRJNA490515 | ENA

Interactome between ASFV and host immune pathway proteins

Project description:Interactome between ASFV and host immune pathway proteins

| PRJNA910475 | ENA

Water purification system

Project description:Water purification system Raw sequence reads

| PRJNA1086135 | ENA

The SARS-CoV-2 RNA-protein interactome in infected human cells

Project description:Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry (RAP-MS), we identify up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrate the SARS-CoV-2 RNA interactome with proteome abundance changes induced by viral infection and link interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrate by genetic perturbation that CNBP and LARP1, two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduces viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.

2020-12-01 | GSE154430 | GEO

The interactome of Pou5f1 enhancer in mouse embryonic stem cells

Project description:We report the application of enyzme-based 4C-Seq technique for exploring Pou5f1 enhancer interactome in mouse ES cells. We explored the interactome of Pou5f1 upstream enhancer in mouse ES cells by using an enzyme digestion based 4C-Seq protocol. The interactome is involved in gene active regulation.

2013-04-28 | E-GEOD-45418 | biostudies-arrayexpress

LncPHx2 RNA-interactome

Project description:LncPHx2 RNA-interactome study realed that LncPHx2 is associated with multiple RNAs Biotinylated DNA probes targeting LncPHx2 were used to precipitate endogenous LncPHx2 and associated RNAs from Hepa 1-6 cells. The associated RNAs were sequenced and 415 unique transcripts were identified.

2015-06-27 | E-GEOD-70342 | biostudies-arrayexpress

LncPHx2 RNA-interactome

Project description:LncPHx2 RNA-interactome study realed that LncPHx2 is associated with multiple RNAs

2015-06-27 | GSE70342 | GEO

Defining the RNA Interactome by Total RNA-Associated Protein Purification

Project description:UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae ) and bacteria (E. coli). In all analyses, SILAC labeling was used to quantify protein recovery in the presence and absence of irradiation. For S.cerevisiae, we also compared crosslinking using 254nm (UVC) irradiation (TRAPP) with 4-thiouracil (4SU) labeling combined with 350nm (UVA) irradiation (PAR-TRAPP). Recovery of proteins not anticipated to show RNA-binding activity was significantly higher in TRAPP compared to PAR-TRAPP. As an example of preferential TRAPP-crosslinking, we tested enolase (Eno1) and demonstrated its strong, but largely sequence independent, binding to RNA in vivo. We speculate that many protein-RNA interactions have biophysical effects on localization and/or accessibility, by opposing or promoting phase separation. Homologous metabolic enzymes showed RNA crosslinking in S. cerevisiae and E. coli, indicating conservation of this property. TRAPP allows alterations in RNA interactions to be followed and we initially analyzed the effects of weak acid stress. This revealed specific alterations in RNA-protein interactions; for example, during late 60S ribosome subunit maturation. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified following phospho-peptide enrichment combined with a bioinformatic pipeline (Xi). TRAPP is quick, simple and scalable, allowing rapid characterization of the RNA-bound proteome in many systems.

2018-09-13 | GSE119867 | GEO

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