Deck 21: Genetics of Complex Traits

Question 1

Which of the following is an important control component when using an RNAi library to screening breast cancer cell lines for genes required for cell profileration?

A) genomic DNA
B) Cy3 dyes
C) Cy5 dyes
D) a normal mammary cell line
E) barcodes

Answer 1

D

Question 2

Genes that are synthetic lethal most likely function in

A) rapidly evolving pathways
B) dispensable processes
C) the same pathway
D) reproductive pathways
E) parallel pathways

Answer 2

E

Question 3

Approximately what proportion of genes have been shown to be essential for viability in yeast?

A) 20%
B) 40%
C) 50%
D) 60%
E) 80%

Answer 3

A

Question 4

Barcodes are used in knock-out and knock-down screen in both yeast cells and human cells.

Question 5

Which of the following is a property of Saccharomyces cerevisiae but not Caenorhabditis elegans?

A) sexual reproduction
B) multicellularity
C) fully sequenced genome
D) efficient homologous recombination
E) ability to take up foreign DNA

Question 6

If A- is the genotype of a query strain,the genotype that is tested for synthetic lethality in a synthetic genetic array is:

A) A^-A^-
B) A^-B⁺
C) A^-B^-
D) A⁺A^-
E) A^-A^-B^- B^-

Question 7

Approximately how many digenic mutant combinations result in a lethal phenotype in budding yeast?

A) 1,000
B) 2,500
C) 25,000
D) 100,000
E) 250,000

Question 8

What is the difference between siRNA and shRNA?

A) siRNA is used for eukaryotes;shRNA is used for prokaryotes
B) siRNA is used for stable silencing;shRNA is used for transient silencing
C) siRNA is 50 nucleotides;shRNA 19-22 bp
D) siRNA is ssRNA;shRNA is dsRNA
E) siRNA is chemically synthesized;shRNA is delivered to the cell as a plasmid

Question 9

A diagram showing all of the functional overlap between genes of a given species can be used to describe its

A) synthetic array.
B) genome architecture.
C) genotype-phenotype relationships.
D) phenological array.
E) phylogenetic history.

Question 10

In a synthetic lethal,which of the following phenotypes is most likely to be non-viable?

A) A⁺B⁺
B) A^-B⁺
C) A⁺B^-
D) A^-B^-
E) A⁺A^-B⁺ B⁺

Question 11

Why is Saccharomyces cerevisiae a useful model organism for functional genetics?

A) It has approximately the same number of protein coding genes as humans do.
B) It has the smallest genome of any organism.
C) The function of every one of its genes is known.
D) It has the smallest genome of any eukaryote.
E) It can exist as a haploid or diploid.

Question 12

Where should barcodes be placed in a gene deletion cassette?

A) flanking the selectable marker
B) flanking one of the homologous fragments
C) flanking both homologous fragments
D) in the middle of the selectable marker
E) in the middle of the homologous fragment

Question 13

shRNA is a type of RNAi.

Question 14

Which of the following is the correct order of steps in a synthetic genetic array screen?

A) mating,sporulation,kan^R selection,assay double mutants
B) sporulation,kan^R selection,mating,assay double mutants
C) mating,kan^R selection,assay double mutants,sporulation
D) kan^R selection,assay double mutants,mating,sporulation
E) mating,kan^R selection,sporulation,assay double mutants

Question 15

Genetic buffering describes

A) the ability of cells to accumulate mutations.
B) loss of mutations through repair and recombination.
C) the accumulation of extra,non-coding DNA in eukaryotic genomes.
D) the ability of one gene to mask variability in another gene.
E) the expansion of introns throughout evolution.

Question 16

Which of the following statements about shRNA is not true?

A) shRNAs are synthetic 19-22bp dsRNAs.
B) shRNA encodes a substrate of RISC.
C) shRNAs encodes ssRNA.
D) shRNA is used to produce siRNA.
E) shRNA can be packaged into a virus.

Question 17

You grow a barcoded yeast deletion set at 4°C and then a copy of the same set at 25°C.Barcodes from the 4°C sample and 25°C are labeled with a green fluorochrome and a red fluorochrome,respectively.How will you identify genes required for growth specifically at cold temperatures?

A) separate the PCR products on an agarose gel and look for red fluorescent bands
B) separate the PCR products on an agarose gel and look for yellow fluorescent bands
C) hybridize the products to a microarray and look for red spots
D) hybridize the products to a microarray and look for green spots
E) separate the PCR products on an agarose gel and look for green fluorescent bands

Question 18

Synthetic genetic arrays involve mating a ________ with __________.

A) haploid wild-type;all inviable deletion mutants.
B) diploid query strain;a haploid wild-type strain.
C) haploid query strain;a diploid wild-type.
D) haploid query strain;all viable haploid deletion mutants.
E) inviable diploid strain;all viable haploid deletion mutants.

Question 19

Which of these would be of the least use in a gene deletion cassette for use in yeast?

A) kanR gene
B) DNA barcode
C) common PCR primer binding sites
D) shRNA
E) yeast DNA sequences

Question 20

Which of the following is not true of the most highly connected nodes in a genetic interaction map?

A) they are the minority of nodes
B) they are also known as hubs
C) they have a greater influence on phenotype than other genes
D) they typically show scale-free architecture
E) they have lowest buffering capacity of any genes

Question 21

Explain why budding yeast (Saccharomyces cerevisiae)is a particularly useful tool for functional genomics.What are the limitations of budding yeast as model organism?

Question 22

Genes of round worms (Caenorhabitis elegans)can be silenced by soaking the worms in siRNA.

Question 23

siRNA contains a stem loop.

Question 24

Budding yeast with the genotype A⁺B⁺ is haploid.

Question 25

A comprehensive collection of deletion mutants is required for synthetic genetic array analysis.

Question 26

How are the gene interaction maps that are made by analysis of synthetic genetic arrays related to protein interaction maps made by e.g.yeast two-hybrid analysis?

Question 27

Retroviruses can be used for targeted gene silencing in mammal cells.

Question 28

In scale-free networks,the number of links shows a normal distribution.

Question 29

In genetic interaction maps,most genes have the same number of links to other genes.

Question 30

The analysis of genetic architecture in model organisms indicates that complex phenotypes are controlled by relatively few genes.

Question 31

RNAi techniques completely knock-out the transcription of their target gene.

Question 32

How could you use shRNA and human cell lines to identify genes to target for cancer therapy? Discuss the methods and expected results and your intepretations.

Question 33

Compare genome sequencing,functional genomics,and systems biology.

Question 34

There are more mutant combinations that cause lethality than there are single mutants that cause lethality.

Question 35

Modifiers in genetic networks control the strength of mutant phenotypes.

Question 36

Up to 85% of introduced deletion casettes will undergo homologous recombination in budding yeast.

Question 37

One pair of PCR primers can amplify any of the barcodes in the genome-wide yeast deletion set.

Question 38

In a genetic interaction map,a line connects two genes that are both required for normal growth.

Question 39

Two crossovers are usually involved when using a yeast deletion cassette to knock-out a gene.

Question 40

Because it cannot be automated,image analysis is the major limitation in phenotyping genome-wide yeast deletion analysis.

Question 41

How would the methods for genome-wide deletion screens change if barcodes were not available?

Question 42

What do synthetic genetic arrays reveal about the function of genes in general?

Question 43

What is the benefit of using barcodes in genome-wide deletion screens?