Fig. 3: REF6 maintains low H3K27me3 levels on late shade-induced genes.

a Venn diagram showing the overlapping genes between 1 h and 7 h shade-induced genes and REF6 bound genes. The source data for shade-induced genes at 1 h and 7 h are from GSE59722. The source data for REF6 binding genes are from GSE65329. The P value was calculated by Fisher’s exact test. b Gene Ontology (GO) analysis of REF6-bound 7 h shade-induced genes. For each point, the size is proportional to the number of genes, and the colours represent the P value, Fisher’s one-tailed test. c Average density plot (left) and violin plot (right) showing the distribution profile of H3K27me3 levels on control genes (all non-induced genes by shade) and 7 h shade-induced genes. d Average density plot (left) and violin plot (right) showing the distribution profile of H3K27me3 levels of 7 h shade-induced genes in the Col-0 and ref6-1. e Average density plot (left) and violin plot (right) showing the distribution profile of H3K27me3 levels of REF6-bound 7 h shade-induced genes in Col-0 and ref6-1. f Relative expression levels of LNG2, EXPA11, XTH22 and XTH23 in Col-0 and ref6-1. g H3K27me3 enrichment on the LNG2, EXPA11, XTH22 and XTH23 loci in Col-0 and ref6-1. The top panels show a schematic representation of the gene structures and the positions of primers. The bottom panels show the effects of shade on H3K27me3 enrichment. The enrichment of H3K27me3 was calculated as input%. In c–e, the source data are from GSE65329. The P value was calculated by Welch’s t-test (two-sided). In f and g, seedlings that were grown under white light for 6 d and then maintained under white light or transferred to shade for 1 h and 8 h. Data are presented as mean values +/− SD (n = 3, where n refers to biological replicates). Different letters indicate statistically significant differences (P < 0.05) by one-way ANOVA with Tukey’s HSD test. Source data are provided as a Source Data file.