Fig. 4

Utilization of TF footprints to identify heat response cis-regulatory elements. a An example of differential TF footprints near a B73 heat-responsive gene. Raw read coverages were normalized by RPGC (reads per genomic content) methods. b Same as a, but for another heat-responsive gene, Zm00001d016255 (ZmHSF13). c Normalized MOA-seq signals near 1kb extended regions of putative summits of heat-enriched TF footprints in three biological replicates under control and heat conditions. d Compared 793 commonly upregulated genes with 11,501 background genes for presence and absence of heat-enriched TF footprints. e Comparisons of interaction terms between SNPs located inside and outside of defined TF footprints located within different categories of reGenes and their 1-kb flanking regions. The definition of RefControl, RefHeat, AltControl, and AltHeat were the same as Fig. 3c. ** indicates p-value < 1e⁻² and ns indicates insignificant