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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.

Show MeSH
An imperfect inverted repeat and its hairpin structure. The hairpin has nine matched base pairs, one mismatch at site I, and one indel (an insertion in the right copy or a deletion in the left copy) at site II
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Fig1: An imperfect inverted repeat and its hairpin structure. The hairpin has nine matched base pairs, one mismatch at site I, and one indel (an insertion in the right copy or a deletion in the left copy) at site II

Mentions: Other proposed mechanisms by which IRs might participate in regulatory processes involve the formation of alternative DNA structures in which the two repeat copies on the same DNA strand pair together to form a hairpin. (An example is shown in Fig. 1.) If both DNA strands of an IR form hairpins simultaneously, the result is a cruciform.Fig. 1


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

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

An imperfect inverted repeat and its hairpin structure. The hairpin has nine matched base pairs, one mismatch at site I, and one indel (an insertion in the right copy or a deletion in the left copy) at site II
© Copyright Policy
Related In: Results  -  Collection

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

Fig1: An imperfect inverted repeat and its hairpin structure. The hairpin has nine matched base pairs, one mismatch at site I, and one indel (an insertion in the right copy or a deletion in the left copy) at site II
Mentions: Other proposed mechanisms by which IRs might participate in regulatory processes involve the formation of alternative DNA structures in which the two repeat copies on the same DNA strand pair together to form a hairpin. (An example is shown in Fig. 1.) If both DNA strands of an IR form hairpins simultaneously, the result is a cruciform.Fig. 1

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