All organisms' genomes mutate, but do some mutate more than others? For example, are individuals with differing lengths of repetitive DNA at a given site in their genome more likely to mutate? To examine this question, next-generation DNA sequencing technology will be used to compare the mutational properties at genomic sites that differ in length in 16 individuals from an experimental population of nematode worms. The DNA sequencing information will be used to test whether 1) sites that differ by short stretches of DNA mutate more than sites that do not and 2) if there is a greater number of single DNA base mutations in the regions flanking the sites that differ in length.
Understanding how differences in mutational properties differ between and within species has implications beyond pure academic interests. Most people who live in an industrialized society will die of diseases with a complex genetic basis; for example, there are a multitude of subtle genetic causes that lead to cancers. If genomic mutation rates differ significantly among individuals within a species, this would have a significant effect on how to best approach the study of such complex diseases. In particular, the understanding of the "rare variant/common variant" conceptual framework that motivates association studies of human diseases would need to be re-evaluated in light of a greater appreciation of the role of rare variants in the human population. If individuals with differing lengths of repetitive DNA at a given site are predisposed to mutation, this will indeed be the case.
Scientific Merit - The main goal of this project is to establish if there is any relationship between the probability that an individual (in this case a nematode worm belonging to the genus Caenorhabditis remanei) is a heterozygote at a locus in which the two alleles are of different lengths (an "indel", short for "insertion or deletion") and the probability that a nearby nucleotide mutates. The starting material was a stock of C. remanei which was bred to be homozygous at all loci, but for which it was subsequently discovered that the genome was not completely homozygous, i.e., some loci were heterozygous. To test this hypothesis, we sequenced the genome of five populations descended from the original stock population which had been allowed to accumulate mutations for 122 generations. At this time we are still analyzing the data in terms of the original question. We have tentatively established that the genome-wide mutation rate per-nucleotide per-generation is approximately four-fold greater than that of two related species, C. briggsae and C. elegans. This result is potentially important from the perspective of theoretical evolutionary biology. C. remanei reproduces by "normal" sexual reproduction, i.e., there are males and females, whereas C. briggsae and C. elegans reproduce primarily (not completely) by self-fertilizing hermaphrodites. Evolutionary theory predicts that the strength of natural selection to reduce the mutation rate should be stronger in self-fertilizing species than in "normal" sexual species. If this tentative result holds up under scrutiny, it would be the first direct evidence that mutation rates have actually evolved in this predicted way. Broader Impacts - The results of this project may ultimately have particular importance for human medical genetics. If sites in the genome where two alleles differ in length do have different mutational properties, this will have a significant impact on the local mutation rate surrounding these sites. The human genome is known to contain many sites where indels are segregating in the population. Therefore, a better understanding of how mutational properties depend on fine-scale genomic context is important to our understanding of the role of new mutations in complex human diseases.
