Krystalynne Morris et al. (2001) International C. elegans Meeting "Abundance, Distribution and Mutation Rate of Homopolymeric Nucleotide Runs in the Genome of Caenorhabditis elegans"

Dee R Denver, Suzanne Randall Estes, Michael Lynch, W Kelley Thomas, Avinash Kewalramani, Katherine Harris, Krystalynne Morris

[International C. elegans Meeting, 2001]

Homopolymeric nucleotide runs are a ubiquitous feature of eukaryotic genomes. Although their dominance in nuclear genomes is clear, homopolymer origins and mechanisms of maintenance and mutation are less obvious. To address these questions, we comprehensively examined the abundance and distribution of homopolymer loci ≥8 nucleotides in length in the genome of C. elegans . There are 148,625 homopolymer loci in the C. elegans genome. The four specific homopolymers are evenly distributed with respect to (+/-) strands of each chromosome. Homopolymer loci are under-represented in exons, show significant clustering in the arms of autosomes, and have significantly different densities between chromosomes. Homopolymers are over-represented in C. elegans genome compared to expectations based on individual nucleotide frequencies. A/T homopolymers vastly outnumber C/G homopolymers, and the size distributions of AT and CG homopolymers differ significantly, particularly for homopolymer loci less than 20 nucleotides in length. A direct investigation of mutation rates at numerous homopolymer loci in a set of C. elegans mutation accumulation lines (Denver, et al. 2000) revealed a significantly higher rate of mutation at C/G loci than at A/T loci. The abundance and distribution of homopolymer loci taken together with direct measures of their mutation rate suggest that differential stability may play a significant role in the maintenance of homopolymer loci. Literature cited: Denver, D.R., Morris, K., Lynch, M., Vassilieva, L., Thomas, W.K. "High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans " Science 289:2342-2344.