PXD065004-1

PXD065004 is an original dataset announced via ProteomeXchange.

Title	Teamwork of clustered low affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers
Description	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 sites, many exhibiting low affinity for NF-κB in vitro. Deletion of these sites demonstrated their collective critical role in transcription. We explored how these “weak” κB sites exert their influence, especially given the typically low nuclear concentration of NF-κB. Using proteomics approaches, we identified additional nuclear factors, including other DNA-binding TFs, that could interact with κB site-bound NF-κB RelA without their direct interaction to DNA. ChIP- seq and RNA-seq analyses suggest that these accessory TFs, referred to as the TF-cofactors of NF-κB, facilitate dynamic recruitment of NF-κB to the clustered κB sites. Overall, the occupancy of NF-κB at promoters and enhancers appears to be defined by a collective contribution from all κB sites, both weak and strong, in association with specific cofactors. This congregation of multiple factors within dynamic transcriptional complexes is likely a common feature of transcriptional programs.
HostingRepository	PRIDE
AnnounceDate	2025-10-13
AnnouncementXML	Submission_2025-10-13_13:05:55.498.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shandy Shahabi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-13 10:22:03	ID requested
⏵ 1	2025-10-13 13:05:56	announced

10.1093/nar/gkaf846;

Shahabi S, Biswas T, Shen Y, Sanahmadi R, Zou Y, Ghosh G, B RelA dimers. Nucleic Acids Res, 53(18):(2025) [pubmed]

submitter keyword: transcription, cofactor, promoter, κB DNA,NF-kappa B (NF-κB)

Gourisankar Ghosh
contact affiliation	UCSD
contact email	gghosh@ucsd.edu
lab head
Shandy Shahabi
contact affiliation	UCSD
contact email	sshahabi@ucsd.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/2025/10/PXD065004

PRIDE project URI

• PRIDE
  1. PXD065004
     1. Label: PRIDE project
     2. Name: Teamwork of clustered low affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers