Academic journal article Genetics

Natural Variation in a Subtelomeric Region of Arabidopsis: Implications for the Genomic Dynamics of a Chromosome End

Academic journal article Genetics

Natural Variation in a Subtelomeric Region of Arabidopsis: Implications for the Genomic Dynamics of a Chromosome End

Article excerpt

ABSTRACT

We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (~3.5 kb), which represents the relatively simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4-kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4-kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated nonhomologous endjoining (NHEJ) events. There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome-healing events associated with terminal deletions of the subtelomeric region as well as the capture of a scrambled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini.

THE transitional region between telomeric repeats that cap the chromosome end and the most distal chromosome-specific sequence is termed the subtelomeric region. The organization of this genomic region varies among eukaryotic organisms (PRYDE et al. 1997). However, some common features can be recognized, including an abundance of repetitive sequences (including microsatellites, blocks of larger tandem repeats, and transposons) (LEVIS et al. 1993; VERSHININ et al. 1995; PEARCE et al. 1996; AMARGER et al. 1998) and the presence of duplicated sequences and/or paralogous genes shared among nonhomologous chromosomal ends (CARLSON et al. 1985; Louis 1995; THOMPSON et al. 1997; 2002). The complex and extensive sequence similarity exhibited among subtelomeric regions suggests that frequent sequence exchange occurs between nonhomologous chromosome ends. A recent study in humans inferred two major processes that generate the patchwork of sequence blocks shared extensively among nonhomologous chromosome ends: chromosomal translocations through nonhomologous end joining (NHEJ) DNA repair and subsequent homologous recombination among the duplicated segments on different chromosomes (LINARDOPOULOU et al. 2005). The role of ectopic recombination between nonhomologous chromosomes has also been shown to underlie the complex organization of the subtelomeric regions in other organisms (Louis and HABER 1990; FREITAS-JUNIOR et al. 2000). As expected for a plastic region of the genome subject to reshuffling through recombination events, subtelomeric regions are highly polymorphic and evolutionarily dynamic (BROUN et al. 1992; ROYLE et al. 1994; BAIRD and ROYLE 1997; MEFFORD and TRASK 2002; EICHLER and SANKOFF 2003).

The role of subtelomeric regions in chromosome stability and function remains elusive. Subtelomeric regions in most organisms generally contain nonfunctional repetitive sequences, and in cases where subtelomeric sequences have been lost or omitted, cell viability and chromosome stability were not affected (see review by MEFFORD and TRASK 2002). However, subtelomeric regions can provide a backup mechanism for acquisition of a new telomeric end through ectopic recombination with shared subtelomeric sequences on nonhomologous chromosome ends (WANG and ZAKIAN 1990). In extreme cases where conventional telomere repeat addition is compromised in budding yeast, amplification of subtelomeric repeats can ensure chromosome maintenance through a so-called ALT alternative telomere lengthening mechanism (LUNDBLAD and BLACKBURN 1993). …

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