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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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Part a shows the number of inverted repeats that are overlapped by NIR others, together with regression lines, plotted for the S. cerevisiae (blue), RA (red), and R (green) genomes. Part b shows the number Nbp of distinct inverted repeats that overlap a given base pair. Both plots are presented in semilog coordinates. There is significant clustering of IRs in the S. cerevisiae genome relative to random, as shown by the larger overlap numbers it attains
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Fig8: Part a shows the number of inverted repeats that are overlapped by NIR others, together with regression lines, plotted for the S. cerevisiae (blue), RA (red), and R (green) genomes. Part b shows the number Nbp of distinct inverted repeats that overlap a given base pair. Both plots are presented in semilog coordinates. There is significant clustering of IRs in the S. cerevisiae genome relative to random, as shown by the larger overlap numbers it attains

Mentions: Figure 8 shows semilog plots of the number of IRs that are overlapped by NIR others (Fig. 8a), and the number of base pairs that are overlapped by Nbp IRs (Fig. 8b), for each of the three genome types. The data for each genome type fit a straight line to high precision. This shows that both Nbp and NIR decrease exponentially with overlap number. It is clear from the figure that the exponential decay rates for the R and RA genomes are essentially the same, and steeper than that for the S. cerevisiae genome, again indicative of IR clustering.Fig. 8


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

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

Part a shows the number of inverted repeats that are overlapped by NIR others, together with regression lines, plotted for the S. cerevisiae (blue), RA (red), and R (green) genomes. Part b shows the number Nbp of distinct inverted repeats that overlap a given base pair. Both plots are presented in semilog coordinates. There is significant clustering of IRs in the S. cerevisiae genome relative to random, as shown by the larger overlap numbers it attains
© Copyright Policy
Related In: Results  -  Collection

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

Fig8: Part a shows the number of inverted repeats that are overlapped by NIR others, together with regression lines, plotted for the S. cerevisiae (blue), RA (red), and R (green) genomes. Part b shows the number Nbp of distinct inverted repeats that overlap a given base pair. Both plots are presented in semilog coordinates. There is significant clustering of IRs in the S. cerevisiae genome relative to random, as shown by the larger overlap numbers it attains
Mentions: Figure 8 shows semilog plots of the number of IRs that are overlapped by NIR others (Fig. 8a), and the number of base pairs that are overlapped by Nbp IRs (Fig. 8b), for each of the three genome types. The data for each genome type fit a straight line to high precision. This shows that both Nbp and NIR decrease exponentially with overlap number. It is clear from the figure that the exponential decay rates for the R and RA genomes are essentially the same, and steeper than that for the S. cerevisiae genome, again indicative of IR clustering.Fig. 8

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
Related in: MedlinePlus