Small RNA-MediatedDe NovoSilencing ofAc/DsTransposons Is Initiated by Alternative Transposition in Maize

Abstract

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 is initiated by alternative transposition, a type of aberrant transposition event that engages the termini of two nearby separate TEs. Alternative transposition during DNA replication can generate Composite Insertions that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two Composite Insertions are transcribed to produce double-stranded RNAs that trigger the production of two distinct classes of small interfering RNAs: a 24-nt class complementary to the TE terminal inverted repeats and noncoding subterminal regions, and a 21- to 22-nt class corresponding to the TE transcribed regions. Plants containing these small interfering RNA-generating Composite Insertions exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. Further, we demonstrate that Composite Insertions can heritably silence otherwise active elements in trans. This study documents the first case of transposon silencing induced by alternative transposition and may represent a general initiating mechanism for silencing of DNA transposons.

Ectopic Expression of a Maize Gene Is Induced by Composite Insertions Generated Through Alternative Transposition

“…A second type of AT is termed SCT (Sister Chromatid Transposition), in which the two TE's are located on sister chromatids (Weil and Wessler 1993;Zhang and Peterson 1999). Recently, SCT has been shown to generate CIs containing inverted duplications of TE sequences that can induce silencing of Ac (Wang et al 2020). Together, these results indicate that Alternative…”

“…A second type of alternative transposition is termed SCT, in which the two TEs are located on sister chromatids ( Weil and Wessler 1993 ; Zhang and Peterson 1999 ). Recently, SCT has been shown to generate CIs containing inverted duplications of TE sequences that can induce silencing of Ac ( Wang et al 2020 ). Together, these results indicate that alternative transpositions are able to copy and mobilize regulatory elements and thereby regulate gene expression patterns, while other alternative transposition events can initiate TE silencing.…”

“…Because our screen was based on the recovery of pericarp pigment, we detected only CI insertions into the p2 locus. In fact, CIs can insert into any location in the genome ( Zhang et al 2014 ; Wang et al 2020 ), not necessarily producing a readily observable phenotype. The occurrence of a pair of active TEs ( Ac/fAc) inserted into one copy of closely linked paralogs ( p1/p2) controlling a visible, nonessential trait provides an ideal system in which to detect such events in real time, in relatively small experimental populations.…”

“…Previous studies have shown that SCT can generate deletions, inverted duplications ( Zhang and Peterson 1999 , 2005 ), sister chromatid fusions, and chromosome breaks ( Yu et al 2010 ); while RET can generate deletions ( Zhang and Peterson 2005 ), direct duplications ( Zhang et al 2013 ), inversions, and translocations ( Zhang and Peterson 1999 , 2004 ; Zhang et al 2009 ). In addition, both SCT and RET can generate novel compound structures termed composite insertions (CIs) ( Zhang et al 2014 ; Wang et al 2020 ).…”

Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes

“…The second pathway involves Pol II‐RDR6‐dependent 21‐ and 22‐nt small RNAs that are corresponding to the transcribed proportion of the Bot1 elements, mainly a predicted ORF (ORF2) that is adjacent to the TNP2 ‐like transposase gene (Figure 7). These 21‐ and 22‐nt small RNAs were recently found to be processed from inverted repeats that are generated by duplication of a proportion of the original TE element (Burgess et al ., 2020; Wang et al ., 2020). These inverted repeats were called ‘ Mu killer ’ and ‘ Ac killer ’, which are transcribed by nearby promoters, produce 21‐ and 22‐nt small RNAs, act in trans to trigger CG and CHG DNA methylation, and heritably silence an active element.…”