Fig. 6

Full-length TEs are preferentially cleaved and produce secondary siRNAs, driving RDR6-RdDM. a Percentage of TEs with cleaved mRNAs in the TE-silent context. b Percentage of TEs with cleaved mRNAs in the TE-active context. In (a) and (b) rdr6 mutants are used to determine which cleavage events are due to primary small RNAs (not RDR6 dependent) or RDR6-dependent secondary siRNAs. c Venn diagram of cleaved TE mRNAs in the TE-active context and their dependence on RDR6-generated secondary siRNAs. d siRNA production from small RNA-cleaved and uncleaved TE mRNAs determined in parts (a–c). Labels above bars indicate the assayed genotype of small RNA alignment. e RdDM pathway categorization of the TE categories shown in (d). f siRNA production in the TE-active context. Small RNA-cleaved and uncleaved TE mRNAs in the TE-silent context are the same as in (d). “New ddm1 cleaved” refers to TE mRNAs that are cleaved in the TE-active context but were not cleaved in the TE-silent context. g TE-active context siRNA production from TE mRNAs with new cleavage sites in the TE-active context compared to the TE-silent context. “Cleavage sites retained & gained in ddm1” refers to TE mRNAs with new cleavage sites plus the retention of the same TE mRNA cleavage sites from the TE-silent context. “Cleavage sites not retained & completely distinct in ddm1” refers to TE mRNAs with new cleavage sites without retention of the same TE mRNA cleavage sites from the TE-silent context. h Of the “Cleavage sites not retained & completely distinct in ddm1” TEs from (g), the number of cleavage sites on the same TE mRNA in the TE-silent and TE-active contexts. Weight of the arrow is determined by how many TE mRNAs transition from 1–2 cleavage sites in the TE-silent context to other numbers of cleavage sites in the TE-active context. The majority of TE mRNAs have one cleavage site in the TE-silent context and a different one cleavage site in the TE-active context