Gene silencing can occur either through repression of transcription, termed transcriptional gene silencing (TGS), or through mRNA degradation, termed post-transcriptional gene silencing (PTGS). Initially, TGS was associated with the regulation of transposons through DNA methylation in the nucleus, whereas PTGS was shown to regulate virus infection through double-stranded RNA in the cytoplasm. However, several breakthroughs in the field have been reported recently that blur this neat distinction. First, in plants TGS and DNA methylation can be induced by either dsRNA or viral infection. Second, a mutation in the plant MOM gene reverses TGS without affecting DNA methylation. Third, in Caenorhabditis elegans mutation of several genes that control RNA interference, a form of PTGS, also affect the regulation of transposons. TGS and PTGS, therefore, appear to form two alternative pathways to control incoming, redundant and/or mobile nucleic acids.