An alternative splicing event amplifies evolutionary differences between vertebrates

Abstract

Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here we show that mammalian-specific skipping of polypyrimidine tract-binding protein 1 (PTBP1) exon 9 alters the splicing regulatory activities of PTBP1 and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. Engineered skipping of the orthologous exon in chicken cells induces a large number of mammalian-like AS changes in PTBP1 target exons. These results thus reveal that a single exon-skipping event in an RNA binding regulator directs numerous AS changes between species. Our results further suggest that these changes contributed to evolutionary differences in the formation of vertebrate nervous systems.

RBM4 Regulates Neuronal Differentiation of Mesenchymal Stem Cells by Modulating Alternative Splicing of Pyruvate Kinase M

“…Nevertheless, the observation that RBM4 overexpression slightly induced exon 9 skipping of PTB in 3A6 cells (Fig. 4A, lane 2) was reminiscent of a recent report that the exon 9-skipping isoform of PTB (PTB-1) is induced during neuronal differentiation of mouse embryonic stem cells (25). We indeed observed that exon 9 skipping of PTB increased gradually during neuronal differentiation of primary MSCs (Fig.…”

Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2

“…A third isoform, PTBP1.2, resulting from the shortening of exon 9 was not tested. It was previously shown that PTBP1.4 was more active than PTBP1.1 for repression of tropomyosin and other exons, but showed equal repression activity for an exon in actinin (Wollerton et al 2001;Gueroussov et al 2015). When assayed for splicing of the Dup175-DS9 exon, PTBP1.1 (isoform 1) had a moderately lower repression index than PTBP1.4 (33.4 compared with 38.1), confirming that the linker 2 sequence can increase splicing repression activity.…”

“…PTBP2 is expressed in neurons, testis, and certain other cells. PTBP1 is expressed in neuronal progenitor cells but is replaced by PTBP2 during early neuronal differentiation (Polydorides et al 2000;Boutz et al 2007;Makeyev et al 2007;Licatalosi et al 2012;Zheng et al 2012;Gueroussov et al 2015;Linares et al 2015). The switch from PTBP1 to PTBP2 alters the splicing of exons that are more sensitive to PTBP1, thus reprogramming neuronal splicing.…”

“…Each gene can produce more than one protein through alternative splicing. For PTBP1, the PTBP1.4 isoform has higher splicing repression activity than PTBP1.1 on some target exons (Wollerton et al 2001;Gueroussov et al 2015). Detailed studies of splicing repression by PTBP1 have examined several exons including the N1-exon of the Src pre-mRNA, exon 9 of GABA A receptor-γ2 subunit, and exon SM of α-actinin (Ashiya and Grabowski 1997;Chan and Black 1997;Southby et al 1999).…”

RNA Splicing

“…Interestingly, just a single exon-skipping event in the RNA-binding protein (RBP), polypyrimidine tract binding protein 1 has been shown to direct numerous alternative splicing changes between species, indicating that a single splicing event can amplify transcriptome diversity between species. 7 The recent observation that the total number of protein-coding genes does not differ much between species, fueled the hypothesis that alternative splicing largely contributes to organism diversity. And indeed, as we move up the phylogenetic tree, alternative splicing complexity increases, with the highest complexity in primates.…”