Crossregulation and Functional Redundancy between the Splicing Regulator PTB and Its Paralogs nPTB and ROD1

Abstract

SummaryAmong the targets of the repressive splicing regulator, polypyrimidine tract binding protein (PTB) is its own pre-mRNA, where PTB-induced exon 11 skipping produces an RNA substrate for nonsense-mediated decay (NMD). To identify additional PTB-regulated alternative splicing events, we used quantitative proteomic analysis of HeLa cells after knockdown of PTB. Apart from loss of PTB, the only change was upregulation of the neuronally restricted nPTB, resulting from decreased skipping of nPTB exon 10, a splicing event that leads to NMD of nPTB mRNA. Compared with knockdown of PTB alone, simultaneous knockdown of PTB and nPTB led to larger changes in alternative splicing of known and newly identified PTB-regulated splicing events. Strikingly, the hematopoietic PTB paralog ROD1 also switched from a nonproductive splicing pathway upon PTB/nPTB knockdown. Our data indicate crossregulation between PTB and its paralogs via nonproductive alternative splicing and a large degree of functional overlap between PTB and nPTB.

Polypyrimidine tract binding proteins (PTB) regulate the expression of apoptotic genes and susceptibility to caspase-dependent apoptosis in differentiating cardiomyocytes

“…However, PTB expression did not alter the steady-state amount of apoptotic gene transcrips ( Figure 3 and data not shown). As expected, expression of either human PTB1 or PTB4 induced a slight decrease in endogenous PTB transcripts (Figure 3, second row from top) and skipping of their target exon 10 in the transcript of endogenous neural PTB (nPTB) 19 (Figure 3).…”

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

“…Data are mean values from three independent experiments and total six replicates (17 replicates for the wild-type); error bars show SE. previously described auto-and cross-regulation of At-PTB1 and At-PTB2, leading to PTB-dependent inclusion of a poison exon (Stauffer et al, 2010). The opposite mode of autoregulation (i.e., PTB-mediated exon skipping) is found for At-PTB3 (Stauffer et al, 2010) and mammalian PTBs (Wollerton et al, 2004;Spellman et al, 2007). Furthermore, it has been reported that PTB-activated exons typically had PTB binding sites downstream of the exon, while PTB-repressed exons contained pyrimidine motifs upstream of or within the cassette exon (Llorian et al, 2010).…”

Control of alternative pre-mRNA splicing by Ca++ signals

“…Hopefully, the now available mammalian RNAi libraries could also be applied for functional screening of genes essential in inducible alternative splicing. Thirdly, splicing-sensitive microarrays and whole genome exon arrays [64,78,82,83,[223][224][225], combined with loss-of-functions of splicing factors (such as knockout or RNAi), will allow the identification of a group of exons/genes controlled by a particular factor during Ca ++ -regulation of splicing. Lastly, bioinformatics approaches with highly predictive RNA elements could also help identify a group of exons regulated by Ca ++ signals, as has been demonstrated for the alternative splicing factor Nova-1 [62].…”

“…The relative levels of positive and negative regulatory factors determine the generation of variant mRNA isoforms in specific cell types [73][74][75]. Brainenriched splicing factors include Nova-1 and -2 [62][63][64][65][66], FOX-1 and -2 [54-61], PTBP2 (nPTB) and neuronal Hu proteins [76][77][78][79][80][81][82][83].…”