Divergence of alternative splicing in Arabidopsis

We investigated genome-wide variation in AS in Arabidopsis thaliana accessions Col and Ler using RNA-seq. We identified many cis-regulatory elements associated with AS events, among which polypyrimidine tracts (e.g., UCUCUC and CUCUCU) were significantly overrepresented, especially in the exons upstream of each AS event. We found that variation in cis-regulatory element sequences contributed to divergence in AS levels, but not to differential gene transcription between the two Arabidopsis accessions. Overall design: RNA-seq analysis of alternative splicing in the first leaf of 14 day old seedlings of two Arabidopsis Col and Ler.