Perturbation—a theme in the study of developmental biology Surgical (removal, transplantation)

Developmental Genetics
Perturbation—a theme in the study of developmental biology
Surgical (removal, transplantation)
Pharmacological (exogenous application of compounds, hormones, inhibitors,
drugs, etc)
Function-blocking antibodies
Developmental Genetics
! a major goal in developmental biology is to identify and understand the functions
of genes that regulate development
! one way to determine whether a gene is important for a developmental process
is to perturb that gene and see whether the process of interest is affected.
! provides information on the genes that control a process, and on the
process itself
Analysis of the phenotypic defects for a mutant provides information about the normal
function of the mutated gene. The interpretation of the gene function from the
phenotype depends on the nature of the mutation.
Main types of mutations:
1. loss-of-function – eliminates or reduces the activity of a gene or gene product.
Examples include deletions, nonsense mutations, point mutations that
compromise the activity of a protein. These are generally recessive mutations.
2. gain-of-function – increases the activity or adds new functions to a gene or gene
product. Examples include overexpression, ectopic expression (expression in a
new place or time), point mutations that eliminate a site of negative regulation on
a protein. These are generally dominant.
3. dominant negative – the product of the mutant gene interferes with the function of
a normal gene product. Examples: a nonfunctional protein that outcompetes the
normal version of the protein for an active site, proteins that form multimers
where the mutant protein “poisons” the complex, antisense or RNAi. These
Disrupting gene function
Forward genetics
-perform screen for mutants with a phenotype of interest
-requires no foreknowledge and tolerates false preconceptions
-one of the most powerful techniques to identify important genes
-example= Drosophila segmentation
Reverse genetics
-disrupting the function of a specific gene of interest
-RNAi, antisense, homologous recombination, insertions
Manipulating gene function
Overexpression—put the coding region under the control of a strong promoter
Downregulation (RNAi, antisense)
Ectopic expression / misexpression – put the coding region under the control of a
promoter that expresses in different times or places.
Genetic mosaics
Gene name—italics (CDC2)
Mutant gene (recessive)—lower case italics (cdc2)
Protein—upper case non-italicized (CDC2)
Working list of Genetic Definitions
gene—the DNA that codes for a protein or RNA product and all it’s cis-regulatory
alleles—variants a gene containing nucleotide sequence differences
-often cause functional alterations
locus—position on a chromosome (may be occupied by a gene)
genome—sum total of an organisms’ genetic material
genotype—genetic composition of an individual
-can be referred to with respect to a single locus (gene) or the entire genome
phenotype—observable characteristics of an organism
-interaction of genotype and environment
heterozygote—individual containing 2 different alleles of a gene
homozygote—individual containing 2 copies of the same allele
dominant allele—manifests phenotypic effect when in the heterozygous state
(designated with a capitalized symbol)
recessive allele—only manifests phenotypic effect as a homozygote
(designated with lower case symbol)
-dominance relationships not always hard and fast
allele specific relationships
depends on level of phenotypic assay
mutation—heritable change in the nucleotide sequence of a gene
-Must be heritable!!
-Can be silent.
epigenetic—mitotically or meiotically heritable change in a gene’s expression which
does not result from a change in the nucleotide sequence
-often involves methylation of DNA bases and chromatin changes
wildtype—the state that is normal or considered normal
-can refer to alleles, proteins, phenotype etc.
mutant—containing a mutation or conditioned by a mutation
-can refer to alleles, proteins, phenotypes
-opposite of wildtype
mutagenesis—experiment designed to induce new mutations
mutagen—an agent that induces mutations (eg. EMS, UV, X-rays, transposons)
screen—experiment designed to identify individuals with particular phenotypes or