The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

Abstract

Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.

RBM10 promotes transformation-associated processes in small cell lung cancer and is directly regulated by RBM5

“…A very recent study in non-transformed mouse cells not only supports our working model, but extends its relevance beyond cancer-based systems [75]. In that study, Rodor et al .…”

An RRM–ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

“…and the recently reported CC motif enriched in RBM10 cross-linked RNAs in a mouse cell line (4). Moreover, a pyrimidine-rich intronic 3΄ segment containing runs of Cs but no GGAs has been directly shown to recruit RBM10 and mediate repression of the alternative exon 9 in NUMB pre-mRNA.…”

RBM10: Harmful or helpful‐many factors to consider

“…The severe impact of RBM10 mutations in these children strongly suggests a critical role for RBM10 in fetal development. This is supported by in vivo and in vitro findings showing RBM10 expression to be: (1) regulated during rat skeletal and cardiac muscle cell differentiation; (2) regulated both temporally and spatially during murine midgestation embryo development; (3) a regulator of mouse embryonic stem cell proliferation and differentiation; and (4) able to influence the alternative splicing of SMN2 . The latter could be of clinical relevance to patients with spinal muscular atrophy who have a homozygous deletion of SMN1 , and thus rely on their SMN2 gene for all SMN protein.…”

“…As predicted by the consensus functional motifs in its primary sequence, RBM10 is a regulator of alternative splicing. This was first demonstrated in 2013/2014, and has since been confirmed by a number of groups . For instance, RBM10 is involved in the alternative splicing of pre‐mRNA from NUMB , FAS , Dlg4 , and SMN2 .…”

“…For instance, many initial functional studies associated RBM10 expression with increased apoptosis, decreased cell proliferation, decreased colony formation, and decreased xenograft tumor growth . Counterintuitively, however, very recent studies have suggested a tumor promoter role for RBM10, and associated RBM10 expression with additional processes and mechanisms of action . This functional dichotomy highlights the importance of not only gaining a deeper understanding of the downstream consequences of RBM10 expression, but identifying the mechanisms responsible for regulating RBM10 itself.…”