Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

Abstract

The nuclear cap-binding protein complex (CBC) participates in 5′ splice site selection of introns that are proximal to the mRNA cap. However, it is not known whether CBC has a role in alternative splicing. Using an RT–PCR alternative splicing panel, we analysed 435 alternative splicing events in Arabidopsis thaliana genes, encoding mainly transcription factors, splicing factors and stress-related proteins. Splicing profiles were determined in wild type plants, the cbp20 and cbp80(abh1) single mutants and the cbp20/80 double mutant. The alternative splicing events included alternative 5′ and 3′ splice site selection, exon skipping and intron retention. Significant changes in the ratios of alternative splicing isoforms were found in 101 genes. Of these, 41% were common to all three CBC mutants and 15% were observed only in the double mutant. The cbp80(abh1) and cbp20/80 mutants had many more changes in alternative splicing in common than did cbp20 and cbp20/80 suggesting that CBP80 plays a more significant role in alternative splicing than CBP20, probably being a platform for interactions with other splicing factors. Cap-binding proteins and the CBC are therefore directly involved in alternative splicing of some Arabidopsis genes and in most cases influenced alternative splicing of the first intron, particularly at the 5′ splice site.

Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

“…The observed genetic interactions between emu and se-1 may provide a clue to the mechanism of action of EMU. Interestingly, mutations in the Arabidopsis genes that encode the two cap-binding complex (CBC) subunits-CAP-BINDING PROTEIN20 (CBP20) and ABSCISIC ACID HYPERSESITIVE1 (ABH1)/CBP80-cause a serrated leaf phenotype and mRNA splicing defects as observed in emu and se-1 mutants (Hugouvieux et al 2001;Papp et al 2004;Kuhn et al 2007;Laubinger et al 2008;Raczynska et al 2010). It is also noteworthy that the abh1-8 mutation enhanced the phyllotaxy defect of ago1-38 mutant inflorescences as seen in emu ago1-27 plants (Gregory et al 2008).…”

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

“…The abh1 and cbp20 mutants are impaired in ABH1/CBP80 and CBP20, the subunits of the CAP binding complex, and are hypersensitive to ABA (Hugouvieux et al, 2001;Papp et al, 2004). ABH1/CBP80 and CBP20 contribute to the regulation of AS and preferentially affect AS of the first intron, particularly at the 59 splice site (Laubinger et al, 2008;Raczynska et al, 2010). The hnRNP-like At-GRP7 (for glycine-rich RNA binding protein 7) that is upregulated by cold and oxidative stress has also been associated with ABA responses (Carpenter et al, 1994;Cao et al, 2006;Kim et al, 2008;Schöning et al, 2008;Schmidt et al, 2010;Streitner et al, 2010).…”

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

“…While most of our current knowledge on AS regulation is based on animal systems, previous work has provided evidence for the presence of SR Reddy and Shad Ali, 2011) and hnRNP proteins (Wachter et al, 2012) and their roles within splicing control in plants. Furthermore, a function of the nuclear cap binding protein complex in controlling AS events in Arabidopsis has been demonstrated (Raczynska et al, 2010). Given that several aspects of AS, such as its prevalent types, have been shown to differ between animals and plants (Reddy, 2007), a thorough analysis of the currently ill-defined plant splicing code is of central importance for our understanding of this process (Reddy et al, 2012).…”