[
International Worm Meeting,
2007]
The insulin/insulin-like growth factor-I signaling (IIS) pathway regulates larval diapause and adult lifespan in Caenorhabditis elegans. To date, many of the 38 insulin-like genes have been identified1), and a few of the genes have been investigated to identify their physiological function by RNAi knockdown. For instance, Murphy and co-workers reported that
ins-7 RNAi knockdown induces larva diapause and an extended lifespan.2) In our previous study, we disrupted Ceinsulin-1 (
ins-18) and Ceinsulin-2 (
ins-17), and elucidated their function on larval diapause and adult lifespan. Disruption of
ins-17 and/or
ins-18 reduced dauer larva formation caused by a crude extract of dauer-inducing pheromone, while the disruption showed no effect on adult lifespan. To investigate redundant function of the insulin-like genes, we disrupted the
ins-7, and then established multiple-gene-disrupted animals. Disruption of
ins-7 induced an extended lifespan as expected. Disruption of
ins-7 and
ins-17 also revealed lifespan extension, suggesting that
ins-17 is not relevant to lifespan regulation. On the other hand, disruption of
ins-7 and
ins-18 revealed no lifespan extension, indicating that
ins-18 is necessary for lifespan extension induced by the gene-disruption of
ins-7. Now we are measuring lifespan of each gene-disrupted animal under
daf-2(-) conditions. 1) Pierce, S. B. et al. (2001) Genes Dev. 15:672. 2) Murphy, C. T. et al. (2003) Nature 424:277.
[
West Coast Worm Meeting,
2004]
Regulatory motifs are short sequences of DNA that regulate the level, timing, and location of gene expression. Identifying these motifs and their functions is crucial in our understanding of gene regulation and disease processes. We developed CompareProspector, a motif-finding program that takes advantage of cross-species sequence comparison to identify putative regulatory motifs from sets of co-regulated genes [1] . We applied CompareProspector to 30 sets of genes with very similar patterns of expression, identified from the C. elegans topomap [2] and individual DNA microarray experiments. The statistical significance of each candidate motif identified was evaluated using criteria such as motif enrichment-the ratio of prevalence of the motif in a given set of promoters to its prevalence elsewhere in the genome, and the expression coherence of genes with the motif. We identified twelve significant regulatory motifs, three of which have literature evidence confirming they are true regulatory motifs. Overall, these twelve motifs are found in the upstream regulatory regions of 2970 different genes, and may be involved in gene regulation in 24 clusters of co-expressed genes. The first known motif, with the consensus TGATAA, matches the consensus of known binding sites for GATA factors. As GATA factors are known to be involved in worm intestine development [3] and hyperdermis development, it is not surprising that the GATA motif is identified from a set intestine-specific genes (F. Pauli, unpublished), mount08 of the topomap, which is enriched in genes from the intestine, and several collagen-related datasets (mount14, 17, and 35 of the topomap). We correctly identified GATA sites in the promoters of genes known to be regulatory by GATA factors. Interestingly, the GATA motif is also identified from several data sets involved in the aging process. This result parallels that of Murphy and colleagues, who independently identified this motif from their data set of DAF-16 target genes [4] . Both our result and the result from Murphy suggest that GATA factors may be involved in worm aging. Motif 2, which is identified in the two heat shock-related data sets, matches the consensus of known binding sites for heat shock factors [5] . Motif 3 matches the consensus of heat shock associated sites (HSAS), a motif that was first predicted computationally to be involved in the heat shock process [6] and later experimentally validated to be involved in ethanol stress response (14 th International C. elegans Conference abstract 1113C). We are currently in the process of validating the rest of the motifs and their individual binding sites using mutagenesis studies of promoters with predicted motifs. 1. Liu, Y., Liu, X.S., Wei, L., Altman, R.B. and Batzoglou, S. (2004) Eukaryotic regulatory element conservation analysis and identification using comparative genomics . Genome Res. 14 , 451-8. 2. Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J.M., Eizinger, A., Wylie, B.N. and Davidson, G.S. (2001) A gene expression map for Caenorhabditis elegans . Science. 293 , 2087-92. 3. Maduro, M.F. and Rothman, J.H. (2002) Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm . Dev Biol. 246 , 68-85. 4. Murphy, C.T., McCarroll, S.A., Bargmann, C.I., Fraser, A., Kamath, R.S., Ahringer, J., Li, H. and Kenyon, C. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans . Nature. 424 , 277-83. 5. Amin, J., Ananthan, J. and Voellmy, R. (1988) Key features of heat shock regulatory elements . Mol Cell Biol. 8 , 3761-9. 6. GuhaThakurta, D., Palomar, L., Stormo, G.D., Tedesco, P., Johnson, T.E., Walker, D.W., Lithgow, G., Kim, S. and Link, C.D. (2002) Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods . Genome Res. 12 , 701-12 .
[
Worm Breeder's Gazette,
1978]
With lots of help from the Medical Research Council, especially Marilyn Dew, we now have a core collection of C. elegans E stocks, and we (Claire, Kari & I) hereby offer to supply requested strains. At John Sulston s request, I have also agreed to handle two other functions: maintaining the genetic map and administering the genetic clearing house. At present, we have no special support for this work. As many of you know, Don Murphy at NIA is exploring the possibility of supporting a stock center, which could be here or somewhere else. At any rate, I think it makes sense to have the mapkeeping and clearing house operations affiliated with the stock collection, and on the advice of John Sulston and Bob Horvitz, I have defined what, with your support and help I propose to do, for the time being at least: 1. Stockkeeping: Keep and supply requests for at least one mutant per mapped gene or know where in North America the mutants can be obtained. 2. Mapkeeping: (a) Solicit new data (actual counts, complementation results, etc.) on both old and new genes, and update the official map records as such data become available. (b) Submit new data for publication in the Newsletter. These data would include, besides linkage results, interesting properties of new or old genes. 3. Genetic clearing house-keeping: (a) Register new lab symbols, which, in accordance with Bob Horvitz s nomenclature paper, are one or two letters, used as non-ized upper case prefixes for strain names and ized lower case prefixes for mutation names. (b) Register new gene names and list them in the Newsletter. The laboratory assigned to a gene name is then responsible for issuing gene numbers. I hereby solicit data, comments, suggestions, etc. What follows is a list of E stocks available, some new map data, and a few clearing house assignments. Please note: We have taken a cue from the E. coli stock center and have not attempted to confirm the gentoypes of all stocks. We certainly have checked all the more obvious phenotypes, such as for unc and dpy mutants, and we ve been careful in handling heterozygotes, but we have not confirmed some of the other mutants, such as cat, che and flu. If you request any of the latter class, it will be useful if you inform us, say upon acknowledging receipt of the stocks, how they checked out, and we can record that information. In the list that follows, if no mutation name is given for a homozygous single mutant, it can be derived from the strain name, (i.e. , strain E769 has the following genotype:
bli-1(
e769)).