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A fitness assay for comparing RNAi effects across multiple C. elegans genotypes

BACKGROUND: RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a...

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Autores principales: Elvin, Mark, Snoek, Laurens B, Frejno, Martin, Klemstein, Ulrike, Kammenga, Jan E, Poulin, Gino B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206879/
https://www.ncbi.nlm.nih.gov/pubmed/22004469
http://dx.doi.org/10.1186/1471-2164-12-510
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author Elvin, Mark
Snoek, Laurens B
Frejno, Martin
Klemstein, Ulrike
Kammenga, Jan E
Poulin, Gino B
author_facet Elvin, Mark
Snoek, Laurens B
Frejno, Martin
Klemstein, Ulrike
Kammenga, Jan E
Poulin, Gino B
author_sort Elvin, Mark
collection PubMed
description BACKGROUND: RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. RESULTS: Here we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which E. coli is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in ppw-1 contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important. CONCLUSIONS: In summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi.
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spelling pubmed-32068792011-11-03 A fitness assay for comparing RNAi effects across multiple C. elegans genotypes Elvin, Mark Snoek, Laurens B Frejno, Martin Klemstein, Ulrike Kammenga, Jan E Poulin, Gino B BMC Genomics Methodology Article BACKGROUND: RNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. RESULTS: Here we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which E. coli is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in ppw-1 contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important. CONCLUSIONS: In summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi. BioMed Central 2011-10-17 /pmc/articles/PMC3206879/ /pubmed/22004469 http://dx.doi.org/10.1186/1471-2164-12-510 Text en Copyright ©2011 Elvin et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Elvin, Mark
Snoek, Laurens B
Frejno, Martin
Klemstein, Ulrike
Kammenga, Jan E
Poulin, Gino B
A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title_full A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title_fullStr A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title_full_unstemmed A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title_short A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
title_sort fitness assay for comparing rnai effects across multiple c. elegans genotypes
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206879/
https://www.ncbi.nlm.nih.gov/pubmed/22004469
http://dx.doi.org/10.1186/1471-2164-12-510
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