Fig. 5

LDL3-mediated H3K4me2 in CIM regulates gene expression on SIM. a H3K4me2 changes during callus formation (C14–C0) in ldl3 compared with WT. b H3K4me2 changes upon shoot induction (C14S1–C14) in ldl3 compared with WT. Each dot represents the square root of RPM. Black dots, all genes; red dots, upregulated genes in C14S1 in WT (UGs_S1); blue dots, downregulated genes in C14S1 in WT (DGs_S1). c Altered gene expression in ldl3 [Log2 (read counts per kilobase million mapped reads: RPKM_ldl3/WT)] before (C14, black dots) and after (C14S1, green dots) shoot induction with reference to hyper H3K4me2 caused by ldl3 [Log2 (RPKM_ldl3/WT)] during callus formation (C14). d On the basis of H3K4me2 changes between WT and ldl3 [Log2 (RPKM_ldl3/WT)] at C14 in (c), genes were divided into three groups (i < 0, 0 < ii < 1, iii > 1) (x-axis). Gene expression fold-changes between WT and ldl3 [Log2 (RPKM_ldl3/WT)] at C14 and C14S1 were calculated and compared across groups. e −log10 [p value (C14 vs C14S1, Wilcoxon signed rank test)] for each group in (d). Source data are provided as a Source Data file