C' elegans

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C. elegans
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Caenorhabditis elegans Nematode (roundworm)
Tiny, eats E. coli, grows on petri plates,
freezable
Great genetics Hermaphroditic Short life cycle
(3.5 days at 20 C) Large brood size (300-1000
progeny) RNAi pioneered in the worm (most genes
have been tested)
Simple anatomy Nearly invariant lineage
pattern of development Adult has 959 cells, 302
of which are neurons 131 other cells normally
undergo apoptosis Transparent (can watch
development happen)
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C. elegans genome
97 Megabases in 6 chromosomes Sequencing
complete (no gaps) Most recent annotations
(WS130, 30th July 2004) predict 23, 475
genes 22,249 protein sequences 1/3 of
predicted proteins are nematode-specific Referenc
e genome Caenorhabditis briggsae (100 million
years diverged)
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C. elegans Reverse Genetics
RNA-mediated interference (RNAi) pioneered in C.
elegans, gt18,000 genes have been tested Can
use PCR-based approaches to screen for
deletions, but CANNOT currently do targeted
gene knockouts Transgenics generated
by microinjection of DNAs into adult
germline (generates an extrachromosomal,
multi-copy array) Bombardment with gene
gun (generates low-copy integrants)
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Genome project name C32F10.2 (cosmid.) Three
-letter Gene name lin-35 (xxx-)
What those three-letter gene names stand
for http//biosci.umn.edu/CGC/Nomenclature/genes
.htm
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C. elegans Blast Server (Sanger
Center) http//www.sanger.ac.uk/cgi-bin/blast/sub
mitblast/c_elegans blastp against Wormpep
database
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Two main websites to access C. elegans
information Wormbase (main data repository,
CHECK HERE FIRST) http//www.wormbase.org/ Caen
orhabditis elegans WWW Server (links to
everything! data, literature, researchers,
protocols, newsgroup, announcements) http//elega
ns.swmed.edu/
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C. elegans nomenclature is very rigid and
logical.
Gene names are italicized, no caps let-60 Alway
s 3 letters - Abbreviation for phenotype or
molecular info Alleles are italicized, no caps,
in parentheses let-60(n2021) Each mutant allele
starts with 1-2 letters indicating lab in which
it was isolated Proteins are all capital
letters LET-60 Predicted genes/proteins from
genome project are ZK792.6 each named cosmid.
or yac.
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Duplication (Dp), Deficiency (Df), Translocation
(T) qDp3(III f) free duplication (involving
part of chromosome III, not attached to another
chromosome) mnDp3(IVX) attached
duplication (involving part of chromosome IV,
attached to X chromosome) arDf1 V deficiency
removing part of chromosome V (deficiency
deletion) eT1(IIIV) reciprocal translocation
between chromosome III and chromosome
V Transgenes Extrachromosomal (Ex) or
Insertional (Is) csEx1 extra-chromosomal
transgenic array (mini-chromosome) csIs3 chrom
osomally integrated transgene/array mpk-1GFP fu
sion of mpk-1 and GFP sequences