Fig. 2

Genome-wide distribution of TE CHH methylation pathways. a CHH methylation levels of the RDR6-RdDM targeted locus TAS3. Track scale is 0–50 %. b TAS3 small RNA size and abundance heat maps in the TE-silent context. R1, R2, and R3 signify independent biological replicates. c Small RNA size and abundance heat maps for all perfectly and uniquely mapping TE small RNAs in the TE-silent context. d Small RNA size and abundance heat maps for all perfectly and uniquely mapping TE small RNAs in the TE-active context. GSE numbers represent the data source. e Heat map representing CHH methylation values for individual TEs (rows). The columns represent different genotypes assayed. Numbers represent the amount of TEs targeted by each corresponding CHH methylation pathway. TEs change position between the TE-silent (left) and ddm1 TE-active (right) panels. The location of the Athila6A TE analyzed in Additional file 3: Figure S2C is shown as an arrow, while the TE shown in Fig. 3a is marked with an arrowhead. Genotypes are color-coded based on the methylation pathway (black = maintenance methylation (no RdDM), red = Pol IV-RdDM, blue = RDR6-RdDM, green = contributes to both Pol IV-RdDM and RDR6-RdDM)