Fig. 5: Transcriptome and translatome analysis of Col-0 and vir-1 seedlings.
From: N6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants
a Number of differentially expressed genes between Col-0 and vir-1 after a 4-h high light (HL) treatment. b Volcano plot of differentially expressed genes between Col-0 and vir-1 after a 4-h HL treatment. Significantly downregulated genes are shown in blue, significantly upregulated genes are shown in red, and genes without significant differences in expression are shown in black. Black vertical lines highlight Log2(fold-change) = 1 or –1; black horizontal line represents FDR of 0.05. c GO enrichment analysis of the differentially expressed genes between Col-0 and vir-1 after a 4-h HL treatment. Statistical test was determined by one-sided hypergeometric test. d Number of differentially translated genes between Col-0 and vir-1 after a 4-h HL treatment. e Volcano plot of differentially translated genes between Col-0 and vir-1 after a 4-h HL treatment, indicated as in (b). f GO enrichment analysis of the differentially translated genes between Col-0 and vir-1 after a 4-h HL treatment. Statistical test was determined by one-sided hypergeometric test. g Number of genes showing differential translation efficiency (TE) between Col-0 and vir-1 after a 4-h HL treatment. h Volcano plot of differential TE genes between Col-0 versus vir-1 after a 4-h HL treatment, indicated as in (b). i GO enrichment analysis of the differential TE genes between Col-0 and vir-1 after a 4-h HL treatment. Statistical test was determined by one-sided hypergeometric test. j Extent of correlation between RNA-seq and Ribo-seq samples after a 4-h HL treatment. Pearson’s correlation coefficient (r) is shown. k Extent of correlation between the transcriptome changes and translatome changes in vir-1 vs. Col-0 after a 4-h HL treatment. Pearson’s correlation coefficient (r) is shown. l, m Normalized distribution of RNA-seq and Ribo-seq reads in Col-0 and vir-1 along the MPH1 (l) and STN8 (m) genes. The fold-change and associated P-value for VIR effect on transcript and footprint levels, as well as the fold-change in the footprint levels given the levels of mRNA (TE) and the corresponding P-value, are shown.
