Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition

Abstract

AbstractTransposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status and generating small RNAs. In this study, we demonstrated thatAc/fActransposable elements are able to induce ectopic gene expression by duplicating and shuffling enhancer elements.Ac/fAcelements belong to thehATfamily of Class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events which involve the termini of two different, nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations and Composite Insertions (CIs). We identified over 50 independent cases of CIs generated byAc/fAcalternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maizepericarp color 2 (p2)gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearbyp1gene, suggesting that the CI-induced activation ofp2is effected by mobilization of thep1enhancer. This is further supported by analysis of a mutant in which the CI is excised andp2expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate Composite Insertions that can control gene expression.SummaryWhen Barbara McClintock originally identified and characterized Transposable Elements (TEs) in maize, she termed them “Controlling Elements” due to their effects on gene expression. Here we show that maizeAc/DsTEs can acquire a genomic enhancer and generate Composite Insertions (CIs) that activate expression of a nearby gene. CIs are structurally variable elements that include TE termini enclosing sequences from an original donor locus, and are formed when the termini of two nearby TEs transpose during S phase from a replicated to unreplicated site. In this way, TEs may acquire genomic enhancers to generate Controlling Elements as described by McClintock.