Lecture 15

Question 1

What is meant by forward genetics

Answer 1

Forward genetics is the method by which you identify the function of a gene and then identify the gene itself

Question 2

How are forward genetic screen carried out

Answer 2

An organism is taken and its genome is randomly mutated using a mutagen. Then, interesting phenotypes are looked for in the offspring of the mutagenized animals. Once the interesting phenotypes have been identified the next stage is to identify the actual gene that the mutation is in

Question 3

What chemical mutagen is commonly used in forward genetic screens

Answer 3

EMS

Question 4

Why are more simple organisms used preferentially over more complex mammalian systems in forward genetic screens

Answer 4

Because the mutagenesis process occurs at random and effects the entire genome the probability if hitting a specific gene is relatively low. This increases the number of mutagenized animals you would need to analyse to find the interesting phenotypes. Thus simpler organisms are used to speed up this process

Question 5

What examples of simple systems are used in forward genetic screens

Answer 5

Drosophila, C. elegans, Zebrafish and Yeast

Question 6

Most genetic screens are done for recessive alleles but domain forward screens can also be done, T or F

Answer 6

T

Question 7

What technique allows you to identify the specific gene mutated in a particular phenotype

Answer 7

Positional cloning/linkage analysis

Question 8

Explain how a forward genetic screen is carried out in flies

Answer 8

Male flies are exposed to a mutagen such as EMS which is then integrated into the body and introduces mutations in the sperm. This generation of males, referred to a P0 are then outcrossed with non-mutagenised wild type female flies. The male offspring from this cross are then collected, these are referred to as the F1 generation. Each male in the F1 will have 4 or 5 mutated genes. These males are then crossed with wild type females once again to produce the F2 generation. The F2 generation will contain both males and females with mutant copies of the genes. This family is then incrossed to see what the homozygous mutants look like.

Question 9

What percentage of the F2 generation of flies produced by a forward genetic screen will show a phenotype if there is one

Answer 9

A quarter

Question 10

How many generations does it take to make a particular mutation homozygous

Answer 10

3 generations; Po, F1 and F2

Question 11

To identify genes that affect a specific process, thousands of F2 families need to be screened, T or F

Answer 11

T

Question 12

What is meant by complementation testing

Answer 12

Complementation testing is used to determine if different mutations that have the same phenotype are alleles of the same gene or if these mutations in fact lie in separate genes.

Question 13

Explain the process of complementation testing

Answer 13

Complementation analysis allows the sorting of mutations into distinct groups that correspond to individual genes. Carriers of a mutation that has the same phenotype are crossed and the offspring produced from this cross are analysed. If ¼ of the offspring produced are homozygous mutants then the mutations fail to complement each other and they are mutant alleles of the same gene. If no offspring with the mutant phenotype are produced then mutations are said to complement each other and lie in different genes

Question 14

What is the name given to the groups of separate genes that when mutated produced the same phenotype

Answer 14

Complementation groups

Question 15

Explain how linkage analysis allows the identification of a particular gene

Answer 15

Linkage analysis involves analysing recombination between an identified allele and a known marker on the same chromosome. This enables the determination of whether the gene and marker are linked in any way. Carriers of the mutation are crossed with carriers of the marker and the number of offspring where crossing over has occurred in, are counted. These are the number of offspring that exhibit both the mutation and the marker. The greater the distance between the gene and the marker on the chromosome the more frequent that crossing over events will occur and the greater the number of offspring produced with both attributes.

Question 16

What is indicated by linkage analysis experiments that reveal few offspring that show both the mutation and the marker

Answer 16

It means that the mutation and the marker lie close to each other and hence crossing over is rare

Question 17

What maker is often used in fruit fly screens

Answer 17

Notch

Question 18

Recall the equation that calculates the genetic distance between mutation and marker in linkage analyses

Answer 18

cM = R/T x 100 (genetic distance = number of recombinant gametes/total number of gametes)

Question 19

How are genetic distances calculated in humans

Answer 19

A correlation between known SNPs and diseased phenotypes are investigated. SNPs act as the markers and over 1m have been identified in humans. The offspring of a diseased individual are analysed to determine if particularly SNPs are always present in the diseased state. If an SNP is always present in diseased offspring but not healthy ones you can determine that the mutant gene is linked to that SNP. You can then correlate the location of the known SNP with known genes to derived candidate genes.

Question 20

What are SNPs

Answer 20

Single polynucleotide polymorphisms are single base pair changes that are frequent in the population, varying from individual to individual but without conferring a disease phenotype

Question 21

What is the result of changes in the regulatory sequences of the DNA

Answer 21

These affect transcription and occur in regulatory sequences such as enhancers

Question 22

What are the downstream implications of changes in the non-coding sequence of the transcript of a gene

Answer 22

These may effect RNA splicing, stability or folding

Question 23

Give an example of a change in the non-coding sequence of a gene transcript

Answer 23

Mutations that lead to the deletion of an intron

Question 24

What are the results of mutations in the coding sequence of a gene

Answer 24

May alter amino acid composition which can impact folding

Question 25

What are the main two types of mutations in the coding sequence

Answer 25

Missense mutations which are characterised by the substitution of an amino acid. Nonsense mutations create premature stop codons which result in a truncated protein

Question 26

Below is a table containing a list of features of loss of function mutations, determine if they are characteristic of amorphic, hypomorphic or antimorphic mutations?

Answer 26

• Antimorphic*
• Antimorphic*
• Amorphic*
• Hypomorphic and amorphic*
• Antimorphic*
• Hypomorphic*
• Hypomorphic*
• Antimorphic*
• Amorphic*
• Amorphic*
• Antimorphic*

Question 27

What is meant by a hypermorphic mutation

Answer 27

Mutation that confers a gain of function of the gene product. This is caused by the overexpression of a transcription unit or overactivity of a gene production.

Question 28

Are hypermorphic mutations recessive or dominant

Answer 28

Dominant