C. elegans Breakout Group



This workshop benefited from several responses received prior to the meeting from members of the C. elegans research community who were provided with the workshop breakout questions.

1. Resource needs for C. elegans

An attempt has been made to prioritize these items, but they are all considered to be high priority.

a. Completion of the remaining genomic sequence.

Genomic studies are best done with a complete genomic sequence.

Cost: currently funded

b. A complete, unigene set of full-length sequenced cDNAs.

The cDNAs will be useful for confirming the expression of predicted genes and patterns of alternative pre-mRNA splicing. They will also be used in microarrays for monitoring genome-wide patterns of transcription, for systematic RNA-mediated interference (RNAi) experiments aimed at transient inactivation of specific gene expression, for two-hybrid libraries, and for in vitro synthesis of protein products to be used in biochemical experiments. Both cDNAs and primer pairs for each cDNA should be available for distribution.

Cost: $3-8 Million

Time: 3 years

c. Central resource for generating gene knockouts (KOs).

We strongly endorse the current pilot project for generating gene knockouts. Top priority should be given to requests from academic researchers for specific KOs, but ultimately KOs of every gene are desired. We also encourage efforts to improve the technology, including the adoption of systematic procedures for outcrossing and homozygosing (or balancing) each KO. A method for targeted gene disruption by homologous recombination would be highly desirable.

Cost: $10-40 Million

Time: depends on technology development

d. Make microarray technology available to community.

We need a central resource to generate whole genome chips and distribute them to the community at an affordable price. The resource might also provide software to analyze data and generate a publicly-accessible gene expression database.

Cost: $1.2 Million

Time: 3 years for initial phase

e. Complete genomic sequence of C. briggsae and possibly another nematode.

Comparisons of C. elegans and C. briggsae, which diverged from each other at least 20 million years ago, have proved to be good predictors of gene structure and functionally important regions, especially regions that regulate transcription. By identifying conserved transcriptional regulatory regions, it may be possible to assemble regulatory cascades simply by searching whole genome sequence for common (and conserved) transcription factor binding sites. There may also be much to learn from sequencing another, more distantly related, nematode, perhaps a parasite.

Cost: $25 Million for C. briggsae

Time: 5 years?

f. Expanded stock center and creation of a vector resource.

A significant increase in genetic stocks will require increased resources for the C. elegans stock center (the Caenorhabditis Genetics Center, or CGC). We also recommend the creation of a center for distribution of commonly-used vectors.

Cost: $0.3 Million per year

Time: As long as needed

g. High density map of DNA dimorphisms for physically mapping genes defined by mutation.

Relating gene to function will continue to involve analyzing mutant phenotypes, characterizing genes, gene products and interactions among genes and gene products. Genetic mapping strains with sequenced polymorphisms every few kb would greatly aid continuing efforts to identify the DNA sequence of genes defined solely by mutant phenotypes. Technology to facilitate displaying large numbers of polymorphisms, possibly using microarrays, is also needed.

Cost: $1 Million, depending on technology development

Time: 3 years

h. Creation of transgenic lines carrying GFP fusions to every gene.

A central resource is needed to generate GFP fusions, create stable transgenic lines carrying these fusions, and analyze the expression patterns as close to cell resolution as possible. These patterns should be catalogued in a publicly-accessible database.

Cost: $10 Million

Time: 5 years

i. Methods and technology improvements

We recommend support for investigator-initiated research projects aimed at improving or creating technologies of use to the community. These would include more efficient transformation, more efficient gene KOs, methods for targeted gene replacement, better regulation of transgenic gene expression, ability to do cell culture, better electrophysiology, and better methods for systematic phenotypic characterization, including automated methods for following cell lineage.

It should perhaps be more widely advertised that NIH enthusiastically funds technology development and that study sections can be very receptive to applications that concentrate on technology development if the proposed technology is shown to have a benefit, if the relevant expertise, both biological and technical, is apparent (collaborations may be useful), and if the proposal is well designed. Two other suggestions for enhancing technology development through standard grants would be, first, to make clear to study sections that significant progress in technology development may not result in prominent publications, and second, to restore the five-year funding period.

Cost: R01 and RFAs

2. Databases

a. The specialized C. elegans genomic database is ACeDB. The C. elegans WWW Server (:http//elegans.swmed.edu) provides a single point of access to all information available about C. elegans on the internet.

b. The current databases are largely meeting the needs of the community, but improvements could and should be made. The best versions of ACeDB must be downloaded to UNIX-based computers. The desirability of developing a rapid Web-based ACeDB is widely recognized and is under development; Web links from the Web-based ACeDB to other genetic databases would be desirable. Some feel that ACeDB should be made more user friendly. A user's manual would be welcome. Another problem is the weak state of literature annotation; for example, very little information is provided about patterns of gene expression or gene function. Better resources detailing C. elegans anatomy, both at the light microscopic and ultrastructural levels, are needed. It should be emphasized that by contrast to yeast and fly genomic databases, which are richly funded, the C. elegans genomic database is almost completely unfunded, except as part of the genomic sequencing project (and a tiny contribution from the CGC for curating genetic map data).

Cost per year: $1 Million

3. Facilitation of research

a. A more user-friendly, Web-based ACeDB (see above) would help, as would Web links from Genbank and EST databases to a central ACeDB server. The gene KO center (see 1.c., above) would be useful to novice worm workers, who might also be advised to collaborate with an experienced worm lab. In addition, we recommend funding for intensive short courses and for mini-sabbaticals for non-worm scientists to work in C. elegans labs.

b. Greater similarity in formats for different genomic databases might promote interactions between model organism communities, as might more user-friendly interfaces between different organism databases. Generally, it is felt that interactions between model organism communities is good and that advances in each field are quickly disseminated by journals, seminars and meetings.

4. Consideration of other model organisms

There was wide agreement that a broader span of animal (and perhaps plant) phylogeny should be represented in molecular genetic studies. It was also suggested that work on two or more model organisms in the same phylum may be important in elucidating the evolution of developmental systems. Electrophysiologists tend to favor organisms other than the five models represented at this meeting.

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