Extended Data Fig. 1: siRNA is associated with recovery of CG methylation in TE genes.

a, Genetic scheme to examine recovery of CG methylation. b–e, CG methylation levels of cellular genes (black dots) and TE genes (red dots) are compared between wild-type plant (x-axis) and corresponding plant (y-axis). Mutations in the maintenance methyltransferase MET1 (b), as well as the triple mutations in the redundant genes, VIM1, VIM2 and VIM3 (c), induced a loss of CG methylation, and the recovery of CG methylation was examined in the F1 (d) and F2 (e) progenies. The F2 plant in panel E was a self-pollinated progeny from the F1, with a genotype of MET1/MET1 VIM1/VIM1 VIM2/VIM2 vim3/vim3. f, Comparison of two individual F1 plants. The re-methylation efficiency for each of the TE genes was similar in the two F1 plants. R represents the pearson’s correlation coefficient between two methylation values in the TE genes. g, Comparison of remethylation in an F1 plant and its F2 progeny. TE genes remethylated in the F1 plant tended to be further remethylated in the F2 progeny. h, CG remethylation in TE genes was associated with the presence of 24-nt siRNAs in an met1 mutant. siRNA-Seq data were obtained from GEO (GSE10967⁶³ and TE genes were classified according to the matching siRNA levels with high (left, RPKM>0.1, 3283 TE genes) or low (right, RPKM<0.1, 372 TE genes) in met1-3 (see Methods for details). The box plot indicates the median (line in the box), the lower and upper quartiles (box), the largest and smallest data points within the interval of 1.5 times the interquartile range from the box (whiskers). i, j, Correlation of CG remethylation in TE genes and the levels of 24-nt siRNAs in met1 mutant. In Fig. 1h–j, TE genes with low CG methylation (mCG <0.1) were excluded and the remaining TE genes (n=3655) were analyzed to avoid division by values near zero.