Fig. 6: Demethylation of H3K27me3 at certain shade-memory-related genes is mediated by PIF7 and REF6.

a Violin plot displaying the REF6 enrichement under N_WL and N_SH 8 h conditions on shade-memory-related genes co-regulated by REF6 and PIF7. b Venn diagram showing the overlapping genes between shade-increased REF6 binding genes (N_SH 8 h vs. N_WL > 1.2), PIF7 bound genes and shade-memory-related genes co-regulated by REF6 and PIF7. The source data for PIF7 bound genes were obtained from GSE156584. c Gene Ontology (GO) analysis of PIF7 targets (bound and regulated genes), PIF7 and REF6 cotargets (bound and regulated genes) and REF6 targets (bound and regulated genes) in shade-memory-related 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. d Violin plot displaying the REF6 enrichement of REF6 and PIF7 co-targets under N_WL and N_SH 8 h. e ChIP‒qPCR analysis of PIF7 enrichment using an anti-MYC antibody at the IAA19, GH3.6 and BGL1 in 35S::PIF7-Flash. f ChIP‒qPCR analysis of H3K27me3 enrichment using anti-H3K27me3 antibody at the IAA19, GH3.6 and BGL1 loci in Col-0, pif7-1 and ref6-1. In a and d, the P value was calculated in a window from the 3 kb upstream REF6 binding summit to the 3 kb downstream by Welch’s t-test (two-sided). In e and f, the sampling conditions are shown in Supplementary Fig. 6a. The top panels show a schematic representation of the gene structures and position of primer and enrichment was calculated as input%. Different letters indicate statistically significant differences (P < 0.05) based on one-way ANOVA with Tukey’s HSD test. Data are presented as mean values +/− SD (n = 3, where n refers to biological replicates). Source data are provided as a Source Data file.