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Schwarz, Erich M.; Antoshechkin, Igor; Bastiani, Carol; Bieri, Tamberlyn; Blasiar, Darin; Canaran, Payan; Chan, Juancarlos; Chen, Nansheng; Chen, Wen J.; Davis, Paul A.; Fiedler, Tristan J.; Girard, Lisa-Christine; Harris, Todd W.; Kenny, Eimear E.; Kishore, Ranjana; Lawson, Daniel; Lee, Raymond; Müller, Hans‐Michael; Nakamura, Cecilia; Ozersky, Phil; Petcherski, Andrei; Rogers, Anthony; Will, Stefan; Tuli, Mary Ann; Auken, Kimberly Van; Daniel, Wang; Durbin, Richard; Strouboulis, John; Stein, Lincoln; Sternberg, Paul W.

doi:10.1093/nar/gkj061

Cited by 74 publications

(63 citation statements)

References 31 publications

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“…K09H11.3 and Y75B7AL.4 were named RGA-3 and RGA-4 for RhoGAP-3 and RhoGAP-4, respectively. RGA-1 and RGA-2 are RhoGAPs expressed in epithelial cells and are the worm orthologues of mammalian RhoGAP1 (ARHGAP1) and ARHGAP20, respectively (Jenna et al, 2005;Schwarz et al, 2006). RGA-3 and RGA-4 belong to a subfamily of RhoGAPs with their GAP domain located at the N-terminus.…”

Section: Resultsmentioning

confidence: 99%

Functions of the novel RhoGAP proteins RGA-3 and RGA-4 in the germ line and in the early embryo ofC. elegans

2007

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We have identified two redundant GTPase activating proteins (GAPs) -RGA-3 and RGA-4 -that regulate Rho GTPase function at the plasma membrane in early Caenorhabditis elegans embryos. Knockdown of both RhoGAPs resulted in extensive membrane ruffling, furrowing and pronounced pseudo-cleavages. In addition, the non-muscle myosin NMY-2 and RHO-1 accumulated on the cortex at sites of ruffling. RGA-3 and RGA-4 are GAPs for RHO-1, but most probably not for CDC-42, because only RHO-1 was epistatic to the two GAPs, and the GAPs had no obvious influence on CDC-42 function. Furthermore, knockdown of either the RHO-1 effector, LET-502, or the exchange factor for RHO-1, ECT-2, alleviated the membrane-ruffling phenotype caused by simultaneous knockdown of both RGA-3 and RGA-4 [rga-3/4 (RNAi)]. GFP::PAR-6 and GFP::PAR-2 were localized at the anterior and posterior part of the early C. elegans embryo, respectively showing that rga-3/4 (RNAi) did not interfere with polarity establishment. Most importantly, upon simultaneous knockdown of RGA-3, RGA-4 and the third RhoGAP present in the early embryo, CYK-4, NMY-2 spread over the entire cortex and GFP::PAR-2 localization at the posterior cortex was greatly diminished. These results indicate that the functions of CYK-4 are temporally and spatially distinct from RGA-3 and RGA-4 (RGA-3/4). RGA-3/4 and CYK-4 also play different roles in controlling LET-502 activation in the germ line, because rga-3/4 (RNAi), but not cyk-4 (RNAi), aggravated the let-502(sb106) phenotype. We propose that RGA-3/4 and CYK-4 control with which effector molecules RHO-1 interacts at particular sites at the cortex in the zygote and in the germ line.

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Section: Resultsmentioning

confidence: 99%

Functions of the novel RhoGAP proteins RGA-3 and RGA-4 in the germ line and in the early embryo ofC. elegans

2007

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“…A BLASTx-search revealed the top-hit C. elegans sequence for a unigene (using E value cut-oV of 1e-05). Subsequently, the RNAi phenotype and GO terms (only of the C. elegans top-hits with observed RNAi phenotypes) were retrieved via WormMart (Schwarz et al 2006) and the GO terms analyzed and visualized with WEGO (Ye et al 2006).…”

Section: Trans-spliced Leader Searchmentioning

confidence: 99%

Exploring the transcriptome of the burrowing nematode Radopholus similis

et al. 2008

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Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more eYcient control measures. For the Wrst high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reXects the nematode population biology. Genes with a role in the parasitism process are identiWed, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three diVerent sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the Wrst molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.Keywords Expressed sequence tag analysis · Trans-spliced leader · Parasitism · G + C content · Wolbachia · Endoparasitic migratory nematode

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“…shtml). The C. elegans miRNA genes, their genomic location and deletion allele information can de accessed directly from WormBase (http://www.wormbase.org) [107].…”

Section: Accession Numbersmentioning

confidence: 99%

Most Caenorhabditis elegans microRNAs are individually not essential for development or viability

et al. 2005

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MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to posttranscriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs or among gene pathways regulated by miRNAs. This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs.

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WormBase: better software, richer content

Cited by 74 publications

References 31 publications

Functions of the novel RhoGAP proteins RGA-3 and RGA-4 in the germ line and in the early embryo ofC. elegans

Functions of the novel RhoGAP proteins RGA-3 and RGA-4 in the germ line and in the early embryo ofC. elegans

Exploring the transcriptome of the burrowing nematode Radopholus similis

Most Caenorhabditis elegans microRNAs are individually not essential for development or viability

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