Arms race in non-coding regions of transposable elements; evolution of anti-silencing and RNAi

Transposable elements (TEs) are among the most dynamic parts of genomes. Since TEs are potentially deleterious, eukaryotes silence them by epigenetic mechanisms such as DNA methylation and RNAi. We have previously reported that Arabidopsis TEs, called VANDALs, counteract the epigenetic silencing by a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to non-coding regions of specific VANDAL copies and induce loss of silent chromatin marks. The sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here we show that RNAi efficiently targets non-coding regions of VANDAL TEs to silence them de novo. Target motifs of VANC, in turn, evolved to escape from RNAi. The escape from RNAi could be the primary event leading to the differentiation of the sequence-specific anti-silencing systems. We propose this selfish behavior of the TEs paradoxically could make them less harmful to the host.