Fig. 6: Circadian rhythm network genes are both differentially expressed and methylated.

a DMGs for the circadian rhythm (GO:0007623) network in msh1 memory line. Only genes identified as DMGs in at least four out of seven comparisons (Gen1 to Gen6 WT vs. MM and Gen1 NM vs. MM) are presented. Scale represents the log2 Fold change of DMP number at specific genes in each comparison. b DEGs from the circadian rhythm (GO:0007623) network in msh1 memory line and msh1 mutant. Only genes identified as DEGs in at least four out of five comparisons (Gen1 WT vs. MM, Gen1 NM vs. MM, Gen5 WT vs. MM, WT vs. msh1 translatome (TRAPseq) and WT vs. msh1 TDNA mutant) are presented. c DMGs and DEGs presented in panels (a) and (b) are positioned in the circadian clock network. The network is adopted from the KEGG database (Circadian rhythm—plant—Arabidopsis thaliana). The hda6 transcriptome data were taken from Yu et al.²⁷ and reanalyzed using our pipeline. Genes associated with differentially expressed sRNA clusters were highlighted with a green star. Source data for generational DMGs are provided as a Source Data file.