PXD023732-2

PXD023732 is an original dataset announced via ProteomeXchange.

Title	PROBER Identifies Proteins Associated with Sequence- Specific DNA in Living Cells
Description	Specific 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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:04.526.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Smarajit Mondal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-21 02:44:42	ID requested
1	2022-07-27 13:29:41	announced
⏵ 2	2023-11-14 08:52:04	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: DNA-Protein Interaction,PROBER, LC-MS/MS

Paul Khavari
contact affiliation	Dept. of Dermatology Stanford University School of Medicine
contact email	khavari@stanford.edu
lab head
Smarajit Mondal
contact affiliation	Stanford University School of Medicine
contact email	mondal@stanford.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/07/PXD023732

PRIDE project URI

• PRIDE
  1. PXD023732
     1. Label: PRIDE project
     2. Name: PROBER Identifies Proteins Associated with Sequence- Specific DNA in Living Cells