Fig. 5

Transcriptional changes directed by OsRKD3 induction. A Venn diagram showing the overlap between differentially expressed genes (DEGs) in OsRKD3 induced and OsRKD3 leaked samples. Blue coloured circle represents DEGs between indOsRKD3 DEX (TD) and indOsRKD3 mock (TM) treatments; purple coloured circle indicates DEGs between indOsRKD3 mock (TM) and non-transgenic (NT) treatments. B Heatmap showing the transcriptional changes of differentially expressed genes found in indOsRKD3 transgenic and non-transgenic plants (two biological replicates per sample). C, D Gene Ontology (GO) analysis showing gene sets enriched in the differentially upregulated (C) and downregulated (D) categories. (E) Distribution of RKD-binding motifs in the upstream regions of OsRKD3 upregulated DEGs. Regulatory regions were defined as 1000 bp upstream of the transcription start site (TSS) and 1000 bp downstream of TSS. RKD motif enrichment and statistical significance was determined using HOMER v4.11. RKD motif density was plotted using a bin size of 20 bp. F Functional analysis of cis-regulatory motifs identified in OsRKD3 targets. The panel represents the promoter activity of HDZip-like/OsHox2 in Arabidopsis protoplasts upon OsRKD3 induction. Top panel: a schematic diagram showing the construct designed to determine promoter activity using a luciferase reporter. Black boxes, RKD-binding motifs. Bottom panel: quantitative measurements of luciferase activity of the promoter. A t-test was performed; ****p < 0.0001. G Heatmap showing the expression, as nomalised FPKM reads, in different rice tissues of OsRKD3 upregulated DEGs that contain RKD sequence motifs