Fig. 3

MNase HS as a proxy for TF-DNA binding. (a) Overlap of high confidence peaks from FEA4 and KN1 ChIP-seq experiments with MNase HS regions based on LCS data. Less than 2 % of co-bound sites and 6 % of all sites do not overlap MNase HS. (b) Read density (reads per million) of LCS are plotted around a consensus TSS of genes bound by KN1 and/or FEA4. Genes co-bound by both TFs in the proximal promoter show a wider range of accessibility. Data are shown for tassel; similar profiles are shown for ear presented in Fig. S9. (c) Examples of intergenic MNase HS sites in tassel, ear, and/or shoot that are co-bound by KN1 and FEA4: a known enhancer element 65 kb upstream of tb1, and a site 6 kb upstream of the gnarley 1 (gn1) locus. (d) Fragment densities from the light MNase digest plotted around high-confidence FEA4 ChIP-seq peaks show strong enrichment at the consensus FEA4 binding motif. (e) Density of ABI3-like motifs were plotted in relation to experimentally validated FEA4 binding sites. The ABI3-like motif was discovered by mining HS regions called by iSeg that overlapped consensus FEA4 binding sites. ABI3-like motifs are most densely positioned within 50 bp of FEA4 motifs. (f) GO terms overrepresented among genes within 1 kb of FEA4-ABI3-like motif modules (ABI3-like motifs within 50 bp of FEA binding sites) and compared with genes within 1 kb of random FEA4 motifs of equal number