Fig. 5

BAF60 has opposite effects than PIF4 on the expression of hypocotyl elongation regulatory genes. a Venn diagram displaying the elements in common between the BAF60 targets missregulated in the Baf60 RNAi line and the PIF4 targets downregulated in the pifq mutant. The values in parentheses (grey) correspond to the common elements expected by chance, while those in black or red represent the observed results. The values in red represent significant enrichment, while those in black are not significantly different from those expected by chance (Chi2 square test). b Gene ontology analysis of the common targets oppositely regulated by PIF4 and BAF60. The red bars represent the input and the black bars the reference. This group of loci is significantly enriched in genes involved in response to auxin, hormones, and light. c Genome Browser snapshots of ATAC-seq, BAF60, and PIF4 ChIP-seq peaks on six common target genes (IAA19, ST2a, XTR7, SDR, HFR1, and BEE1). BAF60-associated peaks are shown in green, PIF4-binding peaks in red, ATAC-seq peaks in blue, annotated genes in black, and G-box motifs in pink. d RT-qPCR analysis showing the relative expression of the indicated genes in 7-day-old seedlings in LD conditions. Values are average ± standard deviation obtained from three independent replicates and asterisks represent significant difference from the wild type (WT; Student’s t-test, P < 0.05). e DNA accessibility measured by FAIRE-qPCR in 7-day-old wild-type and BAF60 RNAi seedlings grown in LD conditions. Higher values correspond to more accessible DNA. Primer pair 1 was used for ST2a, SDR, and HFR1 loci, pair 3 for IAA19 and BEE1 loci, and pair 2 for the XTR7 locus. Error bars represent the standard deviation from three biological replicates and asterisks represent significant difference from the WT (Student’s t-test, P < 0.05)