Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation

Abstract

Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Motif analysis revealed that SRSF10 binding to cassette exons was associated with exon inclusion, whereas the binding of SRSF10 within downstream constitutive exons was associated with exon exclusion. This positional effect was further demonstrated by the mutagenesis of potential SRSF10 binding motifs in two minigene constructs. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Consistent with this observation, cells depleted of SRSF10 expression were far more susceptible to endoplasmic reticulum stress-induced apoptosis than control cells. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.

BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells

“…7). Together, these findings demonstrated that inclusion of exon5a by SRSF10 is consistent with activation mechanism for the protein in splicing regulation 19,21 , and strongly indicated that BCLAF1 is a direct splicing target regulated by SRSF10.…”

“…Strikingly, we found many purine-rich (GA rich) motifs especially within the downstream 200 bp region (5a3) of exon5a, and each constitutes a good match to the binding motif of splicing factor SRSF10 (previously known as SRp38; Supplementary Fig. 6a) 21,29 . Neither exon5 nor exon11 contained a match to the SRSF10 consensus sequence.…”

“…SRSF10 is an atypical SR protein that functions as a sequencedependent splicing activator as well as a key regulator of alternative splicing [19][20][21] . Motif analysis of SRSF10-regulated splicing events in vivo revealed that the binding of SRSF10 to the alternative exon is associated with exon inclusion 21 .…”

“…Motif analysis of SRSF10-regulated splicing events in vivo revealed that the binding of SRSF10 to the alternative exon is associated with exon inclusion 21 . To determine whether SRSF10 specifically binds exon5a to activate its inclusion, we prepared 32 P-labelled 5a1, 5a2 and 5a3 RNA, each containing the putative SRSF10 binding sites, and compared binding in gel shift assays with exon5 RNA.…”

“…Overexpression of BCLAF1-L considerably increased colony-forming efficiency of cells, suggesting protumorigenic capacity for the L isoform in colon cancer cells. Mechanism analysis demonstrated that splicing factor SRSF10 (serine/arginine-rich splicing factor 10), an atypical member of SR proteins and a key regulator of alterative splicing in vivo [19][20][21] , specifically binds to exon5a. SRSF10 activates the inclusion of exon5a, as its loss leads to a dramatic shift of exon5a-containing product to exon5a-lacking product in colon cancer cells.…”