C. elegans Report from Workshop for Genomic Resources for

Geraldine Seydoux gseydoux at bs.jhmi.edu
Mon Mar 8 15:58:19 EST 1999


C. elegans Report from Workshop for Genomic Resources for Non-Mammalian Models
The following report was drafted by a small group of worm breeders during a
recent Workshop for Genomic Resources for Non-Mammalian Models held at the
NIH. We would like this report to serve as a starting point for a larger
discussion among the community. In particular, some have suggested that it
might be a good idea to set up a C. elegans advisory board for genomic
resources, similar to what has been done in the fly field. Anyone
interested in this or any other "genomic" issues is invited to attend a
Genomic Resources workshop which will be held at this year's worm meeting.
Signed: Avery, Chalfie, Kim, Mello, Plasterk, Ruvkun, Strome, Seydoux and
Herman
Report from C. elegans Breakout Session
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.



Please note my new email address: gseydoux at jhmi.edu
Geraldine Seydoux
Dept. of Molecular Biology and Genetics
Johns Hopkins University School of Medicine
725 N. Wolfe Street / 515 PCTB
Baltimore MD 21205-2185
Office tel: 410-614-4622
Lab Phone: 410-614-4623
Fax: 410-502-6718





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