Extended Data Fig. 8: Comparison of FEA4 binding profiles and its target genes between wild type and grx triple mutant.

a, The replicate rates of FEA4 binding peaks identified by ChIP-seq using 3–5 mm ears were about 60% in both wild type (WT, left panel) and the grx triple mutant (triple, right panel). Each replicate was done using more than 30 ears. b, A large portion (>90%) of potential binding peaks (Left) and the corresponding genes (Right) identified for FEA4 were overlap between WT and the grx triple mutants. The number of FEA4 peaks was almost doubled in the grx triple mutants compared to WT. c, The distributions of the high-confident binding peaks of FEA4 in wild type (WT) and the grx triple mutants (triple). ‘1 kb upstream’ and ‘1–3 kb upstream’ represent the regions 1 kb and 1–3 kb upstream of the transcription start sites (TSS), respectively. ‘Downstream’ represents the regions 3 kb downstream of the transcriptional termination sites (TTS). ‘intergenic’ represents the intergenic regions outside the 3 kb upstream of TSS and 3 kb downstream of TTS. d, The TGA motif (TGACG) was enriched in the FEA4-bound promoter regions of both wild type (WT, 56%) and the grx triple mutant (triple, 58.2%). The promoter regions include the regions within 3 kb upstream of TSS and 3 kb downstream of TTS of annotated coding genes. In total 3,059 out of 5,459 and 7,094 out of 12,181 FEA4 binding sites in the promoter regions of WT and triple mutant, respectively, contain at least one TGA motif. e, The overlapping DEGs caused by fea4 mutation with FEA4-bound genes either in wild type (left panel) or grx triple mutant background (right panel). f, On the common FEA4-bound sites present in the 75 overlapping genes, the peaks captured in the grx triple (triple) mutants are significantly more abundant than those captured in wild type (WT). Pileup values representing the aligned reads with a given extension size were shown. In total, 91 binding peaks of FEA4-YFP captured in both wild type and the grx triple mutants are used for analysis. The box plot boundaries show the interquartile range, and the center line is the median, extended to minimum and maximum values, the whiskers represent 1.5-fold to the interquartile range from the lower and upper quartiles. n = 91, P = 3 ×10⁻⁴. P value calculated using two-sided Wilcoxon test.