PXD029392

PXD029392 is an original dataset announced via ProteomeXchange.

Title	Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites
Description	Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:02:50.491.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vytautas Iesmantavicius
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-28 01:53:52	ID requested
1	2023-09-07 02:24:50	announced
2	2023-11-14 09:05:07	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:02:52	announced	2024-10-22: Updated project metadata.

10.1261/rna.079465.122;

Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, B, ü, hler M, Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA, 29(8):1140-1165(2023) [pubmed]

submitter keyword: CCDC174, spliceosome, Protein-RNA interactions, splicing factors, RNA-binding proteins,NRDE2

Marc Buehler
contact affiliation	Senior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
contact email	marc.buehler@fmi.ch
lab head
Vytautas Iesmantavicius
contact affiliation	Friedrich Miescher Institute for Biomedical Research
contact email	vytautas.iesmantavicius@fmi.ch
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/2023/09/PXD029392

PRIDE project URI

• PRIDE
  1. PXD029392
     1. Label: PRIDE project
     2. Name: Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites