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The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome.

Strawbridge EM, Benson G, Gelfand Y, Benham CJ - Curr. Genet. (2010)

Bottom Line: We find that the S. cerevisiae genome is significantly enriched in IRs relative to random.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, University of Chicago, IL 60637, USA. emstrawb@math.uchicago.edu

ABSTRACT
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.

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The percentage of IRs in the S. cerevisiae genome (blue circles) and in a representative RA genome (red x’s) that contain one or more ApT or TpA dinucleotide repeat of length n, for n ≥ 1
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Fig5: The percentage of IRs in the S. cerevisiae genome (blue circles) and in a representative RA genome (red x’s) that contain one or more ApT or TpA dinucleotide repeat of length n, for n ≥ 1

Mentions: We next considered whether this dinucleotide enrichment has an effect on the IR numbers. Figure 5 shows the percentage of IRs in the S. cerevisiae genome, and in a representative RA genome, that contain either n consecutive ApT repeats, or n consecutive TpA repeats. One sees that only small fractions of the IRs in the S. cerevisiae genome contain AT dinucleotide repeats having n > 2, and that these numbers are entirely consistent with random. We note that less than 1% of IRs in either the S. cerevisiae or RA genomes possess dinucleotide repeats with n > 3. This data show that the 12.7% genomic enrichment of IRs is not significant due to expansion of AT dinucleotide repeats, nor are long IRs the result of closely occurring independent dinucleotide repeats (shown in the supplementary materials, SFigure 1). For repeat numbers n = 1 or 2, the IR count is weakly positively correlated with copy length. This correlation is weaker in the S. cerevisiae genome than in the RA randomized genomes, and drops steadily beyond n = 2. This means that longer IRs do not contain more instances of (ApT)n or (TpA)n for a given n than do short IRs. These results show that neither A+T content nor the presence or extension of AT dinucleotide repeats is significantly responsible for the observed enrichment of the S. cerevisiae genome in either total IR numbers or in long IRs.Fig. 5


The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome.

Strawbridge EM, Benson G, Gelfand Y, Benham CJ - Curr. Genet. (2010)

The percentage of IRs in the S. cerevisiae genome (blue circles) and in a representative RA genome (red x’s) that contain one or more ApT or TpA dinucleotide repeat of length n, for n ≥ 1
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908449&req=5

Fig5: The percentage of IRs in the S. cerevisiae genome (blue circles) and in a representative RA genome (red x’s) that contain one or more ApT or TpA dinucleotide repeat of length n, for n ≥ 1
Mentions: We next considered whether this dinucleotide enrichment has an effect on the IR numbers. Figure 5 shows the percentage of IRs in the S. cerevisiae genome, and in a representative RA genome, that contain either n consecutive ApT repeats, or n consecutive TpA repeats. One sees that only small fractions of the IRs in the S. cerevisiae genome contain AT dinucleotide repeats having n > 2, and that these numbers are entirely consistent with random. We note that less than 1% of IRs in either the S. cerevisiae or RA genomes possess dinucleotide repeats with n > 3. This data show that the 12.7% genomic enrichment of IRs is not significant due to expansion of AT dinucleotide repeats, nor are long IRs the result of closely occurring independent dinucleotide repeats (shown in the supplementary materials, SFigure 1). For repeat numbers n = 1 or 2, the IR count is weakly positively correlated with copy length. This correlation is weaker in the S. cerevisiae genome than in the RA randomized genomes, and drops steadily beyond n = 2. This means that longer IRs do not contain more instances of (ApT)n or (TpA)n for a given n than do short IRs. These results show that neither A+T content nor the presence or extension of AT dinucleotide repeats is significantly responsible for the observed enrichment of the S. cerevisiae genome in either total IR numbers or in long IRs.Fig. 5

Bottom Line: We find that the S. cerevisiae genome is significantly enriched in IRs relative to random.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, University of Chicago, IL 60637, USA. emstrawb@math.uchicago.edu

ABSTRACT
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.

Show MeSH