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ProteomicsImmunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in host immune evasion by antigenic variation
RNA-DNA hybrids are widespread epigenetic features of genomes that provide a growing range of activities in transcription, chromatin and DNA replication and repair. Understanding of these diverse functions has been advanced by characterising the proteins that interact with the hybrids, with all such...
ORGANISM(S): Trypanosoma brucei 
2024-01-26 | PXD042146 | Pride
R loops  dna-rna interactors 
ProteomicsActive DNA demethylation during the vertebrate phylotypic period
The vertebrate body plan and organs are shaped during a highly conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of thousands o...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2016-01-27 | PXD001164 | Pride
Zebrafish Dna interactors Development Dna methylation Proteome 
GenomicsChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3
This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates),...
ORGANISM(S): Homo sapiens 
2010-09-17 | E-GEOD-20303 | biostudies-arrayexpress
ProteomicsExpanding the substantial interactome of NEMO using protein microarrays
Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstr...
ORGANISM(S): Homo sapiens 
2010-06-19 | E-GEOD-19841 | biostudies-arrayexpress
UnknownIdentification of proximal SUMO-dependent interactors using SUMO-ID.
Not available
S-EPMC8602451 | biostudies-literature
ProteomicsThe Quantitative Changes in the Yeast Hsp70 and Hsp90 Interactomes upon DNA Damage
The molecular chaperones Hsp70 and Hsp90 participate in many important cellular processes, including how cells respond to DNA damage. In this study, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand the protein network through which Hsp70 and Hsp90 exe...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2014-12-08 | PXD001284 | Pride
Saccharomyces cerevisiae 18o quantitation Ltq orbitrap xl Lc-ms/ms 
TranscriptomicsA comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of inte...
ORGANISM(S): Mus musculus 
2015-06-19 | E-GEOD-67516 | biostudies-arrayexpress
UnknownThe TET2 interactors and their links to hematological malignancies.
Not available
S-EPMC4765929 | biostudies-literature
GenomicsCRISPR screen of genes encoding protein interactors of MCB-613 in parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines
CRISPR screen of genes encoding protein interactors of MCB-613 in parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines
PRJNA1090830 | ENA
TranscriptomicsControlling for gene expression changes in transcription factor protein networks.
The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactio...
ORGANISM(S): Homo sapiens 
2014-04-24 | E-GEOD-57027 | biostudies-arrayexpress
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