Fig. 1

RNA-seq analysis in WT, ∆kmt1/∆dim-5 and ∆kmt2/∆set-1. (a) Graphical representation of identified transcripts. In total, there were 21,475 unique transcripts classified as 10,784 previously annotated protein-coding transcripts and 10,692 unannotated transcripts, that were further subdivided into 2444 natural antisense transcripts and 2268 predicted lincRNAs. (b) Violin plot depicting the expression levels (FPKM, log2) of transcripts belonging to annotated transcripts, NATs and lincRNAs. The black dots indicate median. (c) Heatmap showing the clustering of light-activated and light-repressed genes in WT (q < 0.05) and compared to the same genes in ∆kmt1/∆dim-5 and ∆kmt2/∆set-1. Group A includes genes that were light-activated in WT while Group B represents genes that were light-repressed. Relative expression levels are shown as log2 fold change of LP vs. DD as indicated in the range bar. The overlap among (d) light-activated (q < 0.05) or (e) light-repressed (q < 0.05) genes are represented as Venn diagrams