Fig. 6

Genes with perturbed splicing in GEX1A treatment are associated with stress responses. a and b, Comparison of intron retention between control and GEX1A treatments. Reads numbers for the exons and introns are plotted. The expression of introns (a), but not exons (b), in GEX1A treatments showed a global upregulation. c, Comparison of global alternative splicing between control and GEX1A treatments. The intron retention events increased in the drug-treated samples, while the other AS events (including alternative 5’ splice sites, 3’ splice sites, and exon skipping) decreased in the GEX1A-treated samples. d, A two-dimensional view of the functional annotations of genes with retained introns in GEX1A treatment. The functional classification of genes was done using the DAVID software. The top 40 functional annotations were ordered by the number of genes in each category and selected for the two-dimensional view, which indicates that genes with retained introns were strikingly enriched in the response-to-abiotic-stress category. e, Functional category (biological process) of genes with retained introns in GEX1A treatment. The top 20 categories were ordered by the enrichment scores and selected. f, RT-PCR. The cDNAs were prepared from one-week-old Arabidopsis seedlings treated with 5 μM GEX1A for 6 h, DMSO as control. Gene structure and intron retention of interesting regions from eight genes were shown in IGV program, validation of intron retention of each gene was performed by RT-PCR using intron-flanking primers, with the result shown on the right. The red bar in the IGV program snapshot represents the target amplification region. D6, DMSO 6-h treatment; G6, GEX1A 6-h treatment