Using RNA-Seq and genetics to investigate condition and tissue-specific alternative splicing in plant species

Most protein-coding genes in higher eukaryotes contain introns, segments of the primary, pre-mRNA transcript that are removed during splicing. During splicing, a macromolecular complex called the spliceosome assembles on the pre-mRNA and catalyzes intron removal. Spliceosome assembly and function depend on RNA-binding accessory proteins to recognize intron boundaries. Differential expression and activity of these accessory proteins allow different splice sites to be selected depending on cell type or developmental stage. This variability in splice site selection is called alternative splicing, occurring in nearly every animal and plant species examined thus far. Alternative splicing makes it possible for one gene to produce multiple mRNA species and thus encode different – but similar – proteins. In animals, many processes use alternative splicing as a regulatory mechanism; two of the best studied are sex determination in invertebrates and neuronal cell differentiation in mammals. But the ability to splice also introduces risks – many genetic disorders are due to splicing errors. In plants, we know far less about how splicing occurs and how it is regulated. And yet, studying splicing in plants could yield novel insights into this nearly universal process. Plants live their entire lives in one location and must acclimate to daily and seasonal fluctuations in temperature, water availability, and sunlight. Studying how the splicing machinery in plants adjusts to environmental challenges can illuminate general features of splicing regulation and catalysis in all organisms, including humans. In this talk, I will discuss how my group uses experimental and computational strategies to investigate splicing regulation in plants. In addition to discussing our findings thus far, I will demonstrate software tools we developed to help researchers understand and predict the effects of alternative splicing on gene function.