PXD041633

PXD041633 is an original dataset announced via ProteomeXchange.

Title	Analysis of the interactome of B2-SINE RNA transcripts
Description	B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-28_16:04:44.098.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juan Oses-Prieto
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-18 14:28:29	ID requested
⏵ 1	2025-09-28 16:04:45	announced

10.1016/j.cell.2025.04.030;

Zahavi EE, Koppel I, Kawaguchi R, Oses-Prieto JA, Briner A, Monavarfeshani A, Dalla Costa I, van Niekerk E, Lee J, Matoo S, Hegarty S, Donahue RJ, Sahoo PK, Ben-Dor S, Feldmesser E, Ryvkin J, Leshkowitz D, Perry RB, Cheng Y, Farber E, Abraham O, Samra N, Okladnikov N, Alber S, Albus CA, Rishal I, Ulitsky I, Tuszynski MH, Twiss JL, He Z, Burlingame AL, Fainzilber M, Repeat-element RNAs integrate a neuronal growth circuit. Cell, 188(16):4350-4365.e22(2025) [pubmed]

submitter keyword: B2-SINE RNAs,RNA-Protein interactions, RNA regulators

Mike Fainzilber
contact affiliation	Departments of Molecular Neuroscience and Biomolecular Sciences, Weizmann Institute of Science; Rehovot, Israel.
contact email	mike.fainzilber@weizmann.ac.il
lab head
Juan Oses-Prieto
contact affiliation	UCSF
contact email	joses@cgl.ucsf.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/2025/09/PXD041633

PRIDE project URI

• PRIDE
  1. PXD041633
     1. Label: PRIDE project
     2. Name: Analysis of the interactome of B2-SINE RNA transcripts