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. 2022 Nov 21;11:e78808. doi: 10.7554/eLife.78808

Figure 3. Splicing events sensitive to temperature and loss of FIO1.

(A–B) Analysis of Illumina RNA-seq data presented as bar plots showing the proportion of splicing events of each class, as labelled by SUPPA, which have significantly different usage (false discovery rate [FDR] <0.05) at either (A) varying temperatures or (B) in fio1-3. In (B), events for which the response to temperature changes in fio1-3 are shown in orange. (C) Gene track of Illumina RNA-seq reads showing the change in retention of MAF2 intron 3 in fio1-3, at 20°C. Expression is normalised by the read coverage at the −1 position of the 5’ splice site (5’SS). (D) Boxplot of Illumina RNA-seq analysis showing the change in retention of MAF2 intron 3 at varying temperatures and in fio1-3.

Figure 3—source data 1. Differential gene expression analysis results from Illumina RNA-seq experiment on Col-0 and fio1-3 mutants at four temperatures.
Figure 3—source data 2. Differential splicing analysis results from Illumina RNA-seq experiment on Col-0 and fio1-3 mutants at four temperatures.

Figure 3.

Figure 3—figure supplement 1. Analysis of Illumina RNA-seq data.

Figure 3—figure supplement 1.

(A) Boxplot showing the reduction in overall gene expression of FIO1 in fio1-3. (B) Volcano plots showing the distribution of alternative splicing events from four classes (alternative 5’ splice sites [5’SSs], alternative 3’ splice sites [3’SSs], skipped exons, and retained introns) in the fio1-3 mutant compared to Col-0. For skipped exons and retained introns, a positive ΔPSI means that the feature is retained more in the fio1-3 mutant, whilst a negative ΔPSI means the feature is spliced out more in the fio1-3 mutant. ΔPSIs are unsigned for alternative 5’SSs and 3’SSs. (C) Histogram showing change in the difference between fio1-3 and Col-0 percent splicing index (PSI) between 4 and 28°C (ΔΔPSI). A positive ΔΔPSI indicates that there is a greater deviation from Col-0 splicing levels in fio1-3 at 28°C than at 4°C.
Figure 3—figure supplement 2. Illumina RNA-seq analysis of differential gene expression between Col-0 and fio1-3.

Figure 3—figure supplement 2.

(A–I and K–L) Boxplots showing the increase in overall gene expression of the flowering time activators (A) FT (AT1G65480), (B) SOC1 (AT1G65480), and reduction in the expression of the flowering repressors (C) FLM (AT1G77080), (D) MAF2 (AT5G65050), (E) MAF3 (AT5G65060), (F) MAF4 (AT5G65070), (G) MAF5 (AT5G65080), (H) FLC (AT5G10140), and (I) COOLAIR transcripts expressed antisense to FLC. (J) Gene track of Illumina RNA-seq reads showing the expression of FLC and COOLAIR transcripts at 20°C in Col-0 and fio1-3. The mRNA-level expression of (K) the flowering activator CO (AT5G15840) and (L) the flowering repressor SVP (AT2G22540) was also not affected.