Abstract
BackgroundGenetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits.MethodsIn the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement.ResultsUsing two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions.ConclusionsWe developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.
Highlights
Genetic interactions are keys to understand complex traits and evolution
Instead of lethality or general sickness that may involve many biological processes, these are specific developmental traits. These traits represent different types of phenotypic data: the sex ratio measures a population of a binary output from each animal; the body length measures an individual animal of a continuous variable
A valid quantitative epistasis method should be applicable to both data types and be adapted to a wide range of metazoan phenotypes
Summary
Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. A genetic interaction occurs when two mutations at different loci generate a phenotype that cannot be explained by the additive effect of the two single mutations [1]. Genetic interactions are defined as positive (alleviating) when the combination of mutations shows a phenotype that is milder than the expected additive effect from the two single mutations; and negative (aggravating) when the combined phenotype is more severe than expected [1, 2]. Synthetic lethality screens would miss non-lethal negative genetic interactions and all positive interactions
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