DNA silencing or cleavage is initiated by the biogenesis of small RNAs from host-encoded precursors, which are then bound by effector proteins and lead to the transcriptional silencing or elimination of complementary sequences. Orthologs are indicated as follows: Dicers, green; RNA-dependent RNA polymerase complexes, blue; polymerases, brown; Ago clade Argonautes, yellow; Piwi clade Argonautes, purple; histone and DNA methyltransferases, orange; and chromodomain-containing proteins, gray. Epigenetic modifications are represented as follows: H3K9me, blue; H3K27me, orange; and DNA methylation, green. The targets of small RNA-mediated TGS in each organism are indicated in the right panels.