Gene conversion-like rearrangement at the Kn1-0 tandem duplication
--Julie Mathern and Sarah Hake

The homeobox-containing knotted (kn1) locus of maize is characterized by a series of dominant alleles affecting leaf development. All but one of the Kn1 mutations are caused by insertions of transposable elements into introns. The exceptional Kn1-0 allele consists of a tandem array of two 17kb repeat units (Veit, B et al., Genetics 125:623, 1990), each containing the entire Kn1 transcription unit. Analysis of Kn1-0 derivatives indicates that the duplication itself conditions the mutant phenotype due to the novel context of the proximal transcription unit. Insertion mutagenesis of the Kn1-0 allele produced four derivatives which altered the mutant phenotype to nearly normal. Three of the insertions are Mutator elements, and have inserted within a 316bp region 5' to the proximal transcription unit. One of the derivatives, Kn1-174, contains a Mu1 element. We have shown that the mutant phenotype of Kn1-174 is regulated by methylation of the Mu1 element (Lowe et al., Genetics 132: 813, 1992). When the Mu1 element is hypomethylated, or active, the phenotype is near normal, with mild ligule displacement on early leaves. Conversely, when the Mu1 element is methylated, or inactive, the phenotype is mutant, resembling the Kn1-0 allele.

Further genetic analysis of the Kn1-174 derivative yielded progeny which were completely wild type in phenotype. Unlike the progenitor, this new derivative, Kn1-174a, is stably normal; knotted progeny have not been found in a population of 500 heterozygous Kn1-174a/+ individuals. Sequence data show that Kn1-174a has lost the Mu1 element and instead has sustained a rearrangement. The rearrangement places sequences outside the tandem duplication, 5' to the proximal transcription unit (Fig. 1). Thus both transcription units now have the same 5' sequences for approximately 2.4kb. According to our model for the Kn1-0 mutant phenotype, both transcription units are now in a "wildtype" context.

We propose that gene conversion is responsible for the Kn1-174a rearrangement. We previously documented a high frequency of loss of one of the tandem repeats in Kn1-174 and the other Mu insertion alleles at Kn1-0. The high frequency of repeat loss required active Mu elements (Lowe et al., Genetics 132: 813, 1992). When the Mu element excises, the broken chromatid ends are highly recombinogenic and pair with homologous sequences. Since the Kn1-0 sequences are duplicated, pairing could occur at two different places, at the proximal repeat that contained the Mu element, or at the distal repeat. We propose that the pairing in Kn1-174a was misaligned thus bringing sequences normally 5' to the distal repeat in a position 5' to the proximal repeat. 

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