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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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Distribution of G/C tracts along each chromosome of C. elegans and C. briggsae*. X axis in each graph represents one chromosome whose length was normalized to 1 and Y axis is the number of G/C tracts. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially. The diamond spots on the X axis marked the edge of the genetically defined central gene cluster [24]. * Positions of G/C tracts in C. briggsae were predicted by the method described in text.
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Figure 3: Distribution of G/C tracts along each chromosome of C. elegans and C. briggsae*. X axis in each graph represents one chromosome whose length was normalized to 1 and Y axis is the number of G/C tracts. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially. The diamond spots on the X axis marked the edge of the genetically defined central gene cluster [24]. * Positions of G/C tracts in C. briggsae were predicted by the method described in text.

Mentions: Although the GC content in the C. elegans genome is similar on all the chromosomes [16], the G/C tracts are not distributed uniformly across the chromosomes. C. elegans autosomes can be divided into three genetically defined compartments of the left arm (L), the central gene cluster region (C), and the right arm (R) [24]. We found that more G/C tracts are located in the chromosome arms than in the central regions (Table 1, Figure 2 and 3). While this pattern is fairly subtle on LGIII, it is more obvious on the other chromosomes especially on LGV where only 9% of G/C tracts are located in the central region while 91% reside on the arms of LGV (Table 1, Figure 2 and 3). This non-random distribution of G/C tracts on the autosomes correlates with both the meiotic cross-over distribution [24] and negatively with gene density [16,22,25]. An enrichment of G/C tracts on the chromosome arms of the X chromosome was observed even though the X chromosome does not have a central gene cluster or a meiotic cross-over pattern. The distributions of the intragenic and intergenic G/C tracts do not differ from the overall distribution pattern with more and longer G/C tracts on the arms. Nor is there any distinct pattern with regard to the orientation of G/C tracts on either DNA strand.


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

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

Distribution of G/C tracts along each chromosome of C. elegans and C. briggsae*. X axis in each graph represents one chromosome whose length was normalized to 1 and Y axis is the number of G/C tracts. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially. The diamond spots on the X axis marked the edge of the genetically defined central gene cluster [24]. * Positions of G/C tracts in C. briggsae were predicted by the method described in text.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Distribution of G/C tracts along each chromosome of C. elegans and C. briggsae*. X axis in each graph represents one chromosome whose length was normalized to 1 and Y axis is the number of G/C tracts. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially. The diamond spots on the X axis marked the edge of the genetically defined central gene cluster [24]. * Positions of G/C tracts in C. briggsae were predicted by the method described in text.
Mentions: Although the GC content in the C. elegans genome is similar on all the chromosomes [16], the G/C tracts are not distributed uniformly across the chromosomes. C. elegans autosomes can be divided into three genetically defined compartments of the left arm (L), the central gene cluster region (C), and the right arm (R) [24]. We found that more G/C tracts are located in the chromosome arms than in the central regions (Table 1, Figure 2 and 3). While this pattern is fairly subtle on LGIII, it is more obvious on the other chromosomes especially on LGV where only 9% of G/C tracts are located in the central region while 91% reside on the arms of LGV (Table 1, Figure 2 and 3). This non-random distribution of G/C tracts on the autosomes correlates with both the meiotic cross-over distribution [24] and negatively with gene density [16,22,25]. An enrichment of G/C tracts on the chromosome arms of the X chromosome was observed even though the X chromosome does not have a central gene cluster or a meiotic cross-over pattern. The distributions of the intragenic and intergenic G/C tracts do not differ from the overall distribution pattern with more and longer G/C tracts on the arms. Nor is there any distinct pattern with regard to the orientation of G/C tracts on either DNA strand.

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.

Show MeSH
Related in: MedlinePlus