Toward Improving <i>Caenorhabditis elegans</i> Phenome Mapping With an ORFeome-Based RNAi Library

Rual, Jean François; Cerón, Julián; Koreth, John; Hao, Tong; Nicot, Anne Sophie; Hirozane-Kishikawa, Tomoko; Vandenhaute, Jean; Orkin, Stuart H.; Hill, David E.; Heuvel, Sander van den; Vidal, Marc

doi:10.1101/gr.2505604

Cited by 886 publications

(768 citation statements)

References 42 publications

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“…For RNAi, plasmids were obtained from OpenBiosystems (Rual et al, 2004), sequence verified and seeded on NGM plates as described previously (Lee et al, 2007). For all analysis of cye-1 and additional cell cycle factors, unless noted otherwise, mid-L4 animals were placed on the RNAi plates for 48 hours, dissected and assessed for spatial premature meiotic entry or cell cycle arrest.…”

Section: Rnai Experimentsmentioning

confidence: 99%

Cyclin E and CDK-2 regulate proliferative cell fate and cell cycle progression in the C. elegans germline

et al. 2011

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SUMMARYThe C. elegans germline provides an excellent model for analyzing the regulation of stem cell activity and the decision to differentiate and undergo meiotic development. The distal end of the adult hermaphrodite germline contains the proliferative zone, which includes a population of mitotically cycling cells and cells in meiotic S phase, followed by entry into meiotic prophase. The proliferative fate is specified by somatic distal tip cell (DTC) niche-germline GLP-1 Notch signaling through repression of the redundant GLD-1 and GLD-2 pathways that promote entry into meiosis. Here, we describe characteristics of the proliferative zone, including cell cycle kinetics and population dynamics, as well as the role of specific cell cycle factors in both cell cycle progression and the decision between the proliferative and meiotic cell fate. Mitotic cell cycle progression occurs rapidly, continuously, with little or no time spent in G1, and with cyclin E (CYE-1) levels and activity high throughout the cell cycle. In addition to driving mitotic cell cycle progression, CYE-1 and CDK-2 also play an important role in proliferative fate specification. Genetic analysis indicates that CYE-1/CDK-2 promotes the proliferative fate downstream or in parallel to the GLD-1 and GLD-2 pathways, and is important under conditions of reduced GLP-1 signaling, possibly corresponding to mitotically cycling proliferative zone cells that are displaced from the DTC niche. Furthermore, we find that GLP-1 signaling regulates a third pathway, in addition to the GLD-1 and GLD-2 pathways and also independent of CYE-1/CDK-2, to promote the proliferative fate/inhibit meiotic entry.

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Section: Rnai Experimentsmentioning

confidence: 99%

Cyclin E and CDK-2 regulate proliferative cell fate and cell cycle progression in the C. elegans germline

et al. 2011

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“…Complete listing of all KEGG mappings including graphical representation is available at http:// www.nematode.net (Wylie et al, 2004). RNA interference (RNAi) technology was first developed and has been successfully applied to genome-wide gene silencing to reveal gene functions in C. elegans (Fire et al, 1998;Kamath et al, 2003;Rual et al, 2004;Sonnichsen et al, 2005). Caenorhabditis elegans RNAi phenotypes can be further extrapolated in understanding functions of orthologous genes in other nematodes, especially the parasitic nematodes in which complexity of obligate parasitic life cycles and lack of proper laboratory culture system makes high-throughput screening impractical .…”

Section: Functional Categorization and Other Sequence Analysismentioning

confidence: 99%

Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis

Yin

Martin

McCarter

et al. 2006

International Journal for Parasitology

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The heartworm Dirofilaria immitis is a filarial parasitic nematode infecting dogs and other mammals worldwide causing fatal complications. Here, we present the first large-scale survey of the adult heartworm transcriptome by generation and analysis of 4005 expressed sequence tags, identifying about 1800 genes and expanding the available sequence information for the parasite significantly. Brugia malayi genomic data offered the most valuable information to interpret heartworm genes, with about 70% of D. immitis genes showing significant similarities to the assembly. Comparative genomic analyses revealed both genes common to metazoans or nematodes and genes specific to filarial parasites that may relate to parasitism. Characterization of abundant transcripts suggested important roles for genes involved in energy generation and antioxidant defense in adults. In particular, we proposed that adult heartworm likely adopted an anaerobic electron transfer-based energy generation system distinct from the aerobic pathway utilized by its mammalian host, making it a promising target in developing next generation macrofilaricides and other treatments. Our survey provided novel insights into the D. immitis transcriptome and laid a foundation for further comparative studies on biology, parasitism and evolution within the phylum Nematoda. q

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“…To know whether down-regulation of these proteins has a critical effect on larval development of C. elegans, we observed the RNAi phenotypes of these genes for two generations in CN condition. RNAi phenotypes of sams-1 (Gottschalk et al, 2005), pmt-2 (Sönnichsen et al, 2005), R07H5.8 (Sönnichsen et al, 2005), eef-1A.1 (Simmer et al, 2003), and rla-0 (Rual et al, 2004) were previously reported that they showed larval developmental defects. Unlike those previous reports, we found that RNAi of two out of six CS down-regulated genes, F25H2.10 (rla-0) and R07H5.8, caused severe larval arrest phenotype in the second generation in CN.…”

Section: Discussionmentioning

confidence: 90%

Cholesterol-Responsive Metabolic Proteins Are Required for Larval Development in Caenorhabditis elegans

Kawasaki

Jeong

Yun

et al. 2013

Molecules and Cells

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Caenorhabditis elegans, a cholesterol auxotroph, showed defects in larval development upon cholesterol starvation (CS) in a previous study. To identify cholesterol-responsive proteins likely responsible for the larval arrest upon CS, a comparative proteomic analysis was performed between C. elegans grown in normal medium supplemented with cholesterol (CN) and those grown in medium not supplemented with cholesterol (cholesterol starvation, CS). Our analysis revealed significant change (more than 2.2-fold, p < 0.05) in nine proteins upon CS. Six proteins were down-regulated [CE01270 (EEF-1A.1), CE08852 (SAMS-1), CE11068 (PMT-2), CE09015 (ACDH-1), CE12564 (R07H5.8), and CE09655 (RLA-0)], and three proteins were up-regulated [CE29645 (LEC-1), CE16576 (LEC-5), and CE01431 (NEX-1)]. RNAi phenotypes of two of the down-regulated genes, R07H5.8 (adenosine kinase) and rla-0 (ribosomal protein), in CN were similar to that of larval arrest in CS, and RNAi of a down-regulated gene, R07H5.8, in CS further enhanced the effects of CS, suggesting that downregulation of these genes is likely responsible for the larval arrest in CS. All three up-regulated genes contain putative DAF-16 binding sites and mRNA levels of these three genes were all decreased in daf-16 mutants in CN, suggesting that DAF-16 activates expression of these genes.

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Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library

Cited by 886 publications

References 42 publications

Cyclin E and CDK-2 regulate proliferative cell fate and cell cycle progression in the C. elegans germline

Cyclin E and CDK-2 regulate proliferative cell fate and cell cycle progression in the C. elegans germline

Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis

Cholesterol-Responsive Metabolic Proteins Are Required for Larval Development in Caenorhabditis elegans

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