PXD064029-1

PXD064029 is an original dataset announced via ProteomeXchange.

Title	UV-crosslinking mapping of LARP6 interaction sites with RNA
Description	To map the regions of LARP6 that interacts directly with RNA, we developed a mass spectrometry-based approach termed IP-OOPS (Immunoprecipitation coupled with Orthogonal Organic Phase Separation. This approach combines the isolation of UV-C crosslinked RNA–protein adducts via Orthogonal Organic Phase Separation, with the ability to map protein regions that are attached to RNA by sequential Arg-C or Lys-C digestion, followed by trypsin digestion after purification of RNA-bound fragments, as pioneered in the RBDmap method (Castello et al., 2016). We used GFP-trap beads were used to purify LARP6-RNA complexes from UV-crosslinked MDA-MB231 cells that stably expressed GFP-LARP6 (Dermit et al., 2020). The RNA-crosslinked LARP6 was then isolated from the immunoprecipitated LARP6 fraction, using an initial OOPS, before partial digestion with Arg-C or Lys-C, which generated smaller segments, with or without RNA adducts. The RNA-bound segments were further purified from the unbound segments via a second OOPS, followed by trypsin digestion, releasing MS-detectable peptides that were adjacent to a crosslinked region. The crosslinked peptides themselves are undetectable in this approach, due to the addition of the unknown RNA mass, but released peptides after the second phase separation can be readily identified, which map to regions adjacent to the crosslink sites. In our study, Crosslink-adjacent peptides were only detected from the initial Arg-C digests.
HostingRepository	PRIDE
AnnounceDate	2026-01-22
AnnouncementXML	Submission_2026-01-22_09:09:05.968.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Faraz Mardakheh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-18 18:00:19	ID requested
⏵ 1	2026-01-22 09:09:06	announced

Dataset with its publication pending

submitter keyword: LC-MS/MS

RNA-protein interactions

Organic phase separation

RNA crosslinking

Faraz Mardakheh
contact affiliation	Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU The United Kingdom.
contact email	faraz.mardakheh@bioch.ox.ac.uk
lab head
Faraz Mardakheh
contact affiliation	Department of Biochemistry, University of Oxford
contact email	f.mardakheh@qmul.ac.uk
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/2026/01/PXD064029

PRIDE project URI

• PRIDE
  1. PXD064029
     1. Label: PRIDE project
     2. Name: UV-crosslinking mapping of LARP6 interaction sites with RNA