The arms race in noncoding regions of transposable element: the 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 through epigenetic mechanisms such as DNA methylation and RNAi. We have previously reported that Arabidopsis TEs, called VANDALs, counteract epigenetic silencing through a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to noncoding regions of specific VANDAL copies and induce a loss of silent chromatin marks. Sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here, we show that RNAi efficiently targets noncoding regions of VANDAL TEs to silence them de novo. Target motifs of VANC, in turn, evolved to escape RNAi. Escaping RNAi could be the primary event leading to the differentiation of sequence-specific anti-silencing systems. We propose that this selfish behaviour of TEs paradoxically could make them less harmful to the host.