Abstract
BackgroundIn 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.ResultsIn 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.ConclusionThe 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.
Highlights
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
G/C tracts are over-represented in the C. elegans genome 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
G/C tracts are over-represented in Caenorhabditis briggsae To determine if the location and orientation of G/C tracts are conserved in closely related nematode species, we investigated the G/C tract conservation in C. briggsae, a closely related species of C. elegans
Summary
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. Many of the functions of non-coding DNA are poorly understood One such non-coding DNA element is guanine-rich DNA, which has been characterized in several functional domains: the telomeres, the ribosomal DNA and, in mammals, the immunoglobulin heavy-chain switch regions [2]. These G-rich DNA elements all have stretches of consecutive guanines and have the capacity to form secondary structures such as G-quadruplex or G4 DNA by Hoogsteen bonding [3]. Many studies have suggested a possible role for G-rich motifs in chromosome dynam-
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