WormBase: a multi-species resource for nematode biology and genomics

Harris, Todd W.; Chen, Nansheng; Cunningham, Fiona; Tello-Ruiz, Marcela K.; Antoshechkin, Igor; Bastiani, Carol; Bieri, Tamberlyn; Blasiar, Darin; Bradnam, Keith; Chan, Juancarlos; Chen, Chao-Kung; Chen, Wen J.; Davis, Paul A.; Kenny, Eimear E.; Kishore, Ranjana; Lawson, Daniel; Lee, Raymond Y. N.; Müller, Hans‐Michael; Nakamura, Cecilia; Ozersky, Philip; Petcherski, Andrei; Rogers, Anthony; Sabo, Aniko; Schwarz, Erich M.; Auken, Kimberly Van; Wang, Qinghua; Durbin, Richard; Strouboulis, John; Sternberg, Paul W.; Stein, Lincoln

doi:10.1093/nar/gkh066

Cited by 611 publications

(171 citation statements)

References 18 publications

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“…The spe-38(eb44) mutation was isolated from an ethyl methanesulfonate (EMS) mutagenesis conducted by Mako Saito and Tim Schedl (M. Saito and T. Schedl, personal communication). Descriptions of all other strains can be found in WormBase (Harris et al, 2004). Many strains were constructed in a him-5(e1490) genetic background, which increases the frequency of males without causing adverse effects on sperm (Nelson and Ward, 1980).…”

Section: Methodsmentioning

confidence: 99%

TheCaenorhabditis elegans spe-38gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization

et al. 2005

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A mutation in the Caenorhabditis elegans spe-38 gene results in a sperm-specific fertility defect. spe-38 sperm are indistinguishable from wild-type sperm with regards to their morphology, motility and migratory behavior. spe-38 sperm make close contact with oocytes but fail to fertilize them. spe-38 sperm can also stimulate ovulation and engage in sperm competition. The spe-38 gene is predicted to encode a novel four-pass (tetraspan) integral membrane protein. Structurally similar tetraspan molecules have been implicated in processes such as gamete adhesion/fusion in mammals, membrane adhesion/fusion during yeast mating, and the formation/function of tight-junctions in metazoa. In antibody localization experiments, SPE-38 was found to concentrate on the pseudopod of mature sperm, consistent with it playing a direct role in gamete interactions.

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Section: Methodsmentioning

confidence: 99%

TheCaenorhabditis elegans spe-38gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization

et al. 2005

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“…DNAStar 5.05 sequence analysis software (DNAStar, Madison, WI) was used to assemble continuous cDNA sequences. Gene-specific primers for 3Ј-and 5Ј-RACE were designed according to the predicted mRNA sequence of numr-1 and numr-2 published in WormBase, version WS201 (Harris et al, 2004) and are presented in supplementary material Table S1.…”

Section: Rapid Amplification Of Cdna Endsmentioning

confidence: 99%

Molecular characterization ofnumr-1andnumr-2: genes that increase both resistance to metal-induced stress and lifespan inCaenorhabditis elegans

Tvermoes

Boyd

Freedman

2010

Journal of Cell Science

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SummaryTo define the mechanisms involved in the molecular response to the carcinogenic metal cadmium, two novel metal-inducible genes from C. elegans were characterized: numr-1 and numr-2 (nuclear localized metal responsive). numr-1 and numr-2 sequences and cellular patterns of expression are identical, indicating that these are functionally equivalent genes. Constitutive transcription of numr-1 and numr-2 is developmentally regulated and occurs in the intestine, in head and tail neurons, and vulva muscles. Exposure to metals induces numr-1 and numr-2 transcription in pharyngeal and intestinal cells. Other environmental stressors do not affect transcription, indicating that these are metal-specific, stress-responsive genes. NUMR-1 and NUMR-2 target to nuclei and colocalize with HSF-1, suggesting that they may be components of nuclear stress granules. Nematodes overexpressing NUMR-1 and NUMR-2 are resistant to stress and live longer than control animals; likewise reducing expression increases sensitivity to metals and decreases neuromuscular functions. Upstream regulatory regions of both genes contain potential binding sites for DAF-16 and SKN-1, which are components of the insulin-IGF-like signaling pathway. This pathway regulates longevity and stress responses in C. elegans. NUMR-1 and NUMR-2 may function to promote resistance to environmental stressors and longevity, which is mediated by the insulin-IGF-like signaling pathway.Key words: C. elegans, Cadmium, Stress response, Lifespan, LongevityJournal of Cell Science increase in the steady-state mRNA level following a 24-hour cadmium exposure (Cui et al., 2007). A second C. elegans gene, originally designated F08F8.1, was subsequently identified based on sequence identity. These genes are now designated numr-1 and numr-2 (nuclear localized metal responsive), respectively.In the present report, the genomic organization, in vivo cellular patterns of expression, effects of transition metals and other stressors on transcription, and phenotypes associated with increased and decreased expression of numr-1 and numr-2 are presented. Phenotypes associated with these genes include changes in neuromuscular activities, as well as increased resistance to metal toxicity and increased lifespan. Results Sequence analysis of numr-1 and numr-2numr-1 and numr-2 were located less than 1 kb apart in a divergent orientation on chromosome III (Fig. 1). numr-1 mRNA was predicted to be encoded by a single exon. By contrast, numr-2 mRNA was predicted to be encoded by five exons, the first of which was ~99% identical to the numr-1 exon. Sequences of the full-length mRNAs and the exon arrangement for numr-1 and numr-2 were determined using 3Ј-and 5Ј-RACE. The sequence of the 3Ј-end of numr-1 was consistent with that reported in WormBase (version WS201). Using 3Ј RACE, however, cDNAs from predicted exons 2-5 of numr-2 were not isolated. This suggested that numr-2 was annotated incorrectly and that it also was a single exon gene. Sequences for the 5Ј-ends of numr-1 and numr-2 were 100% iden...

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“…The degree of deviation can be statistically quantified by the bootstrap method. Users may choose alternative classification scheme defined using the evidence codes of Gene Ontology Annotation (GOA) 37,38) instead of the five gene groups defined above.…”

Section: Gene Prediction Accuracy Classificationmentioning

confidence: 99%

G-language System as a platform for large-scale analysis of high-throughput omics data

Arakawa

Tomita

2006

J. Pestic. Sci.

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The advent of high-throughput measurement technologies has resulted in the rapid accumulation of "omics" information including genome, transcriptome, proteome, and metabolome data. This increase in data acquisition has lead to a demand for an efficient computational platform for in silico analysis. The G-language software suite provides a comprehensive workbench for large-scale omics research and systems biology. The suite includes a bioinformatics research framework G-language Genome Analysis Environment, which contains a Gene Prediction Accuracy Classification benchmarking tool for the quantification of the sensitivity of genome informatics analysis methods to genome annotation completeness. Omics data processed in this environment can be visualized with KEGG-based pathway mapping web service, and Genome-based Modeling System enables automatic prototyping of metabolic pathway models from the genome. The software suite covers various domains of omics, with the goal of integrating all of these data for research into systems biology.

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WormBase: a multi-species resource for nematode biology and genomics

Cited by 611 publications

References 18 publications

TheCaenorhabditis elegans spe-38gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization

TheCaenorhabditis elegans spe-38gene encodes a novel four-pass integral membrane protein required for sperm function at fertilization

Molecular characterization ofnumr-1andnumr-2: genes that increase both resistance to metal-induced stress and lifespan inCaenorhabditis elegans

G-language System as a platform for large-scale analysis of high-throughput omics data

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