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Figure 1. 

Cold transcriptional responses of the three rice varieties. (a) Cold treatment phenotypes of the three rice varieties; the white scale bar represents 2 cm. (b) Principal component analysis (PCA) of the RNA-seq data. (c) Statistics of differentially expressed genes (DEGs). (d) Overlap analysis of DEGs at the 24 h time point. (e) Gene ontology (GO) enrichment analysis of genes with higher expression in KH and LJ compared to YD at the 24 h time point. (f) Selected cold-induced genes with higher expression in KH and LJ compared to YD.

Figure 2. 

Chromatin accessibility and transcription factor binding motif enrichment analysis. (a) Distribution of DNase-seq data relative to gene structures. (b) Distribution of chromatin accessibility signals relative to gene structures. (c) TOBIAS TF footprinting analysis of ACRs in KH at the 24 h time point; the differential binding score in TOBIAS is a normalized statistic summarizing the overall footprint score change of a TF's motifs between two conditions relative to background. (d) TF binding motif enrichment analysis in the promoter ACRs of DEGs: the enrichment ratio is defined as the proportion of transcription factor footprints present in promoter-associated ACRs of a specific gene set divided by that in all promoter-associated ACRs.

Figure 3. 

DAP-seq data analysis of 23 cold-induced transcription factors. (a) Expression profiles of the 23 cold-induced transcription factors. (b) Clustering of DAP-seq sample signals based on the overlap (Szymkiewicz–Simpson) coefficient. (c) Number of peaks in DAP-seq samples and their distribution relative to gene structures. (d) TF motif enrichment analysis based on DAP-seq signals; the most significant motif identified through de novo prediction is used as the representative motif for the TF.

Figure 4. 

DAP-seq defines potential TF-target gene regulatory relationships. (a) Number of potential target genes for each TF defined by DAP-seq and DNase-seq. The top panel shows the number of target genes defined by promoters containing DAP-seq signals, while the bottom panel shows the number of target genes defined by promoters containing overlapping signals from both DAP-seq and DNase-seq. (b) In vitro binding of TFs to the promoters of stress-related genes; the different colored tracks represent distinct transcription factor families.