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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of C. elegans daf-19(+) and daf-19(-) mutants

ABSTRACT: By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of daf-19(+) and daf-19(-) animals. Experiment Overall Design: There 4 samples.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: BCGSC BC Cancer Agency

PROVIDER: E-GEOD-6563 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics.

Chen Nansheng N Mah Allan A Blacque Oliver E OE Chu Jeffrey J Phgora Kiran K Bakhoum Mathieu W MW Newbury C Rebecca Hunt CR Khattra Jaswinder J Chan Susanna S Go Anne A Efimenko Evgeni E Johnsen Robert R Phirke Prasad P Swoboda Peter P Marra Marco M Moerman Donald G DG Leroux Michel R MR Baillie David L DL Stein Lincoln D LD

Genome biology 20060101 12

<h4>Background</h4>The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes.<h4>Results</h4>By screening for genes possessing canonical X-box sequences in promoters of three C ...[more]

PMID: 17187676

Similar Datasets

Analysis of expression of genes regulated by DAF-19

Project description:By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of daf-19(+) and daf-19(-) animals. Keywords: Microarry analysis; DAF-19; X-box motif; C. elegans; transcription; comparative genomics

2006-12-21 | GSE6563 | GEO

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

Project description:Cilia are ubiquitous cell surface projections that modulate various sensory- and motility based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. As new components required for cilium biogenesis and function remain unidentified, we sought to further define and validate the transcriptional targets of the ciliogenic C. elegans RFX transcription factor DAF-19. To this end, transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using selectively staged embryos where ciliogenesis occurs in most ciliated sensory neurons (CSNs). Statistical comparisons between the two populations revealed 881 differentially regulated genes with 1.5-fold change or greater. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional-GFP fusions revealed CSN-specific expression patterns for 9 of 12 candidate genes. We show that two uncharacterized candidate genes, which we term dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and interestingly, is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK-7/CCRK-related serine-threonine kinase that is necessary for the proper function of intraflagellar transport (IFT), a process critical for cilium biogenesis. Together, our comparative microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover—in addition to DYF-17 and DYF-18—cellular components important for cilium formation and function. 4 daf-19,daf12; 4 daf-12; 4 WT

2011-07-25 | E-GEOD-25633 | biostudies-arrayexpress

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

2011-07-26 | GSE25633 | GEO

The RFX transcription factor gene, daf-19, has dual funcitons in ciliated and non-ciliated neurons

Project description:Cilia are required for many sensory and motility related functions and are involved in growing number of genetic disorders termed ciliopathies. DAF-19, RFX type transcription factor controls expression of many cilia structure and function related genes. To this end, transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using selectively staged larval stages where cilia mature and maintained, structurally as well as functionally.

2018-01-31 | GSE96068 | GEO

Adult C. elegans: Control daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

Project description:Transcriptional profiling of adult C. elegans comparing daf-16(-); daf-2(-) animals with adult daf-2(-) animals.

2010-01-01 | GSE18561 | GEO

Caenorhabditis elegans

Project description:The RFX transcription factor gene, daf-19, has dual funcitons in ciliated and non-ciliated neurons

| PRJNA378754 | ENA

Expression analysis of C. elegans wild-type N2 and rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutants

2013-11-14 | GSE52340 | GEO

Expression analysis of C. elegans genes daf-9 and daf-12 mutant

Project description:Investigation of whole genome gene expression level changes in C. elegans genes daf-9 and daf-12 mutant,compared to the wild-type strain NimbleScan softwareM-bM-^@M-^Ys implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249). A nine chip study using total RNA recovered from three separate wild-type cultures of C.elegans and three separate cultures of daf-9 mutantM-oM-<M-^Lthree separate cultures of daf-12 mutant.The C. elegans 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 13,187 genes are collected from the authoritative data source including Wormbase.

2012-10-18 | E-GEOD-41661 | biostudies-arrayexpress

Expression analysis of C. elegans genes daf-9 and daf-12 mutant

2012-10-18 | GSE41661 | GEO

Expression analysis of C. elegans wild-type N2 and rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutants

Project description:Investigation of whole genome gene expression level changes in C. elegans rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutant compared to the wild-type N2 strain. The mutants have altered longevity phenotypes. The mutants analyzed in this study are further described in Di Chen, Patrick Wai-Lun Li, Benjamin A. Goldstein, Waijiao Cai, Emma Lynn Thomas, Fen Chen, Alan E. Hubbard, Simon Melov and Pankaj Kapahi, Germline Signaling Mediates the Synergistically Prolonged Longevity by Double Mutations in daf-2 and rsks-1 in C. elegans, Cell Reports (CELL-REPORTS-D-13-00388). A 47 chip study using total RNAs from C. elegans wild-type N2 (9 replicates), rsks-1 mutant (9 replicates), daf-2 mutant (9 replicates), daf-2 rsks-1 double mutant (10 replicates) and daf-16; daf-2 rsks-1 triple mutant (10 replicates) measured gene expression levels at the whole genome level.

2013-11-14 | E-GEOD-52340 | biostudies-arrayexpress

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