Poly-G-poly-C tracts in the genomes of CaenorhabditisReport as inadecuate




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BMC Genomics

, 8:403

First Online: 07 November 2007Received: 24 July 2007Accepted: 07 November 2007

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.

List of abbreviationsCGHcomparative genomic hybridization

DSBdouble-stranded break

ESTexpressed sequence tag

HRRhomolog recognition region

KOGconserved orthologous groups

LGlinkage group or chromosome

SAGEserial analysis of gene expression

SNPsingle nucleotide polymorphisms.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-8-403 contains supplementary material, which is available to authorized users.

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Author: Yang Zhao - Nigel J O-Neil - Ann M Rose

Source: https://link.springer.com/article/10.1186/1471-2164-8-403







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