<i>De Novo</i> Identification of Single Nucleotide Mutations in <i>Caenorhabditis elegans</i> Using Array Comparative Genomic Hybridization

Maydan, Jason S.; Okada, Hatsumi; Flibotte, Stéphane; Edgley, Mark L.; Moerman, Donald G.

doi:10.1534/genetics.108.100065

Cited by 16 publications

(18 citation statements)

References 16 publications

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“…Single nucleotide polymorphism (SNP) mapping using the polymorphic Hawaiian isolate CB4856 is a more common approach [21]. Oligonucleotide array comparative genome hybridization (aCGH) has also been used successfully to identify point mutations and deletions in complex pools of genomic DNA [22, 23]. In this case, custom-made arrays with overlapping 50-mer probes are used to identify SNPs and insertions or deletions (indels).…”

Section: Genome-wide Mutagenesismentioning

confidence: 99%

Forward and reverse mutagenesis in C. elegans

Kutscher

Shaham

2014

WormBook

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Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal.

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Section: Genome-wide Mutagenesismentioning

confidence: 99%

Forward and reverse mutagenesis in C. elegans

Kutscher

Shaham

2014

WormBook

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“…In an accompanying article in this issue, Maydan et al (2009) describe that this method can be extended to identify single nucleotide alterations. We use CGH as a cost-effective alternative method to manual DNA sequencing, whose implementation is made easy through the ability to outsource the microarray synthesis and hybridization to NimbleGen and the use of software described in Maydan et al (2009).…”

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confidence: 99%

“…Using an automated oligonucleotide design program (see accompanying article by Maydan et al 2009), we designed an oligonucleotide array containing 379,690…”

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confidence: 99%

“…This 352-kb region encompasses the 41-kb genomic interval (14,888,929,495) in the fosmid WRM067cF11 that rescues the ot119 and ot201 mutant phenotypes. DNA isolated from ot119 and ot201 and a wild-type reference were differentially labeled and hybridized to the array (as described in more detail in Maydan et al 2009). Given the similar genetic behavior of ot119 and ot201, we focused on variants that are present at roughly the same location in both data sets Figure 2 for explanation of the stippled interval.…”

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confidence: 99%

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Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

et al. 2009

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We apply here comparative genome hybridization as a novel tool to identify the molecular lesion in two Caenorhabditis elegans mutant strains that affect a neuronal cell fate decision. The phenotype of the mutant strains resembles those of the loss-of-function alleles of the cog-1 homeobox gene, an inducer of the fate of the gustatory neuron ASER. We find that both lesions map to the cis-regulatory control region of cog-1 and affect a phylogenetically conserved binding site for the C2H2 zinc-finger transcription factor CHE-1, a previously known regulator of cog-1 expression in ASER. Identification of this CHE-1-binding site as a critical regulator of cog-1 expression in the ASER in vivo represents one of the rare demonstrations of the in vivo relevance of an experimentally determined or predicted transcription-factor-binding site. Aside from the mutationally defined CHE-1-binding site, cog-1 contains a second, functional CHE-1-binding site, which in isolation is sufficient to drive reporter gene expression in the ASER but in an in vivo context is apparently insufficient for promoting appropriate ASER expression. The cis-regulatory control regions of other ASEexpressed genes also contain ASE motifs that can promote ASE neuron expression when isolated from their genomic context, but appear to depend on multiple ASE motifs in their normal genomic context. The multiplicity of cis-regulatory elements may ensure the robustness of gene expression.

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“…One such example is comparative genomic hybridization (CGH), a technique that has been extensively used in human genetics to quantify chromosomal copy number aberrations (Kallioniemi et al 1992). In C. elegans oligonucleotide CGH arrays have been used to detect deletions (Jones et al 2007;Maydan et al 2007) and to identify single-nucleotide alterations that were previously mapped (Maydan et al 2009;O'Meara et al 2009). Although WGS is by far the most efficient method for identifying singlenucleotide alteration, CGH arrays offer a useful alternative for detecting structural variations.…”

Section: Non-wgs-based Approachesmentioning

confidence: 99%

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

2016

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The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans. In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.

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De Novo Identification of Single Nucleotide Mutations in Caenorhabditis elegans Using Array Comparative Genomic Hybridization

Cited by 16 publications

References 16 publications

Forward and reverse mutagenesis in C. elegans

Forward and reverse mutagenesis in C. elegans

Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

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