Fig. 4: Shade barely affects global genome-wide binding of REF6.
a Scatterplots of normalized REF6 ChIP-seq signal intensity in log2 for overlap regions between the N_WL and N_SH 8 h conditions. The profiles were generated after merging two biological replicates. The P value was calculated by t-test (two-sided). Average density plot (b) and violin plot (c) displaying the REF6-HA enrichement on N_WL&N_SH 8 h REF6 bound genes (5109) under N_WL and N_SH 8 h conditions. The P value was calculated by Welch’s t-test (two-sided). The profiles were generated after merging two biological replicates. d Representative genome browser view of REF6-HA binding to the LNG2, EXPA11, XTH22 and XTH23 loci in proREF6::REF6-HA/ref6-1 under N_WL and N_SH 8 h conditions. e ChIP‒qPCR analysis of REF6-HA enrichment using an anti-HA antibody at the LNG2, EXPA11, XTH22 and XTH23 loci in proREF6::REF6-HA/ref6-1. TA3 is a transposon and served as a negative control. The top panels show a schematic representation of the gene structures and positions of primers. REF6 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 technical replicates). Source data are provided as a Source Data file.
