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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 six regions of the S. cerevisiae genome are shown where the highest levels of IR overlap are attained. Here IRs are represented by blue arrows, one arrow for each copy, pointing toward the center of symmetry. The flanking genes are shown in black with the arrow indicating transcriptional direction. Regions (a–b), (c), (d), (e–f) are located on chromosomes 3, 9, 11, and 13 respectively
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Fig9: The six regions of the S. cerevisiae genome are shown where the highest levels of IR overlap are attained. Here IRs are represented by blue arrows, one arrow for each copy, pointing toward the center of symmetry. The flanking genes are shown in black with the arrow indicating transcriptional direction. Regions (a–b), (c), (d), (e–f) are located on chromosomes 3, 9, 11, and 13 respectively

Mentions: Parameters reflective of clustering also have very high extreme values. In the S. cerevisiae genome there is a base pair that is overlapped by Nbp = 11 different IRs, while the maximum achieved in any of the 50 RA genomes was Nbp = 7. The largest number attained in any of the 50 R randomizations was Nbp = 6. The distribution of IRs in six representative highly overlapped regions are shown in Fig. 9. The number of IRs in each of these regions is quite high. Each has at least one base pair with Nbp ≥ 11 and contains at least one IR with NIR ≥ 10. In every case the region of highest overlap occurs in the 3′ flank of a gene. These examples suggest a preference for clustering to occur in intergenic regions, and specifically at the 3′ ends of genes, within either tandem or convergent intergenic regions.Fig. 9


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

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

The six regions of the S. cerevisiae genome are shown where the highest levels of IR overlap are attained. Here IRs are represented by blue arrows, one arrow for each copy, pointing toward the center of symmetry. The flanking genes are shown in black with the arrow indicating transcriptional direction. Regions (a–b), (c), (d), (e–f) are located on chromosomes 3, 9, 11, and 13 respectively
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
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Fig9: The six regions of the S. cerevisiae genome are shown where the highest levels of IR overlap are attained. Here IRs are represented by blue arrows, one arrow for each copy, pointing toward the center of symmetry. The flanking genes are shown in black with the arrow indicating transcriptional direction. Regions (a–b), (c), (d), (e–f) are located on chromosomes 3, 9, 11, and 13 respectively
Mentions: Parameters reflective of clustering also have very high extreme values. In the S. cerevisiae genome there is a base pair that is overlapped by Nbp = 11 different IRs, while the maximum achieved in any of the 50 RA genomes was Nbp = 7. The largest number attained in any of the 50 R randomizations was Nbp = 6. The distribution of IRs in six representative highly overlapped regions are shown in Fig. 9. The number of IRs in each of these regions is quite high. Each has at least one base pair with Nbp ≥ 11 and contains at least one IR with NIR ≥ 10. In every case the region of highest overlap occurs in the 3′ flank of a gene. These examples suggest a preference for clustering to occur in intergenic regions, and specifically at the 3′ ends of genes, within either tandem or convergent intergenic regions.Fig. 9

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