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Poly-G/poly-C tracts in the genomes of Caenorhabditis.

Zhao Y, O'Neil NJ, Rose AM - BMC Genomics (2007)

Bottom Line: However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans.Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants.The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of British Columbia, Life Sciences Centre, Room 1364 - 2350 Health Sciences Mall, Vancouver, BC, V6T1Z3, Canada. yzhaocn@interchange.ubc.ca

ABSTRACT

Background: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts.

Results: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggsae. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants.

Conclusion: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

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Length distribution of G/C tracts in C. elegans genome.
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Figure 1: Length distribution of G/C tracts in C. elegans genome.

Mentions: Although statistically no G/C tracts containing 18 or more consecutive Gs are expected in the 100 Mbp C. elegans genome, 396 G/C tracts were found. They are over-represented in the C. elegans genome, especially compared to the human (200 in 3.3 Bbp) and yeast (1 in 12 Mbp) genomes. These G/C tracts range in size from 18 to 32 base pairs and the frequency decreases with increased length (Figure 1). The tracts are distributed throughout the genome along all six chromosomes. The five autosomes have approximately 50 to 70 tracts each, while the X chromosome has more than 100 tracts. The density of G/C tracts on LGX is 6.1 per Mbps compared to 2.7 per Mbps of LGV (longest chromosome in C. elegans) (Table 1).


Poly-G/poly-C tracts in the genomes of Caenorhabditis.

Zhao Y, O'Neil NJ, Rose AM - BMC Genomics (2007)

Length distribution of G/C tracts in C. elegans genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211496&req=5

Figure 1: Length distribution of G/C tracts in C. elegans genome.
Mentions: Although statistically no G/C tracts containing 18 or more consecutive Gs are expected in the 100 Mbp C. elegans genome, 396 G/C tracts were found. They are over-represented in the C. elegans genome, especially compared to the human (200 in 3.3 Bbp) and yeast (1 in 12 Mbp) genomes. These G/C tracts range in size from 18 to 32 base pairs and the frequency decreases with increased length (Figure 1). The tracts are distributed throughout the genome along all six chromosomes. The five autosomes have approximately 50 to 70 tracts each, while the X chromosome has more than 100 tracts. The density of G/C tracts on LGX is 6.1 per Mbps compared to 2.7 per Mbps of LGV (longest chromosome in C. elegans) (Table 1).

Bottom Line: However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans.Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants.The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of British Columbia, Life Sciences Centre, Room 1364 - 2350 Health Sciences Mall, Vancouver, BC, V6T1Z3, Canada. yzhaocn@interchange.ubc.ca

ABSTRACT

Background: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts.

Results: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggsae. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants.

Conclusion: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

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