Biology Reference
In-Depth Information
C. elegans genetic networks provides evidence suggesting
that network structure and topology may be conserved
across organisms
[2]
. Therefore, these hubs may represent
general buffers of phenotypic variation because they are
capable of enhancing the phenotypic consequences associ-
ated with mutations in numerous different genes. This
finding emphasizes the importance of identifying genes
capable of multiple genetic interactions, since, in theory,
genetic network hubs may have the potential to act as
general modifiers of genetic diseases in humans
[65]
.
Furthermore, comparative analysis of functional
networks derived from S. cerevisiae, S. pombe, C. elegans
and D. melanogaster demonstrated that conservation of
biological interactions is maintained between species, but
mainly at the module level rather than at the level of
individual genes or proteins
[82]
. Another study noted
similar module-level conservation when comparing chem-
ical genetic interactions between S. cerevisiae and S. pombe
[83]
, providing additional evidence to support conservation
of general genetic network properties and suggesting that
a complete yeast genetic network may serve as a template
to guide experimental and computational analysis, as well
as predicting genetic interaction hubs in complex organ-
isms where genome-wide combinatorial perturbation
analysis is more technically challenging.
Gain-of-Function Alleles
Systematic analysis of deletion mutant alleles, both indi-
vidually and in combination, have made an enormous
impact on gene function discovery. However, while loss-of-
function genetic analyses identify functionally coherent
gene modules and the connections between them, they are
not always sufficient for elucidating pathway architecture.
Historically, dominant gain-of-function (GOF) mutations
have provided an incredibly powerful means for deter-
mining gene position within a regulatory cascade (
[89]
for
example). The availability of low- and high-copy plasmid
libraries in which the expression of every yeast open reading
frame (ORF) is controlled by the endogenous
[90
92]
or an
e
inducible promoter
[93
95]
has enabled systematic and
genome-wide investigation of GOF and gene dosage effects
in wild-type and mutant strain backgrounds to complement
previous genetic interaction studies
[96,97]
.
Recently, a barcoded high-copy plasmid library was
developed and screened for dosage suppression. Dosage
suppressors of 41 temperature-sensitive different alleles of
essential genes were identified
[92]
. An average of ~5
different genes were found to suppress the temperature-
sensitive phenotype of each essential genemutant, suggesting
that, albeit more rare than LOF interactions such as synthetic
lethality, dosage suppression is also a common genetic
interaction. Furthermore, while they tend to connect func-
tionally related genes, dosage suppression interactions often
overlap with negative genetic interactions and physical
interactions that occur within the essential pathway of the
query gene; however, most interactions are novel, suggesting
that dosage suppression represents a prevalent and distinct
type of interaction that is rich in novel functional information
[92]
. Dosage suppression can identify pathway components
that act downstream of the query gene, and therefore this type
of genetic interaction offers the potential to decipher gene
order and the directionality of biological circuits. Ultimately,
we anticipate that a global dosage suppression map will be
a major contributor to the construction of a complete and
high-resolution cellular landscape comprising all types of
genetic and physical interaction.
e
EXPANDING GENETIC NETWORKS:
MUTANT ALLELES, CONDITIONS
AND PHENOTYPES
Conditional Alleles and Essential Genetic
Interactions
Most yeast genetic interaction studies conducted thus far
have focused on non-essential gene deletion alleles.
However, a truly comprehensive and genome-wide genetic
network must also include interactions involving essential
genes. Mapping of essential genetic interactions is possible
through the development of several strain collections where
subsets of the ~1000 essential yeast genes are individually
altered to produce either conditional alleles
[84
86]
or
hypomorphic alleles that are compatible with viability
[87]
.
Studies combining SGA analysis with a conditional allele
collection showed that essential genes also act as hubs in the
genetic network, engaging in synthetic lethal interactions
five times more often than non-essential genes
[22]
. Another
study emphasized the importance of essential genes for
deciphering the complex relationship between genetic and
physical interaction networks
[17]
. Essential genes tend to
be highly conserved between species at the level of both
sequence similarity
[88]
and fitness
[76,80]
and, as a result,
continued analysis of essential gene interactions will
provide a key resource for future comparative studies to
assess the extent of genetic network conservation.
e
Condition-Specific Genetic Interactions
Although the majority of yeast genes are not required for
viability under standard laboratory conditions, a large-scale
survey of fitness demonstrated that nearly all yeast deletion
mutants (97%) exhibit a growth defect in at least one
chemical or environmental stress condition
[98]
. Further-
more, while the average gene shares a negative genetic
interaction with ~2% of ORFs in the yeast genome, subsets
of genes, such as those involved in metabolic processes, are
statistically under-represented in the genetic interaction
network
[2]
. These findings suggest that the lack of severe
