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E-GEOD-21467

ABSTRACT: Gene expression profile of Caenorhabditis elegans RNAi mutants deficient in ung-1

OTHER RELATED OMICS DATASETS IN: PRJNA125817

PROVIDER: E-GEOD-21467 | ExpressionAtlas | 2015-09-15

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-21467-analysis-methods.tsv	Tabular
	E-GEOD-21467-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-21467-configuration.xml	Xml
	E-GEOD-21467-percentile-ranks.tsv	Tabular
	E-GEOD-21467.condensed-sdrf.tsv	Tabular

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Project description:Yilmaz2016 - Genome scale metabolic model - Caenorhabditis elegans (iCEL1273) This model is described in the article: A Caenorhabditis elegans Genome-Scale Metabolic Network Model. Yilmaz LS, Walhout AJ. Cell Syst 2016 May; 2(5): 297-311 Abstract: Caenorhabditis elegans is a powerful model to study metabolism and how it relates to nutrition, gene expression, and life history traits. However, while numerous experimental techniques that enable perturbation of its diet and gene function are available, a high-quality metabolic network model has been lacking. Here, we reconstruct an initial version of the C. elegans metabolic network. This network model contains 1,273 genes, 623 enzymes, and 1,985 metabolic reactions and is referred to as iCEL1273. Using flux balance analysis, we show that iCEL1273 is capable of representing the conversion of bacterial biomass into C. elegans biomass during growth and enables the predictions of gene essentiality and other phenotypes. In addition, we demonstrate that gene expression data can be integrated with the model by comparing metabolic rewiring in dauer animals versus growing larvae. iCEL1273 is available at a dedicated website (wormflux.umassmed.edu) and will enable the unraveling of the mechanisms by which different macro- and micronutrients contribute to the animal's physiology. This model is hosted on BioModels Database and identified by: MODEL1604210000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Project description:Sequencing of Caenorhabditis elegans deletion mutants treated with RNAi

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The DREAM complex functions as conserved master regulator of somatic DNA repair capacities

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Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents.

Project description:The nematode Caenorhabditis elegans has been used extensively to study responses to DNA damage. In contrast, little is known about DNA repair in this organism. C. elegans is unusual in that it encodes few DNA glycosylases and the uracil-DNA glycosylase (UDG) encoded by the ung-1 gene is the only known UDG. C. elegans could therefore become a valuable model organism for studies of the genetic interaction networks involving base excision repair (BER). As a first step towards characterization of BER in C. elegans, we show that the UNG-1 protein is an active uracil-DNA glycosylase. We demonstrate that an ung-1 mutant has reduced ability to repair uracil-containing DNA but that an alternative Ugi-inhibited activity is present in ung-1 nuclear extracts. Finally, we demonstrate that ung-1 mutants show altered levels of apoptotic cell corpses formed in response to DNA damaging agents. Increased apoptosis in the ung-1 mutant in response to ionizing radiation (IR) suggests that UNG-1 contributes to repair of IR-induced DNA base damage in vivo. Following treatment with paraquat however, the apoptotic corpse-formation was reduced. Gene expression profiling suggests that this phenotype is a consequence of compensatory transcriptomic shifts that modulate oxidative stress responses in the mutant and not an effect of reduced DNA damage signaling. C. elegans RNAi mutants deficient in ung-1 and the corresponding wild-type N2, were subjected to Affymetrix whole C. elegans genome microarrays. Triplicates were run for each sample group.

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