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PXD023732 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePROBER Identifies Proteins Associated with Sequence- Specific DNA in Living Cells
DescriptionSpecific DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) of identifying and quantifying proteins associating with specific DNA sequences in living cells, we developed proximal biotinylation by episomal recruitment (PROBER). PROBER uses high copy episomes to amplify SNR along with proximity proteomics (BioID) to identify the transcription factors (TFs) and additional gene regulators associated with DNA sequences of interest. PROBER quantified steady-state and inducible association of TFs and associated chromatin regulators to target DNA sequences and quantified binding quantitative trait loci (bQTLs) due to single nucleotide variants. PROBER identified alterations in gene regulator associations due to cancer hotspot mutations in the hTERT promoter, indicating these mutations increase promoter association with specific gene activators. PROBER offers an approach to rapidly identify proteins associated with specific DNA sequences and their variants in living cells.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSmarajit Mondal
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListbiotinylated residue
InstrumentQ Exactive HF; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-21 02:44:42ID requested
12022-07-27 13:29:41announced
22023-11-14 08:52:04announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: DNA-Protein Interaction,PROBER, LC-MS/MS
Contact List
Paul Khavari
contact affiliationDept. of Dermatology Stanford University School of Medicine
contact emailkhavari@stanford.edu
lab head
Smarajit Mondal
contact affiliationStanford University School of Medicine
contact emailmondal@stanford.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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