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ProteomicsBANC-seq to identify genome-wide transcription factor binding affinities to native chromatin
BANC-seq (Binding Affinities to Native Chromatin by sequencing) allows determination of absolute apparent binding affinites of transcription factors to native chromatin in a genome-wide manner. In this study, we establish the method and show that chromatin and DNA sequence define binding affinites o...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2023-02-09 | PXD038502 | Pride
Dna pulldowns Transcription factors Tmt Proteomes Binding affinity Absolute quantification 
ProteomicsA quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood
The interaction between transcription factors and genomic DNA forms the basis for spatio-temporal control of gene expression. Therefore, these interactions and their impact on disease and cellular fate are extensively studied on a global level, mainly using techniques based on next-generation sequen...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-03-01 | MSV000079550 | MassIVE
ProteomicsDetermining DNA-protein binding affinities and specificities from crude lysates using a combined SILAC/TMT labeling strategy
Gene expression is driven by the binding of transcription factors to regulatory elements in the genome, such as enhancers and promoters. A powerful technique to study DNA-protein interactions is affinity purification followed by mass spectrometry. Classic affinity purifications coupled to quantitati...
ORGANISM(S): Homo sapiens (Human) 
2023-10-08 | PXD041674 | Pride
Tmt Silac Dna pulldowns Paqman 
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 
ProteomicsTeamwork of clustered low affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers
Non-consensus binding sites of transcription factors are often observed within the promoters and enhancers of various genes; however, their effect on transcriptional strength is unclear. Within the promoters and enhancers of NF-κB-responsive genes, we identified clusters of non- consensus κB DNA sit...
ORGANISM(S): Mus musculus (Mouse) 
2025-10-13 | PXD065004 | Pride
Transcription Cofactor Promoter Κb dna Nf-kappa b (nf-κb) 
ProteomicsQuantitative Proteomics Identify a Novel DNA Repair-Dependent Role for Hepatocyte Nuclear Factor 4α
Hepatocyte nuclear factor 4 (HNF4) is a transcription factor that acts as a master regulator of genes in several endodermal-derived tissues, including the intestine in which it plays a central role during development and tumorigenesis. To better delineate the mechanisms by which HNF4 can interfere d...
ORGANISM(S): Homo sapiens (Human) 
2019-11-12 | PXD008365 | Pride
Gfp-trap Colorectal cancer Dna repair Human Silac Hnf4alpha Quantitative proteomics Bioid 
ProteomicsIsolation of repaired chromatin of UVC-irradiated human skin fibroblasts
To further study and understand the DNA damage responses, we developed aniFOUND, a new method for capturing under native conditions the repaired DNA and the proteins associated with it after UVC irradiation. hTert-immortalised human skin fibroblasts were irradiated with 20 J/m2 UVC and the nascent D...
ORGANISM(S): Homo sapiens (Human) 
2021-03-10 | PXD012997 | Pride
Dna damage responses Human fibroblasts Nucleotide excision repair-ner Dna repair Uv-c radiation Mass spectrometry Anifound Chromatin 
ProteomicsGlobal profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry
Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quan...
ORGANISM(S): Homo sapiens (Human) 
2018-05-02 | PXD007132 | Pride
Transcription Dna-protein interactions Binding affinity Chromatin 
ProteomicsHuntingtin interactome in human striatal neurons derived from iPSCs upon the induction of double strand break (DSB) DNA damage response
Huntington’s Disease (HD), a progressive neurodegenerative disorder with no disease-modifying therapies, is caused by a CAG repeat expansion in the HD gene encoding polyglutamine-expanded huntingtin (HTT) protein. Mechanisms of HD cellular pathogenesis and cellular functions of the normal and mutan...
ORGANISM(S): Homo sapiens (Human) 
2026-03-16 | PXD059660 | Pride
Huntington’s disease Protein interactions Huntingtin Dna damage Neurodegeneration 
ProteomicsProteomic analyses identify ANP32A and CAND1 as androgen receptor and splice variant coactivators, whose interactions are regulated by DNA-dependent protein kinase
ARv7, the most prevalent androgen receptor (AR) variant in castration resistant prostate cancer (CRPC), lacks the AR ligand binding domain (LBD) making it resistant to LBD-targeting pharmacological inhibitors, such as enzalutamide. Identifying new prostate cancer therapeutic targets by defining key ...
ORGANISM(S): Homo sapiens (Human) 
2026-04-06 | PXD021462 | Pride
Prostate cancer Coregulators And cand1 Dna-dependent protein kinase Androgen receptor Androgen receptor splice variant Anp32a 
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