Global Analyses of Light-Regulated Alternative Splicing in Plants

Light is one of the most important factors influencing plant growth and development. Changes of light condition dramatically affect developmental programs throughout the life cycle of plants. Light-sensing photoreceptors play major roles in regulating these processes via signal transduction and gene regulation. Although various levels of gene expression are known to be modulated by photoreceptors, regulation at the pre-mRNA splicing step is less discussed. We have performed mRNA sequencing to analyze transcriptome changes during light exposure in the moss Physcomitrella patens. Our data showed that light induces intensive alternative splicing. Light-responsive intron retention preferentially occurred in transcripts for photosynthesis and translation, which reveals that light-mediated splicing regulation has transcript specificity. Moreover, intron retention was rapidly induced by light but misregulated in photoreceptor-deficient and -knockout mutants, suggesting the involvement of photoreceptors in splicing regulation. Preliminary data indicate the red/far-red photoreceptor phytochrome physically interacts with splicing regulators in the nucleus in a red-light dependent manner. We therefore propose that when plants expose to light, alternative splicing is rapidly fine-tuned to re-organize certain metabolic processes and regulate gene expression. Photoreceptors directly participate in regulation of alternative splicing through interacting with regulatory proteins to modulate splicing activity.