Project description:We identified PRP4 kinase-A (PRP4ka) in a forward genetic screen based on an alternatively-spliced GFP reporter gene in Arabidopsis thaliana (Arabidopsis). Prp4 kinase, which was the first spliceosome-associated kinase shown to regulate splicing in fungi and mammals, has not yet been studied in plants. Analysis of RNA-seq data from the prp4ka mutant revealed widespread perturbations in alternative splicing. A quantitative iTRAQ-based phosphoproteomics investigation of the mutant identified phosphorylation changes in several serine/arginine-rich proteins, which regulate constitutive and alternative splicing, as well as other splicing-related factors. The results demonstrate the importance of PRP4ka in alternative splicing and suggest that PRP4ka may influence alternative splicing patterns by phosphorylating a subset of splicing regulators.
Project description:We revisited the transcriptomes of Arabidopsis seedlings by analyzing alternatively spliced variants during early photomorphogenesis. Half of the expressed transcripts have alternatively spliced forms; many were previously uncharacterized. Light regulated AS for 19.2% of the genes expressed, intron retention being the most prevalent type of alternative splicing. We observed distinct groups of transcripts with differential expression levels or with AS, which implies that transcription and AS target different sets of genes. More than one-third of the AS transcripts with retained introns were translatable. In summary, these AS variants could play regulatory roles and increase the proteome complexity in photomorphogenic Arabidopsis
