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PXD029470

PXD029470 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePROBER Identifies Proteins Associated with Programable Sequence-Specific DNA in Living Cells
DescriptionDNA-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 that associate 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 short DNA sequences of interest. PROBER quantified steady-state and inducible association of TFs and corresponding chromatin regulators to target DNA sequences as well as binding quantitative trait loci (bQTLs) due to single nucleotide variants. PROBER identified alterations in regulator associations due to cancer hotspot mutations in the hTERT promoter, indicating these mutations increase promoter association with specific gene activators. PROBER provides an approach to rapidly identify proteins associated with specific DNA sequences and their variants in living cells.
HostingRepositoryPRIDE
AnnounceDate2022-07-27
AnnouncementXMLSubmission_2022-07-27_13:14:37.105.xml
DigitalObjectIdentifierhttp://dx.doi.org/10.6019/PXD029470
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterSmarajit Mondal
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListbiotinylated residue
InstrumentQ Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-11-01 05:00:55ID requested
12022-07-27 13:14:37announced
Publication List
10.1038/S41592-022-01552-W;
Keyword List
submitter keyword: PROBE, BioID, BASU, bQTL, TERT, SNP
Contact List
Paul Khavari
contact affiliationCARL J. HERZOG PROFESSOR OF DERMATOLOGY STANFORD UNIVERSITY SCHOOL OF MEDICINE, STANFORD, CA 94305
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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