Biology Reference
In-Depth Information
reveal the genetic relationship of two hypomorphic alleles. For genes that act in the
same pathway, determining their genetic hierarchy often requires comprehensive
analysis of the genetic, cell biological, and biochemical information about how
genes and their products interact. There are no universal rules to integrate all of this
information for ordering genes into biological pathways. Indeed, many strategies
that successfully revealed the order of genes are highly context-specific. Below, we
discuss several examples as case studies for developing approaches to order genes
that regulate a biological process.
B. Genetic Ordering of Pathways
1. Epistatic Analysis for Gene Ordering
As some components in a genetic pathway may play positive regulatory roles and
others play negative roles, it is common that genes in the same pathway exhibit the
opposite phenotypes when mutated. Epistatic analysis is a powerful way to order
these components into a signaling hierarchy. The term ''epistatic'' was first coined in
1909 by Bateson to describe a masking effect in which an allele at one locus prevents
the allele at another locus from exhibiting its phenotypes (
Bateson, 1909; Cordell,
2002
). Similarly, epistasis defined by molecular geneticists refers to a genetic
situation in which the phenotype of a mutation in one gene is masked by the
phenotype of the mutation in the other (
Avery and Wasserman, 1992
). This defini-
tion views a phenotype as a qualitative trait; so it is also termed ''compositional
epistasis'' to set it apart from ''statistical epistasis'' used by population geneticists for
quantitative differences of allele-specific effects in a population (
Phillips, 2008
).
Compositional epistatic analysis is particularly suitable for ordering genes whose
mutations cause opposite phenotypes. It has been used in C. elegans to successfully
construct pathways in various developmental processes such as the development of
the vulva (
Sternberg and Horvitz, 1989
), sex determination (
Goodwin and Ellis,
2002
), and dauer formation (
Thomas et al., 1993
). To perform epistatic analysis,
double mutants carrying two mutations giving opposite phenotypes are constructed.
The mutant phenotype that the double mutant adopts indicates the gene that is
epistatic (downstream of) to the other. Two assumptions should be met prior to
epistatic analysis. First, the two genes analyzed should be involved in the same
pathway. Second, the opposite defective phenotypes should be direct opposite states
of a genetic event assayed. For example, in vulval development, there are six VPCs.
Normally, only three of these six VPCs give rise to progeny that form the vulva. A
mutation in lin-1, encoding a transcription factor, causes more than three VPCs to
adopt vulval fates, which produces the Muv phenotype. Conversely, mutations in lin-
3, encoding an inductive cue for vulval formation, cause a reduction in vulval
induction, which can lead to the Vulvaless (Vul) phenotype. These opposite pheno-
types, Muv and Vul, are two opposite states in the same vulval induction pathway.
Thus, epistatic analysis is applicable for ordering these two genes. As the lin-1;lin-3
double mutant displays a Muv phenotype,
lin-1 is epistatic (downstream) of lin-3.
Search WWH ::
Custom Search