Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1
Creators
- 1. University of Chicago
- 2. The Hong Kong University of Science and Technology
Description
2′-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we used RNA affinity purification, followed by mass spectrometry to identify Nm-binding proteins. The Nm-binding protein candidates exhibit enriched binding at known Nm sites. Some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to skipped exons, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1-binding sites, and N m depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.
Data availability
All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The sequencing data are accessible in the Gene Expression Omnibus through accession numbers GSE294792, GSE294793, and GSE294794. Published Nm-mut-seq dataset of internal mRNA (GSE174518); ENCODE datasets of eCLIP experiments targeting FUBP3 (ENCSR486YGP), IGF2BP1 (ENCSR744GEU), and IGF2BP3 (ENCSR993OLA); and their IgG control (GSE77629) were used for analysis.Additional details
Identifiers
- DOI
- 10.1126/sciadv.ady3894
- Other
- oai:uchicago.tind.io:16400
Funding
- National Institutes of Health
- RM1 HG008935
- National Institutes of Health
- R01 HL155909
- Howard Hughes Medical Institute