ArticleGenome research2003
Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 37 citations in OpenAlex.
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- Assessing the efficiency of RNA interference for maize functional genomics.Plant physiology · 2007Article
- Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants.Plant physiology · 2006Article
- Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae.Genetics · 2006Article
- Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans.Genetics · 2006Article
- Analysis of RNA silencing in agroinfiltrated leaves of Nicotiana benthamiana and Nicotiana tabacum.Plant molecular biology · 2005Article
- Article
- Functional constraint and divergence in the G protein family in Caenorhabditis elegans and Caenorhabditis briggsae.Molecular genetics and genomics : MGG · 2005Article
- Protein evolution in the context of Drosophila development.Journal of molecular evolution · 2005Article
- Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library.Genome research · 2004Article
- Evolutionary rate depends on number of protein-protein interactions independently of gene expression level.BMC evolutionary biology · 2004Article
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding genome-wide links between genotype and phenotype has generally been difficult due to both the complexity of phenotypes, and until recently, inaccessibility to large numbers of genes that might underlie a trait. To address this issue, we establish the association between particular RNAi phenotypes in Caenorhabditis elegans and sequence characteristics of the corresponding proteins and DNA. We find that genes showing RNAi phenotypes are long and highly expressed with little noncoding DNA and high rates of synonymous site substitution (KS). In addition, genes conferring RNAi phenotypes have significantly lower rates of nonsynonymous site substitution (KA). Collectively, these sequence features explain nearly 20% of the difference between the sets of loci that display or lack a RNAi-mediated effect, and reflect aspects both of the RNAi mechanism and the biological function of the genes. For example, the particularly low rate of evolution of genes in the sterility RNAi phenotype class suggests a role of C. elegans life history in shaping these patterns of sequence and expression characteristics on phenotypes. This approach also allows prediction of a set of heretofore-uncharacterized loci for which we expect future RNAi studies to reveal phenotypic effects (i.e., false negatives in present screens).
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