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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. briggsae based on genome assembly CB3. X axis of each graph represents the physical length of each chromosome and Y axis is the ordinal number. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially.
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Figure 4: Distribution of G/C tracts along each chromosome of C. briggsae based on genome assembly CB3. X axis of each graph represents the physical length of each chromosome and Y axis is the ordinal number. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially.

Mentions: Based on the knowledge that the two genomes exhibit extensive colinearity [22,27,28], we used the genomic positions of the C. elegans orthologs of the G/C tracts' associated genes in C. briggsae to create a predicted genomic distribution map of G/C tracts in C. briggsae. In the C. briggsae plots (Figure 3), G/C tracts are also dispersed across every chromosome in the C. briggsae genome. Because there are fewer G/C tracts on each chromosome, the curves are beneath their C. elegans counterparts. The slope of the C. briggsae line illustrates that the G/C tracts are distributed evenly across the chromosomes. Both the analysis presented here (Figure 3) and a more recent analysis based on the chromosome-based assembly of C. briggsae genome (Wormbase CB3 [23,28]) result in a similar pattern (Figure 4). Thus, although there is no specific patterning to the position or the orientation of the tracts, the number and dispersed location of them in these two species is suggestive of a biological role.


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. briggsae based on genome assembly CB3. X axis of each graph represents the physical length of each chromosome and Y axis is the ordinal number. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Distribution of G/C tracts along each chromosome of C. briggsae based on genome assembly CB3. X axis of each graph represents the physical length of each chromosome and Y axis is the ordinal number. Each G/C tract from the left end to the right end of one chromosome was numbered sequentially.
Mentions: Based on the knowledge that the two genomes exhibit extensive colinearity [22,27,28], we used the genomic positions of the C. elegans orthologs of the G/C tracts' associated genes in C. briggsae to create a predicted genomic distribution map of G/C tracts in C. briggsae. In the C. briggsae plots (Figure 3), G/C tracts are also dispersed across every chromosome in the C. briggsae genome. Because there are fewer G/C tracts on each chromosome, the curves are beneath their C. elegans counterparts. The slope of the C. briggsae line illustrates that the G/C tracts are distributed evenly across the chromosomes. Both the analysis presented here (Figure 3) and a more recent analysis based on the chromosome-based assembly of C. briggsae genome (Wormbase CB3 [23,28]) result in a similar pattern (Figure 4). Thus, although there is no specific patterning to the position or the orientation of the tracts, the number and dispersed location of them in these two species is suggestive of a biological role.

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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