Proteomics

Dataset Information

0

Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites


ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Early Embryonic Cell

SUBMITTER: Vytautas Iesmantavicius  

LAB HEAD: Marc Buehler

PROVIDER: PXD029392 | Pride | 2023-09-07

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
1841_mqpar.xml Xml
1841_proteinGroups.txt Txt
1963_mqpar.xml Xml
1963proteinGroups.txt Txt
F1_190930_DH_1841_Nrde2D174R__S13.raw Raw
Items per page:
1 - 5 of 47
altmetric image

Publications

Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.

Flemr Matyas M   Schwaiger Michaela M   Hess Daniel D   Iesmantavicius Vytautas V   Ahel Josip J   Tuck Alex Charles AC   Mohn Fabio F   Bühler Marc M  

RNA (New York, N.Y.) 20230503 8


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 1  ...[more]

Similar Datasets

2023-05-04 | GSE179744 | GEO
2017-05-24 | GSE98779 | GEO
2021-06-16 | GSE144906 | GEO
2021-06-16 | GSE144905 | GEO
2021-06-16 | GSE144874 | GEO
2024-01-03 | GSE252348 | GEO
2010-09-29 | GSE24179 | GEO
2022-03-31 | GSE176144 | GEO
2015-12-01 | GSE75517 | GEO
2018-02-22 | GSE97015 | GEO