Epigenetics of Alternative Splicing in Plants

Plants use complex gene regulatory mechanisms to overcome environmental changes. Alternative splicing (AS) of pre-mRNAs makes an important contribution to modulate the transcriptome. Recent evidence supports the co-transcriptional regulation of AS in plants, hence the chromatin state as shown for mammals can impact AS. However, how dynamic changes in the chromatin influence the AS process remains poorly understood. We analyzed sequencing data of an epigenetic Recombinant Inbred Line (epiRIL) and compared it to its wild type parent (Columbia, Col-wt) under normal temperature and cold stress to understand how DNA methylation and chromatin differences modulate AS. We found that exons exhibit higher DNA methylation and nucleosome occupancy level than introns in both Col-wt and the epiRIL. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, also exhibit distinctive nucleosome occupancy compared with the flanking regions that may aid in their recognition by the splicing machinery. Variation in DNA methylation and nucleosome occupancy affects global as well as core circadian clock genes (CCA1 and LHY) splicing patterns. Collectively, our data show that epigenetic differences in an identical genetic background are sufficient to modulate AS in plants.