Molecular Correlates of Genes Exhibiting RNAi Phenotypes in Caenorhabditis elegans

Cutter, Asher D.

doi:10.1101/gr.1659203

Cited by 30 publications

(21 citation statements)

References 47 publications

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“…However, several analyses have detected selection on codon usage bias in the genome of C. elegans (Stenico et al 1994;Duret 2000;Cutter et al 2003b;Cutter and Ward 2005). If selection is relaxed, codon usage bias decays very slowly over time (Marais et al 2004).…”

Section: Discussionmentioning

confidence: 99%

Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans

2006

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An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, extending even between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using ''scattered'' samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is shaped largely by population subdivision due to self-fertilization coupled with long-and short-range migration between subpopulations.

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Section: Discussionmentioning

confidence: 99%

Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans

2006

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“…Varying frequencies for silencing of an endogenous target have been reported in many different RNAi studies (Chuang and Meyerowitz, 2000;Fuhrmann et al, 2001;Cutter et al, 2003;Kamath et al, 2003;Waterhouse and Helliwell, 2003;Kerschen et al, 2004;Wang et al, 2005). One important note is that in many of these published studies the silencing efficiency was evaluated based on the severity of an anticipated phenotype.…”

Section: Discussionmentioning

confidence: 99%

Assessing the Efficiency of RNA Interference for Maize Functional Genomics

et al. 2007

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A large-scale functional genomics project was initiated to study the function of chromatin-related genes in maize (Zea mays). Transgenic lines containing short gene segments in inverted repeat orientation designed to reduce expression of target genes by RNA interference (RNAi) were isolated, propagated, and analyzed in a variety of assays. Analysis of the selectable marker expression over multiple generations revealed that most transgenes were transmitted faithfully, whereas some displayed reduced transmission or transgene silencing. A range of target-gene silencing efficiencies, from nondetectable silencing to nearly complete silencing, was revealed by semiquantitative reverse transcription-PCR analysis of transcript abundance for the target gene. In some cases, the RNAi construct was able to cause a reduction in the steady-state RNA levels of not only the target gene, but also another closely related gene. Correlation of silencing efficiency with expression level of the target gene and sequence features of the inverted repeat did not reveal any factors capable of predicting the silencing success of a particular RNAi-inducing construct. The frequencies of success of this large-scale project in maize, together with parameters for optimization at various steps, should serve as a useful framework for designing future RNAi-based functional genomics projects in crop plants.

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“…Indeed, codon bias is highly correlated with several other genic features such as protein length (Akashi 1996;Eyre-Walker 1996;Comeron et al 1999;Duret and Mouchiroud 1999;, recombination rate (Kliman and Hey 1993;Comeron et al 1999;Marais et al , 2003Hey and Kliman 2002), rate of protein evolution (Akashi 1996;Cutter et al 2003), gonad-biased expression (via a correlation with rate of protein evolution) (Meiklejohn et al 2003), expression level (reviewed in Akashi 2001; see also Sharp and Li 1986;Bulmer 1988;Duret and Mouchiroud 1999;Hey and Kliman 2002), and gene density (Hey and Kliman 2002). To test this hypothesis, we partitioned our data by median values of all known correlates of codon bias in both D. melanogaster and C. elegans: protein length, recombination rate, expression level, gene density, and rate of protein evolution.…”

Section: Resultsmentioning

confidence: 99%

X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis

2005

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Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.

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Molecular Correlates of Genes Exhibiting RNAi Phenotypes in Caenorhabditis elegans

Cited by 30 publications

References 47 publications

Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans

Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans

Assessing the Efficiency of RNA Interference for Maize Functional Genomics

X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis

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