PXD029470 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | PROBER Identifies Proteins Associated with Programable Sequence-Specific DNA in Living Cells |
Description | 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 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. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:54:40.298.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD029470 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Smarajit Mondal |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | biotinylated residue |
Instrument | Q Exactive Plus |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-11-01 05:00:55 | ID requested | |
1 | 2022-07-27 13:14:37 | announced | |
⏵ 2 | 2023-11-14 08:54:40 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: BASU, bQTL, TERT, SNP,PROBE, BioID |
Contact List
Paul Khavari |
contact affiliation | CARL J. HERZOG PROFESSOR OF DERMATOLOGY STANFORD UNIVERSITY SCHOOL OF MEDICINE, STANFORD, CA 94305 |
contact email | khavari@stanford.edu |
lab head | |
Smarajit Mondal |
contact affiliation | Stanford University School of Medicine |
contact email | mondal@stanford.edu |
dataset submitter | |
Full Dataset Link List
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/PXD029470 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029470
- Label: PRIDE project
- Name: PROBER Identifies Proteins Associated with Programable Sequence-Specific DNA in Living Cells