PXD029392 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_09:04:59.150.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 |
Dataset History
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. |
Publication List
Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, B, ΓΌ, hler M, Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA, 29(8):1140-1165(2023) [pubmed] |
Keyword List
submitter keyword: CCDC174, spliceosome, Protein-RNA interactions, splicing factors, RNA-binding proteins,NRDE2 |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029392
- Label: PRIDE project
- Name: Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites