Rapid single nucleotide polymorphism mapping in C. elegans

Davis, Matthew L.; Hammarlund, Marc; Harrach, Tracey; Hullett, Patrick; Olsen, Shawn; Jørgensen, Erik M.

doi:10.1186/1471-2164-6-118

Cited by 306 publications

(277 citation statements)

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“…PCR and sequencing of the unc-73 gene in our mutants revealed mutations in the Rho-specific GEF domain. ox317 and ox322 failed to complement each other and were mapped with SNPs (Davis et al 2005) to an interval on Chromosome I slightly left of cosmid E01A2 (−1.66) and very close to cosmid F28H1 (−1.87). Fine mapping was aided by picking Dpy non-Unc and Unc non-Dpy recombinants from ox317 , but failed to complement unc-73(ev802), and sequencing confirmed that ox317 and ox322 carried mutations in the Rho-GEF domain of unc-73.…”

Section: Mapping Identification and Outcrossing Of Suppressor Mutatmentioning

confidence: 99%

Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans

Williams¹,

Lutz

Charlie³

et al. 2007

Genes Dev.

146

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The G␣ q pathway is essential for animal life and is a central pathway for driving locomotion, egg laying, and growth in Caenorhabditis elegans, where it exerts its effects through EGL-8 (phospholipase C␤ [PLC␤]) and at least one other effector. To find the missing effector, we performed forward genetic screens to suppress the slow growth and hyperactive behaviors of mutants with an overactive G␣ q pathway. Four suppressor mutations disrupted the Rho-specific guanine-nucleotide exchange factor (GEF) domain of UNC-73 (Trio). The mutations produce defects in neuronal function, but not neuronal development, that cause sluggish locomotion similar to animals lacking EGL-8 (PLC␤). Strains containing null mutations in both EGL-8 (PLC␤) and UNC-73 (Trio RhoGEF) have strong synthetic phenotypes that phenocopy the arrested growth and near-complete paralysis of G␣ q -null mutants. Using cell-based and biochemical assays, we show that activated C. elegans G␣ q synergizes with Trio RhoGEF to activate RhoA. Activated G␣ q and Trio RhoGEF appear to be part of a signaling complex, because they coimmunoprecipitate when expressed together in cells. Our results show that Trio's Rho-specific GEF domain is a major G␣ q effector that, together with PLC␤, mediates the G␣ q signaling that drives the locomotion, egg laying, and growth of the animal.[Keywords: G␣ q ; Trio; Rho; phospholipase C␤; C. elegans] Supplemental material is available at http://www.genesdev.org.

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Section: Mapping Identification and Outcrossing Of Suppressor Mutatmentioning

confidence: 99%

Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans

Williams¹,

Lutz

Charlie³

et al. 2007

Genes Dev.

146

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“…Affected and unaffected F2 progeny were collected and used for SNP mapping as previously described (40). Genomic DNA from mutant worms carrying genes localizing to chromosome I were used for PCR using W06D4.1 specific primers, to chromosome III with T21C12.2 primers, and to chromosome X with F42D1.2 primers (sequences available on request).…”

Section: Methodsmentioning

confidence: 99%

“…4, we figured that some of the genes identified in our screen would represent alleles of upstream enzymes in the tyrosine degradation pathway. Consequently, we used a PCR-based SNP-based mapping technique to localize the mutant genes and then sequenced genomic DNA of mutants that localize near F42D1.2, T21C12.2, or W06D4.1 (data not shown) (40). Among our mutants we identified the strains ALF103 (F42D1.2(baf1)) and ALF104 (W06D4.1(baf2)) through sequencing.…”

Section: A Pilot Genetic Screen Identifies Mutants Resistant To the Ementioning

confidence: 99%

The Caenorhabditis elegans K10C2.4 Gene Encodes a Member of the Fumarylacetoacetate Hydrolase Family

Fisher

Page

Lithgow

et al. 2008

Journal of Biological Chemistry

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In eukaryotes and many bacteria, tyrosine is degraded to produce energy via a five-step tyrosine degradation pathway. Mutations affecting the tyrosine degradation pathway are also of medical importance as mutations affecting enzymes in the pathway are responsible for type I, type II, and type III tyrosinemia. The most severe of these is type I tyrosinemia, which is caused by mutations affecting the last enzyme in the pathway, fumarylacetoacetate hydrolase (FAH). So far, tyrosine degradation in the nematode Caenorhabditis elegans has not been studied; however, genes predicted to encode enzymes in this pathway have been identified in several microarray, proteomic, and RNA interference (RNAi) screens as perhaps being involved in aging and the control of protein folding. We sought to identify and characterize the genes in the worm tyrosine degradation pathway as an initial step in understanding these findings. Here we describe the characterization of the K10C2.4, which encodes a homolog of FAH. RNAi directed against K10C2.4 produces a lethal phenotype consisting of death in young adulthood, extensive damage to the intestine, impaired fertility, and activation of oxidative stress and endoplasmic stress response pathways. This phenotype is due to alterations in tyrosine metabolism as increases in dietary tyrosine enhance it, and inhibition of upstream enzymes in tyrosine degradation with RNAi or genetic mutations reduces the phenotype. We also use our model to identify genes that suppress the damage produced by K10C2.4 RNAi in a pilot genetic screen. Our results establish worms as a model for the study of type I tyrosinemia.

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“…To clone tu439, we used RFLP-SNP mapping (35) and next-generation sequencing (50). In brief, we mapped btr-1 to an approximately 160-kb region on chromosome II between the markers F38A3 and F37H8.…”

Section: Resultsmentioning

confidence: 99%

New Role for DCR-1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27

et al. 2013

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Bacillus thuringiensis produces toxins that target invertebrates, including Caenorhabditis elegans. Virulence of Bacillus strains is often highly specific, such that B. thuringiensis strain DB27 is highly pathogenic to C. elegans but shows no virulence for another model nematode, Pristionchus pacificus. To uncover the underlying mechanisms of the differential responses of the two nematodes to B. thuringiensis DB27 and to reveal the C. elegans defense mechanisms against this pathogen, we conducted a genetic screen for C. elegans mutants resistant to B. thuringiensis DB27. Here, we describe a B. thuringiensis DB27-resistant C. elegans mutant that is identical to nasp-1, which encodes the C. elegans homolog of the nuclear-autoantigenic-sperm protein.Gene expression analysis indicated a substantial overlap between the genes downregulated in the nasp-1 mutant and targets of C. elegans dcr-1/Dicer, suggesting that dcr-1 is repressed in nasp-1 mutants, which was confirmed by quantitative PCR. Consistent with this, the nasp-1 mutant exhibits RNA interference (RNAi) deficiency and reduced longevity similar to those of a dcr-1 mutant. Building on these surprising findings, we further explored a potential role for dcr-1 in C. elegans innate immunity. We show that dcr-1 mutant alleles deficient in microRNA (miRNA) processing, but not those deficient only in RNAi, are resistant to B. thuringiensis DB27. Furthermore, dcr-1 overexpression rescues the nasp-1 mutant's resistance, suggesting that repression of dcr-1 determines the nasp-1 mutant's resistance. Additionally, we identified the collagen-encoding gene col-92 as one of the downstream effectors of nasp-1 that play an important role in resistance to DB27. Taken together, these results uncover a previously unknown role for DCR-1/Dicer in C. elegans antibacterial immunity that is largely associated with miRNA processing.

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Rapid single nucleotide polymorphism mapping in C. elegans

Abstract: Background: In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two-and three-factor mapping to measuring recombination across whole chromosomes.

Cited by 306 publications

References 5 publications

Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans

Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans

The Caenorhabditis elegans K10C2.4 Gene Encodes a Member of the Fumarylacetoacetate Hydrolase Family

New Role for DCR-1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27

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Rapid single nucleotide polymorphism mapping in C. elegans

Abstract: Background: In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two-and three-factor mapping to measuring recombination across whole chromosomes.

Cited by 306 publications

References 5 publications

Trio’s Rho-specific GEF domain is the missing Gαq effector in C. elegans

Trio’s Rho-specific GEF domain is the missing Gαq effector in C. elegans

The Caenorhabditis elegans K10C2.4 Gene Encodes a Member of the Fumarylacetoacetate Hydrolase Family

New Role for DCR-1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27

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Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans

Trio’s Rho-specific GEF domain is the missing Gα_q effector in C. elegans