RRC ID 46299
Author Chu JS, Johnsen RC, Chua SY, Tu D, Dennison M, Marra M, Jones SJ, Baillie DL, Rose AM.
Title Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs.
Journal Genetics
Abstract The issue of heterozygosity continues to be a challenge in the analysis of genome sequences. In this article, we describe the use of allele ratios to distinguish biologically significant single-nucleotide variants from background noise. An application of this approach is the identification of lethal mutations in Caenorhabditis elegans essential genes, which must be maintained by the presence of a wild-type allele on a balancer. The h448 allele of let-504 is rescued by the duplication balancer sDp2. We readily identified the extent of the duplication when the percentage of read support for the lesion was between 70 and 80%. Examination of the EMS-induced changes throughout the genome revealed that these mutations exist in contiguous blocks. During early embryonic division in self-fertilizing C. elegans, alkylated guanines pair with thymines. As a result, EMS-induced changes become fixed as either G→A or C→T changes along the length of the chromosome. Thus, examination of the distribution of EMS-induced changes revealed the mutational and recombinational history of the chromosome, even generations later. We identified the mutational change responsible for the h448 mutation and sequenced PCR products for an additional four alleles, correlating let-504 with the DNA-coding region for an ortholog of a NFκB-activating protein, NKAP. Our results confirm that whole-genome sequencing is an efficient and inexpensive way of identifying nucleotide alterations responsible for lethal phenotypes and can be applied on a large scale to identify the molecular basis of essential genes.
Volume 190(4)
Pages 1225-33
Published 2012-4
DOI 10.1534/genetics.111.137208
PII genetics.111.137208
PMID 22267497
PMC PMC3316639
MeSH Alleles* Animals Base Sequence Caenorhabditis elegans / drug effects Caenorhabditis elegans / genetics* Caenorhabditis elegans / metabolism Caenorhabditis elegans Proteins / genetics* Caenorhabditis elegans Proteins / metabolism Chromosome Mapping Chromosomes / drug effects Chromosomes / genetics Chromosomes / metabolism Crosses, Genetic Crossing Over, Genetic Gene Duplication Gene Frequency* Genes, Lethal Genetic Complementation Test Genome, Helminth* Hermaphroditic Organisms / genetics Hermaphroditic Organisms / metabolism Heterozygote Male Mesylates / adverse effects Mesylates / pharmacology Mutation* Organisms, Genetically Modified / genetics Organisms, Genetically Modified / metabolism Polymorphism, Single Nucleotide
IF 3.564
Times Cited 9
WOS Category GENETICS & HEREDITY
Resource
C.elegans tm4719