Figure 1

Overview of RNA editing in plant nuclear transcripts. (A) Statistics of RNA editing sites in nuclear protein-coding transcripts, pre-miRNAs, and mitochondrial and chloroplast transcripts. The number of editing sites in the nuclear protein-coding transcripts (blue histogram) is measured by left y axis and that of the pre-miRNAs (green curve) or the mitochondrial and chloroplast transcripts (red curve) by right y axis. The 12 editing patterns are shown on the x axis. “M” represents the editing sites in the mitochondrial transcripts and none has been detected in the chloroplast transcripts. (B) Novel elements surrounding the editing sites. The 100-nt sequences (x axis) surrounding the editing sites of nuclear protein-coding transcripts were analyzed by using WebLogo. Results of three different editing patterns (A-to-U, G-to-U, and C-to-G) in the nuclear transcripts and C-to-U editing in the mitochondrial transcripts (“M”) are shown. The inset in the upper right corner shows the result for random sequences. (C) GO term enrichment analysis of edited nuclear protein-coding genes. Results of C-to-U and A-to-G edited genes produced by GO::TermFinder are shown. The GO terms, significantly enriched in edited genes (corrected P-value < 1.00E-07), are listed at the bottom. “All” represents all the protein-coding genes (the circle outside the pie chart). “Edited” represents the edited protein-coding genes (the inner pie chart). The percentage was calculated by dividing the number of the “All” (or the “Edited”) genes with the certain GO term by the number of all the listed “All” (or “Edited”) genes. (D) Clustering analysis of RNA editing sites. MPSS data from 17 libraries were analyzed. The ratio of the expression value of all the edited reads to that of the total reads surrounding the editing site was calculated. Only the sites with ratios more than 2% were clustered. The ratio values were represented by the color intensity shown at the bottom. On the right, the transcripts with mitochondrion- or chloroplast-related functions are in orange or green shadows respectively. See details of the 17 libraries in Additional File 9: Data S7 or the MPSS plus database (http://mpss.udel.edu/at/).