siRNA-mediated de novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize

Although Transposable Elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maize Ac/Ds transposon system. This silencing was initiated by Alternative Transposition (AT), a type of aberrant transposition event that engages the termini of two nearby separate TEs. AT during DNA replication can generate Composite Insertions (CIs) that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two CIs are transcribed to produce dsRNAs that trigger the production of two distinct classes of siRNAs: a 24-nt class complementary to the TE terminal inverted repeats (TIRs) and non-coding sub-terminal regions, and a 21-22 nt class corresponding to the TE transcribed regions. Plants containing these siRNA-generating CIs exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. This study documents the first case of TE silencing attributable to transposon self-initiated AT and may represent a general initiating mechanism for silencing of DNA transposons. Article summary Transposable Elements (TEs) are often silenced by their hosts, but how TEs are initially recognized for silencing remains unclear. Here we describe two independent loci that induce de novo heritable silencing of maize Ac/Ds transposons. Plants containing these loci produce dsRNA and Ac -homologous small interfering RNAs, and exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. We show that these loci comprise inverted duplications of TE sequences generated by Alternative Transposition coupled with DNA re-replication. This study documents the first case of transposon silencing induced by AT and may represent a general initiating mechanism for TE silencing.