Size-dependent palindrome-induced intrachromosomal recombination in yeast

Lisnić, Berislav; Svetec, Ivan‐Krešimir; Štafa, Anamarija; Zgaga, Zoran

doi:10.1016/j.dnarep.2008.11.017

Cited by 13 publications

(15 citation statements)

References 48 publications

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“…IR-mediated recombination events in E. coli were found to be dramatically reduced with increased spacer length (Bi and Liu 1996). Similar results were also found by others (Chalker et al 1993; Kogo et al 2007; Lisnic et al 2009). Thus, short-spacer, long-copy IRs are likely to be the most structurally and/or mutationally susceptible in the genome.…”

Section: Resultssupporting

confidence: 90%

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

et al. 2010

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Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3′ flanks of genes than in their 5′ flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered.Electronic supplementary materialThe online version of this article (doi:10.1007/s00294-010-0302-6) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 90%

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

et al. 2010

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“…The palindrome is flanked by the remnants of two copies of a transposable element, similar to the inserted sequences. In yeast, palindromes were shown to mediate gene amplification and intra-chromosomal recombination and may lead to genomic instability [58], [59]. Goodwin et al [46] hypothesized that accessory chromosomes originated through an ancient horizontal transfer from an unknown donor species.…”

Section: Discussionmentioning

confidence: 99%

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

2013

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Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen Zymoseptoria tritici. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB) cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of Z. tritici originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for adaptive evolution in this and other fungal pathogens.

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“…Moreover, FISH revealed a subtelomeric localization of BvMSat05 clusters on some chromosomes, hence, the head to head junction of head to tail arrays typical for BvMSat05 may result from breakage-fusion-bridge cycles as postulated for tandem repeats near at terminal regions of rye chromosomes [60]. It has been reported that palindromic sequences may induce genomic instability through provoking double strand breaks and recombination [61]. Therefore, the head to head junction may also be the result of DNA repair following possible double strand breaks within BvMSat05 arrays.…”

Section: Discussionmentioning

confidence: 99%

Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

et al. 2010

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BackgroundRepetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c0t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences.ResultsAnalysis of 1763 c0t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions.ConclusionThe c0t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c0t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes.

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Size-dependent palindrome-induced intrachromosomal recombination in yeast

Cited by 13 publications

References 48 publications

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

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