Intrachromosomal excision of a hybrid Ds element induces large genomic deletions in Arabidopsis

Abstract

Transposon activity is known to cause chromosome rearrangements in the host genome. Surprisingly, extremely little is known about Dissociation (Ds)-induced chromosome rearrangements in Arabidopsis, where Ds is intensively used for insertional mutagenesis. Here, we describe three Arabidopsis mutants with reduced fertility and propose that excision of a hybrid Ds element induced a large genomic deletion flanking Ds. In the mutants anat and haumea, the deletion mechanism consists of a local Ds transposition from replicated into unreplicated DNA followed by Ds excision, where one end of the newly transposed element and one end of the Ds transposon at the donor site served as substrate for transposase. Excision of this hybrid element reminiscent of a macrotransposon leads to loss of the chromosomal piece located between the two ends, including one full Ds element and the flanking genomic sequence. This mechanism was found to be responsible for several other deletions and occurs at a genetically trackable frequency. Thus, it could be applied to efficiently generate deletions of various sizes in the vicinity of any existing Ds element present in the genome. In the mutant tons missing, a mechanism that involves endogenous repetitive sequences caused a large flanking deletion at a position unlinked to the starter locus. Our study of Ds transposition in Arabidopsis revealed previously undescribed mechanisms that lead to large genomic deletions flanking Ds elements, which may contribute to genome dynamics and evolution. genome evolution ͉ rearrangements ͉ transposition

A Segmental Deletion Series Generated by Sister-Chromatid Transposition of Ac Transposable Elements in Maize

“…A possible clue to the mechanism is provided by McClintock (1953), who determined that Ds was still present on each of the mutant chromosomes she tested. This result is exactly what would be predicted for SCT of doubleDs: A chromosome-breaking Ds structure should be retained at the deletion junction, whereas deletions derived by standard transposition followed by excision of a macrotransposon as proposed by Page et al (2004) would often not contain Ds in association with the deletion-bearing chromosome.…”

“…The authors suggest that these large deletions were formed through a two-step process in which normal transposition of Ds is followed immediately by intrachromosomal excision of a hybrid Ds element. However, the deletion endpoints reported by Page et al (2004) do not end precisely at the Ds termini, suggesting that the formation of these deletions probably involved other cellular functions in addition to the Ac transposase. Transposition of simple Ac/Ds elements is not known to induce large deletions in maize, and their occurrence in Arabidopsis may reflect a loss of normal transposition controls in the nonnative host.…”

“…Some large deletions have been found in maize following excision of compound elements composed of Ac/Ds termini flanking genomic sequences (Ralston et al 1989;Dowe et al 1990). More recently, Page et al (2004) identified several large deletions ($100 kb) in Arabidopsis that were apparently generated during Acinduced excision of a simple Ds element. The authors suggest that these large deletions were formed through a two-step process in which normal transposition of Ds is followed immediately by intrachromosomal excision of a hybrid Ds element.…”

Genome Rearrangements in Maize Induced by Alternative Transposition of ReversedAc/DsTermini

“…An alternative model (Page et al 2004) proposed that deletions flanking Ds elements in Arabidopsis result from a hybrid transposition mechanism involving two sequential steps: First, a newly replicated Ds element inserts into a nearby unreplicated region and forms a pair of Ds elements in reversed orientation. Second, the 59 end of one Ds and the 39 end of the other Ds excise, leading to deletion of the internal sequence.…”

Female gametophytic mutants of Arabidopsis thaliana identified in a gene trap insertional mutagenesis screen

“…1A), and that the segregation ratio of Kan r is consistent with a single insertion (Table 1), we conclude that only a short piece of the 3'-end of the Ds is present on chromosome 1. In contrast the Ds insertion on chromosome 3 appears to be associated with a deletion, as was reported for several other lines that were generated using this transposon system (Oh et al, 2003;Page et al, 2004, Boavida et al, 2009.…”