Integrative analysis revealed the molecular mechanism underlying RBM10‐mediated splicing regulation

Abstract

RBM10 encodes an RNA binding protein. Mutations in RBM10 are known to cause multiple congenital anomaly syndrome in male humans, the TARP syndrome. However, the molecular function of RBM10 is unknown. Here we used PAR-CLIP to identify thousands of binding sites of RBM10 and observed significant RBM10–RNA interactions in the vicinity of splice sites. Computational analyses of binding sites as well as loss-of-function and gain-of-function experiments provided evidence for the function of RBM10 in regulating exon skipping and suggested an underlying mechanistic model, which could be subsequently validated by minigene experiments. Furthermore, we demonstrated the splicing defects in a patient carrying an RBM10 mutation, which could be explained by disrupted function of RBM10 in splicing regulation. Overall, our study established RBM10 as an important regulator of alternative splicing, presented a mechanistic model for RBM10-mediated splicing regulation and provided a molecular link to understanding a human congenital disorder.

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

“…Differential splicing analyses comparing RBM10 LoF mutant tumors (n = 32) and samples WT for all splicing factor genes (n = 87) identified exon inclusion as the primary alternative splicing event in both LUAD and BLCA (Figure 4C; Figure S3A; Tables S2 and S3). This is consistent with earlier reports correlating the overexpression of RBM10 in HEK293 cells with exon skipping (Wang et al, 2013). …”

“…Interestingly, RBM10 expression has also been shown to correlate with retention of the introns flanking the exons that are skipped due to its activity (Wang et al, 2013; Figure S3C), and we observed the corresponding normal splicing of these introns upon RBM10 loss in LUAD (Figure 4D). The majority of genes with this pattern of altered splicing by RBM10 LoF mutation were upregulated compared to RBM10 WT samples, suggesting that RBM10-mediated cassette exon repression acts as an overall gene regulatory mechanism.…”

“…RBM10 is an RNA-binding protein associated exclusively with splicing repression (Wang et al, 2013), typically acting by binding in the intronic regions both up- and downstream of cassette exons. It is most frequently mutated in LUAD (Cancer Genome Atlas Research Network, 2014) and BLCA (Table S2), and the mutations are mutually exclusive with other splicing factor gene mutations (Figure 4A).…”

Comparative transcriptome analysis reveals that the extracellular matrix receptor interaction contributes to the venous metastases of hepatocellular carcinoma

“…The read alignment BAM files produced by TopHat and the Hg19 alternative events annotations downloaded from the MISO main page served as an input. The software computed the percentage of transcripts that were spliced to include exons, known as the PSI (Ψ) [26]:…”

Barcelona conference on epigenetics and cancer 2016 – beyond cancer genomes

“…25,26 NUMB isoform switch is regulated by RBM10, which, importantly, is one of the most frequently mutated genes in lung cancer. 27,28,29,30 This work opens a possible therapeutical avenue to regulate NUMB splicing with chemically modified antisense oligonucleotides, thereby reversing the effect on proliferation, which is the topic of ongoing investigation.…”