GeneACeDB-compara

import of WormBase-Compara data for CGC name projection

Analysis of expression of genes regulated by DAF-19

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

C9orf72/ALFA-1 controls TFEB/HLH-30-dependent metabolism through dynamic regulation ofrag GTPases.

The objective of this experiment was to determine changes in gene expression upon loss of alfa-1 in C.elegans under well-fed and starvation conditions. The human C9orf72 has an orthologue in C. elegans based on sequence homology, which is the F18A1.6 gene and also recently named as alfa-1 (ALS/FTD-associated gene homolog 1). We analyzed the domain structure of ALFA-1 and found that it shares the same DENN domains as human C9orf72, including the uDENN, cDENN, and dDENN domains. We obtained a mutant strain of the alfa-1 gene, which has a mutant allele (ok3062) of 486 bp deletion and 24 bp insertion in the region of exon 3 and exon 4. To understand the changes in gene expression in the alfa-1 mutant C. elegans, we performed the microarray gene expression profiling experiments under the defined conditions.

Ethanol-response genes and their regulation

The nematode shows responses to acute ethanol exposure that are similar to those observed in humans, mice, and Drosophila, namely hyperactivity followed by uncoordination and sedation. We used in this report the nematode Caenorhabditis elegans as a model system to identify and characterize the genes that are affected by ethanol exposure and to link those genes functionally into an ethanol-induced gene network. By analyzing the expression profiles of all C. elegans ORFs using microarrays, we identified 230 genes affected by ethanol. While the ethanol response of some of the identified genes was significant at early time points, that of the majority was at late time points, indicating that the genes in the latter case might represent the physiological consequence of the ethanol exposure. We further characterized the early response genes that may represent those involved directly in the ethanol response. These genes included many heat shock protein genes, indicating that high concentration of ethanol acts as a strong stress to the animal. Interestingly, we identified two non-heat-shock protein genes that were specifically responsive to ethanol. glr-2 was the only glutamate receptor gene to be induced by ethanol. T28C12.4, which encodes a protein with limited homology to human neuroligin, was also specific to ethanol stress. Finally, by analyzing the promoter regions of the early response genes, we identified a regulatory element, TCTGCGTCTCT, that was necessary for the expression of subsets of ethanol response genes. Groups of assays that are related as part of a time series. Keywords: time_series_design

Inferred_from_orthology

Orthologous gene name inferred from approved gene name in other species. Names are assigned using WormBase gene nomenclature guidelines.

Low-intensity microwave irradiation does not substantially alter gene expression in late larval and adult C. elegans

Reports that low-intensity microwave radiation can induce heat-shock reporter gene expression in the nematode, Caenorhabditis elegans, have recently been reinterpreted as a subtle thermal effect caused by very slight heating. This study used a microwave exposure system (1.0 GHz, 0.5 W power input; SAR 0.9-3 mW kg-1 for 6-well plates) that minimises the temperature differential between sham and exposed conditions to 0.1C. Comparable measurement and simulation studies of SAR distribution within this exposure system are presented. We compared 5 Affymetrix gene-arrays of pooled triplicate RNA populations from sham-exposed L4/adult worms against 5 gene-arrays of pooled RNA from microwave-exposed worms (taken from the same source population in each run). Few genes showed consistent expression changes across all 5 comparisons, and all such expression changes appeared modest after applying standard normalisation procedures ( 30% up- or down-regulated). The number of statistically significant differences in gene expression (846) was less than the false-positive rate expected by chance (1131). As one example, an apparent up-regulation of the vit-3 vitellogenin gene by microwave exposure was not mirrored by similar changes affecting the other co-regulated members of the same vit gene family. We conclude that the pattern of gene expression in L4/adult C elegans is not substantially perturbed by low-intensity microwave radiation, and that the minor changes observed in this study may well be explicable as false positives. As a check on the sensitivity of the Affymetrix gene-arrays used, we also compared RNA samples from N2 worms subjected to a sub-heat-shock treatment (28C) against controls kept at 26 C (but using only 2 gene arrays per condition). After similar normalisation, many more genes (3712) showed substantial expression changes (i.e. > 2-fold at p < 0.05), including a group of six heat-shock genes which were strongly but unexpectedly down-regulated (by > 10-fold). However, further replication and confirmation by real-time RT-PCR would be needed to establish how many of these changes might also be false positives. Experimenter name: Adam Dawe Experimenter phone: +27 21 959 2364 adam@sanbi.ac.za Experimenter institute: South African National Bioinformatics Institute Experimenter address: University of Western Cape, Old Chemistry Building, University of Western Cape, Modderdam Road, Bellville 7530, Capetown Experimenter zip/postal_code: 7530 Experimenter country: South Africa Keywords: Microwave radiation, gene expression, gene arrays, Caenorhabditis elegans