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causes a Protruding-vulva (Pvl) phenotype, we first compiled a list of 539 genes
whose reduction in activity was reported to result in the Pvl phenotype from a
number of whole-genome RNAi screens (
Kamath et al., 2003; Rual et al., 2004;
Simmer et al., 2003
). We then performed a focused RNAi screen on these genes by
examining anchor cell invasion using differential interference contrast (DIC) optics.
Through these efforts, we identified 99 genes that are required for anchor cell
invasion. Most of these genes have not been previously implicated in cell invasion,
potentially expanding new targets for cancer therapeutics.
2. Gene Expression Profiling Approach
Examination of gene expression at a genome-wide scale within the whole organ-
ism, specific tissues, and even single cells has proven to be a valuable approach in
identifying pathway components and characterizing gene function (
Grant and
Wilkinson, 2003
). Genes responsible for the same biological process tend to be
regulated in a similar manner. By profiling gene expression changes associated with
a biological process, it is possible to identify a common set of genes whose expres-
sion dynamics and spatiotemporal localization share the same pattern under differ-
ent conditions and in various mutant backgrounds.
A way to measure expression levels of genes is to quantify transcripts of corre-
sponding genes, which can now be readily achieved through a variety of high-
throughput technologies at a genome-wide level, including hybridization-based
approaches and sequence-based approaches (
Wang et al., 2009
). A typical example
of hybridization-based approaches is a DNA microarray assay that profiles expres-
sion of individual genes at a genomic scale through hybridization of oligonucleotide
DNA probes with fluorescently labeled cDNAs of nearly every gene. Unlike hybrid-
ization techniques, sequence-based approaches obtain quantitative gene expression
data by sequencing gene transcripts. For example, SAGE, a sequencing-based
method, quantifies gene expression by counting the number of times a particular
transcript is found in a pool of short diagnostic sequence tags isolated from an
mRNA sample (
Velculescu et al., 1995
). Recently, with advances in deep sequencing
technologies, RNA-Seq, a new high-throughput and more precise sequencing-based
method, allows quantification of all transcripts by directly sequencing fragmented
cDNA (30-400 bp) converted from a population of RNA (
Wang et al., 2009
). In
addition to acquiring information about levels of gene expression, a project aimed to
profile spatiotemporal patterns of gene expression at a large scale (localizome) has
been initiated (
Dupuy et al., 2007
). In this project, worms have been engineered to
express transgenes in which the open reading frame of GFP was placed downstream
of the proximal promoters of 1610 predicted genes. The expression of GFP from
these promoters has been characterized using a worm sorter that profiles tissue
expression at various developmental stages in a high-throughput fashion. The rele-
vant expression data can be found at the web site
http://localizome.dfci.harvard.edu/
.
The ultimate goal of this project is the characterization of all of the
20,000 genes in
the C. elegans genome.
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