Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana

How stable and temperature-dependent variations in DNA methylation and nucleosome occupancy influence alternative splicing (AS) remains poorly understood in plants. To answer this, we generated transcriptome, whole-genome bisulfite, and MNase sequencing data for an epigenetic Recombinant Inbred Line (epiRIL) of A. thaliana at normal and cold temperature. For comparative analysis, the same data sets for the parental ecotype Columbia (Col-0) were also generated, whereas for DNA methylation, previously published high confidence methylation profiles of Col-0 were used. Significant epigenetic differences in an identical genetic background were observed between Col-0 and epiRIL lines under normal and cold temperatures. Our transcriptome data revealed that differential DNA methylation and nucleosome occupancy modulate expression levels of many genes and AS in response to cold. Collectively, DNA methylation and nucleosome levels exhibit characteristic patterns around intron-exon boundaries at normal and cold conditions, and any perturbation in them, in an identical genetic background is sufficient to modulate AS in Arabidopsis.

Automated summary

This study investigates the influence of stable and temperature-dependent variations in DNA methylation and nucleosome occupancy on alternative splicing in plants using an epigenetic Recombinant Inbred Line and the parental ecotype Columbia. The results show significant epigenetic differences between the two lines in response to normal and cold temperatures, affecting gene expression levels and alternative splicing. The patterns of DNA methylation and nucleosome levels around intron-exon boundaries are shown to modulate alternative splicing in Arabidopsis.