A mechanism underlying position-specific regulation of alternative splicing

Abstract

Many RNA-binding proteins including a master regulator of splicing in developing brain and muscle, polypyrimidine tract-binding protein 1 (PTBP1), can either activate or repress alternative exons depending on the pre-mRNA recruitment position. When bound upstream or within regulated exons PTBP1 tends to promote their skipping, whereas binding to downstream sites often stimulates inclusion. How this switch is orchestrated at the molecular level is poorly understood. Using bioinformatics and biochemical approaches we show that interaction of PTBP1 with downstream intronic sequences can activate natural cassette exons by promoting productive docking of the spliceosomal U1 snRNP to a suboptimal 5′ splice site. Strikingly, introducing upstream PTBP1 sites to this circuitry leads to a potent splicing repression accompanied by the assembly of an exonic ribonucleoprotein complex with a tightly bound U1 but not U2 snRNP. Our data suggest a molecular mechanism underlying the transition between a better-known repressive function of PTBP1 and its role as a bona fide splicing activator. More generally, we argue that the functional outcome of individual RNA contacts made by an RNA-binding protein is subject to extensive context-specific modulation.

Validation and Classification of Atypical Splicing Variants Associated With Osteogenesis Imperfecta

“…Variants in probands PUMC-276, PUMC-290, PUMC-15, PUMC-105, PUMC-369, and PUMC-189 belong to this case. It was known that by binding to different locations of sequences, polypyrimidine tract-binding protein1 (PTBP1) can induce either exon skipping or inclusion (Hamid and Makeyev, 2017). Sanz et al (2010) reported that variants affecting PPT region resulted in the exon skipping.…”

Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis

“…PTBP1 acts as a master regulator of splicing to activate or repress alternative exons depending on the pre-mRNA recruitment position. This regulation plays an important role mainly in the growth and differentiation of neuronal cells (Vuong et al, 2016;Hamid and Makeyev, 2017). PTBP1 blocks up-frameshift 1 (UPF1), a nonsense-mediated mRNA decay (NMD) protein, from binding to 3' untranslated regions (UTRs) to preserve the capacity of long 3' UTRs to regulate gene expression and the ability of NMD to accurately detect aberrant mRNAs (Ge et al, 2016).…”

An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands

“…The stem loops 3 and 4 are responsible for interactions with the splicing regulators FUS ( 33 ) and PTBP1 ( 34 ), respectively. Polypyrimidine tract binding protein 1 (PTBP1) is a well-studied splicing factor that promotes or represses spliceosome assembly depending on the position of the cis RNA element with respect to the splice site ( 35 ). The stem loop 4 is essential for splicing ( 36 ) and recently, the U2 snRNP component SF3A1 was shown to establish direct contacts with U1 snRNA stem loop 4 during spliceosome assembly ( 37 ).…”