Figure 4

Genes with abnormal splicing in NaCl treatments are closely associated with stress response and transcriptional activation. (A) Venn diagram of the overlap of differential alternative splicing (DAS) genes in 50, 150 or 300 mM NaCl treatments. (B) A two-dimensional (2-D) view of the relationship between the genes with abnormal splicing and their functional annotations. The functional classification of genes was done by the DAVID software. Top 30 of the functional annotations that were ordered by the enrichment scores were selected for the 2-D view. (C) A network generated by Mapman indicates that genes with aberrant splicing are involved in various stress response pathways, including hormone-signaling pathways, MAPK-signaling pathways and transcription regulation. (D) The representative AS events in six stress-responsive genes validated by RT-PCR and visualized by IGV browser. In the RT-PCR validation, the red asterisk (*) to the right side denotes the alternative splice form. The red arrow on the top indicates an increase (pointing upward) or decrease (pointing down) in AS events at that salt concentration. In the IGV visualization, the exon-intron structure of each gene is given at the bottom of each panel. The grey peaks above the exon-intron structure indicate the RNA-seq read density across the gene. The red arrows represent alternative splice sites. The blue arcs in CIPK3 indicate splice junction reads that support the junctions. (E) Enrichment of biological processes in DAS genes and genes without DAS. The top 10 functional categories in DAS genes are shown. In the stress-related and RNA processing categories, the possibility of genes that undergo AS is much higher than the possibility of genes that are not alternatively spliced.