Fig. 3
From: Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Initiation of TCM and TCdM loci and inheritance of tgDMRs depend on siRNAs. a Fraction of TCM or TCdM DMRs between F1 hybrids and the mid-parent value (MPV) in different genomic features, including gene body, flanking regions of 5′ (− 2 kb to the transcription start site, TSS) and 3′ (transcription termination site, TTS, to + 2 kb), TEs, and intergenic regions excluding TEs in MB, BM, and whole genome (genome). b, c Distribution (y-axis) of CHH methylation (b) and 24-nt siRNA (c) (reads per ten million, RPTM) levels in the genic regions of the F1 hybrids and their parents. Double asterisks indicate statistical significance (P < 0.01, two-sided Wilcoxon signed-rank test). d Levels of 24-nt siRNAs (RPTM, y-axis) in the MB (black), BM (gray), and MB:mop1 (red) hybrid lines. Location of siRNA loci relative to the center (light grey) of TCM and TCdM regions is shown in x-axis. e Density (y-axis) of the methylation difference between the hybrids and their MPV among TCM (left panel) and TCdM (right panel) loci in the BM (black), MB (gray), and MB:mop1-1 (pink). Scale of changes (0 = no change) is shown in x-axis. Double asterisks indicate statistical significance (P < 0.01, two-sided Wilcoxon signed-rank test) of the methylation difference between the MB:mop1-1 and BM (black) or MB (grey). f Levels of 24-nt siRNAs (RPKM, y-axis) in BM6S3 (red) and its recurrent parent Mo17 (violet). Location of siRNA loci relative to the center (light grey) of transgenerational DMRs is shown in x-axis. “Total” represents siRNA expression of all windows of the whole genome