Exam 4

Question 1

In CRISPR/Cas9 mutagenesis a synthetic gRNA (guide RNA) functions
A. as a ribozyme to cut DNA
B. to promote single nucleotide substitutions within the complementary DNA
C. as a selectable marker within embryonic stem cells
D. as a template from which the inserted DNA is synthesized
E. to target Cas9 to specific sites in the genome

Answer 1

E. to target Cas9 to specific sites in the genome

Question 2

In a human pedigree for a family segregating a gain-of-function allele of FGFR1, you might expect
that “filled” circles (females) or squares (males) represent individuals who are:
A. homozygous for the mutant allele
B. heterozygous for the mutant allele
C. recessive
D. unaffected phenotypically
E. dead

Answer 2

B. heterozygous for the mutant allele

Question 3

Reporter genes are useful tools for many kinds of experiments and can often be made by cloning
PCR-amplified segments of genomic DNA upstream of cDNAs for fluorophores like GFP, then injecting
or electroporating these constructs into embryos. Nevertheless, this approach has some caveats,
including:
A. the cloned segment of genomic DNA may not contain all necessary cis-regulatory elements
B. the reporter construct often alters expression of the native gene being “reported on”
C. analyses of reporter expression require the embryo to be histologically “fixed” to prevent RNA
degradation
D. all of the above
E. none of the above

Answer 3

A. the cloned segment of genomic DNA may not contain all necessary cis-regulatory elements

Question 4

Alleles are considered to have additive effects when…
A. each copy adds precisely one unit of a value to trait expression
B. each copy has a discernible influence on the phenotype
C. epistasis is unidirectional
D. similar alleles at other loci can compensate, leading to redundancy
E. only discrete phenotypes are present

Answer 4

B. each copy has a discernible influence on the phenotype

Question 5

Sets of phenotypic traits are sometimes considered to be modular because:
A. Genes normally have weak pleiotropic effects within sets of traits but stronger effect between
sets of traits.
B. Genetic and cellular interactions within sets of traits are stronger and more frequent than
between sets of traits.
C. Environmental factors rarely effect more than one trait.
D. All of the above.
E. None of the above

Answer 5

B. Genetic and cellular interactions within sets of traits are stronger and more frequent than

Question 6

Studies of the gene regulatory network of sea urchin micromere and skeletal development showed
that transcription factor Pmar1 is genetically upstream of transcription factor HesC in a double
negative gate, and that injection of Pmar1 mRNA results in the formation of too many micromeres.
Given your knowledge of gene regulatory logic, how else could you generate an excess of
micromeres?
A. by injecting mRNA for membrane-tethered form of beta-catenin
B. by injecting HesC protein
C. by injecting a morpholino for HesC
D. by injecting mRNA for a downstream differentiation gene like Sm27
E. by injecting Cas9 and guide RNA targeting Pmar1

Answer 6

C. by injecting a morpholino for HesC

Question 7

Simulation analyses of gene regulation in Drosophila have suggested that:
A. very precise levels of gene expression are required for normal development
B. normal domains of final gene expression can be obtained even when some early genes are
deleted entirely
C. hedgehog acts upstream of engrailed to pattern segment morphology
D. pleiotropic effects of early genes extend to segments and other larval traits
E. a wide range of parameter values produce the same final gene expression domains

Answer 7

E. a wide range of parameter values produce the same final gene expression domains

Question 8

A gene is considered to be “haploinsufficient” when…
A. the mutant phenotype is present in some anatomical locations but not others
B. mutations lead to phenotypes in gametes but not somatic cells
C. transgenes fail to rescue the phenotype
D. more than a single wild-type allele is required for normal development or homeostasis
E. a defective protein product interferes with normal function of the wild-type protein

Answer 8

D. more than a single wild-type allele is required for normal development or homeostasis

Question 9

Transcriptional adaptation refers to:
A. the phenomenon in which non-sense mediated decay of transcripts can induce higher levels of expression from functionally similar genes
B. the observation that gene expression often changes as cell types differentiate during
development
C. the mechanism by which RNA perdurance in the cytoplasm of cells is controlled with
exonucleases that attack polyA tails of mature mRNAs
D. short-term physiological regulation of gene expression in response to environmental conditions
E. the finding that genes located within chromosomal inversions can acquire mutations allowing
them to function together as a “supergene” in determining individual phenotypes

Answer 9

A. the phenomenon in which non-sense mediated decay of transcripts can induce higher levels of expression from functionally similar genes

Question 10

In genetics, the term “penetrance” refers to the proportion of genotypically mutant individuals that
actually express a mutant phenotype; if all genotypically mutant individuals actually look like mutants,
the allele is said to be “fully penetrant.” But imagine you are studying a human “disease gene” and
discover a mutant allele that is only 5% penetrant, even when homozygous. A plausible explanation
would be:
A. Spontaneously arising revertant alleles allow restoration of function.
B. The allele affects only non-coding sequence.
C. Alleles segregating at other loci impact the degree of genetic robustness among individuals.
D. Recombination machinery in somatic cells allows homology-directed repair using genes with
similar sequences as templates.
E. The locus is affected by X-chromosome inactivation in female individuals

Answer 10

C. Alleles segregating at other loci impact the degree of genetic robustness among individuals.

Question 11

Whether or not a cell expresses a particular gene depends on:
A. both activating and repressive influences of transcription factors
B. the prior developmental history of the cell
C. what epigenetic modifications have occurred
D. all of the above
E. none of the above

Answer 11

D. all of the above

Question 12

Studies of human genome variation have indicated that:
A. Most homozygous loss of function mutations are not lethal.
B. Icelanders are more prone to mutation than other populations.
C. Loss of function alleles are derived invariably from paternal genomes.
D. Individuals can be heterozygous or homozygous for loss of function mutations.
E. Loss of function mutations are usually X-linked.

Answer 12

D. Individuals can be heterozygous or homozygous for loss of function mutations.

Question 13

Mathematical analyses of linear genetic pathways suggest that hypomorphic alleles are more likely
to be recessive if:
A. mutations are in coding sequence
B. genes undergo non-sense mediated decay
C. there are more genes in the pathway
D. all genes are physically linked
E. genes encode transcription factors

Answer 13

C. there are more genes in the pathway

Question 14

Which statement is true about the mechanism of non-homologous end-joining?
A. it is used by cells to repair double strand breaks and often leads to small deletions or insertions
B. it is used by cells to repair double strand breaks by crossing over without insertions or
deletions
C. it is an important mechanism exploited in CRISPR techniques to allow error-free gene editing
D. it is an important mechanism that allow for targeted mutagenesis coupled with viability
selection in mouse embryonic stem cells
E. all of the above

Answer 14

A. it is used by cells to repair double strand breaks and often leads to small deletions or insertions

Question 15

Which of the following can explain pleiotropy?
A. A gene is tightly linked to another gene on the same chromosome.
B. A gene product acts in more than one genetic pathway.
C. A gene is required in several different cell types.
D. Both A and C.
E. Both B and C.

Answer 15

E. Both B and C.

Question 16

In studies on even skipped (eve) gene expression in Drosophila, a set of “deletion” constructs was
used to…
A. assess whether regions of sequence upstream of eve were required for reporter gene expression at specific anatomical locations.
B. determine which transcription factors bind to particular sequence motifs upstream of eve.
C. test the roles of cis-regulatory elements that had been previously identified using
computational methods applied to whole-genome sequence.
D. evaluate whether nucleotides adjacent to the “optimal” cis-regulatory elements were required
for gene expression.
E. modify the eve locus, allowing alterations in protein distribution to be assessed using an anti-
Eve antibody.

Answer 16

A. assess whether regions of sequence upstream of eve were required for reporter gene expression at specific anatomical locations.

Question 17

Imagine you are studying a developmental process using the zebrafish system and you have
undertaken a reverse genetic screen to test roles for candidate genes identified by single cell RNA-
seq. You therefore plan to design and order CRISPR/Cas9 reagents, which you will inject into
embryos. To have the best chance of observing a phenotype if the gene functions in the process of
interest, you ought to design your reagents to:
A. induce a premature stop codon in the first exon
B. interfere with RNA splicing
C. block translation from mature mRNA
D. prevent any transcript from being made
E. target 3’ UTRs to block polyadenylation

Answer 17

D. prevent any transcript from being made

Question 18

Regulation of Drosophila even skipped (eve) depends in part on:
A. different transcriptional repressors that block expression outside of every stripe
B. different transcriptional activators that drive expression specifically in every stripe
C. transcription factors of the segment polarity class
D. both A and C
E. both B and C

Answer 18

A. different transcriptional repressors that block expression outside of every stripe

Question 19

Studies of several model organisms suggest that if a mutation has an observable effect at all, it
could reasonably be expected to influence
A. every trait
B. at least 5 traits
C. 30% of traits
D. 30–45 traits
E. less than one trait

Answer 19

B. at least 5 traits

Question 20

Analyses of differential gene expression by single cell RNA-sequencing often depend on:
A. Capturing intact genomes from hundreds to thousands of cells at a time and then
reconstructing gene expression using computational methods, with simplifying assumptions
about alternative splicing as well as RNA perdurance.
B. In vitro translation of RNAs to capture of gene products using customized “panels” of
antibodies, thereby permitting detection by mass spectrometry with subsequent clustering in
two or sometimes three dimensions for visualization.
C. Incubation of fixed (i.e., preserved) embryos with antisense riboprobes that simultaneously
recognize as many as 10,000 different transcripts expressed at high levels, with subsequent
“deconvolution” using computational approaches to resolve temporal and spatial heterogeneity
in gene expression.
D. Reverse-transcribing mRNAs isolated from individual cells, sequencing cDNAs tagged according to cell-of-origin, assessing similarities and differences among transcriptomes in many-dimensional space, and then visualizing clusters of cells in two-dimensional space.
E. Antibody-labeling of chromatin-associated proteins (like histones with specific marks) that
reliably indicate transcriptional activity at many genes throughout the genome, followed by
histological detection using multi-colored probes that can then allow clustering and visualizing
in two-dimensional space.

Answer 20

D. Reverse-transcribing mRNAs isolated from individual cells, sequencing cDNAs tagged according to cell-of-origin, assessing similarities and differences among transcriptomes in many-dimensional space, and then visualizing clusters of cells in two-dimensional space.

Question 21

Differentiation can be described as…
A. a change in gene expression during a cell’s lifetime
B. a mechanism by which genes are selectively lost or amplified during embryonic development
C. a process by which a cell becomes specialized to perform a specific function
D. a gradual change in cellular attributes, like shape or size
E. a technique required to restore totipotentiality to mature cells, so they can be used in cloning
experiments

Answer 21

C. a process by which a cell becomes specialized to perform a specific function

Question 22

In trying to understand the buffering of phenotypes against genetic and environmental
perturbation, embryologist Conrad Waddington envisaged an “epigenetic landscape” in which an
embryo, represented as a ball, rolled downhill through certain valleys but not others. In Waddington’s
imagery, the surface of this landscape was dictated by underlying:
A. genes and their interactions
B. histone modifications
C. transcription factors and cofactors
D. environmental conditions
E. mature mRNAs

Answer 22

A. genes and their interactions

Question 23

Analyses of gene regulation in an ascidian have shown that correct expression of a transcriptional
reporter gene requires…
A. maximally efficient binding of transcription factors to their DNA targets
B. precise epigenetic coding, detectable in the form of histone marks
C. core promoter sequences longer than 100 bp
D. moderate affinity interactions between cis-regulatory elements and trans-acting factors
E. removal of Otx binding sites

Answer 23

D. moderate affinity interactions between cis-regulatory elements and trans-acting factors

Question 24

Which statement is true of Bardett-Biedl syndrome?
A. It only arises when all 19 cilia genes are mutated simultaneously.
B. It reflects the functional requirements for primary cilia in the development of many traits.
C. The mutations known identify all of the genes required for ciliogenesis in humans.
D. It represents a good candidate for CRISPR-based gene therapy given the specificity of the
mutations.
E. It is specific to XYY males.

Answer 24

B. It reflects the functional requirements for primary cilia in the development of many traits.

Question 25

Which of the following statements about differentiation is true?
A. Differentiation happens only at embryonic stages and involves temporally predictable
alterations in gene expression.
B. Differentiation is limited to cell lineages that develop from long-term stem cells (like blood or
skin) and involves a terminal state of maturation in which gene expression ceases because the
cell dies or the nucleus is lost.
C. Differentiation is primarily a mechanism for tumor suppression and acts in parallel to the
classical P53 / Retinoblastoma pathway, except in elephants which have extra copies of the
P53 gene, TP53.
D. Differentiation inevitably alters the number of genes within the genome, and so irreversibly
limits the potential of cells to develop along other pathways.
E. Differentiation occurs both in embryos and adults and involves alterations in gene expression that result from dynamic changes in transcription factor complements as cells mature.

Answer 25

E. Differentiation occurs both in embryos and adults and involves alterations in gene expression that result from dynamic changes in transcription factor complements as cells mature.

Question 26

“Consanguineous” mating refers to reproduction involving individuals who are related to one
another (siblings, first or second cousins, cousins once removed, etc.). A principal risk of such matings
is that:
A. offspring fertility will be impacted because of inversions
B. alleles are more likely to be neomorphic
C. co-dominant alleles will interfere with each other
D. epistatic interactions will predominate
E. deleterious recessive alleles will be brought to homozygosity

Answer 26

E. deleterious recessive alleles will be brought to homozygosity

Question 27

Which of the following statements is true about histological analyses of gene expression (also
known as “in situ hybridization”)?
A. The method reveals the spatial distribution of a protein product.
B. The method relies on computational tools to infer expression in cells that were not sampled.
C. The method is similar to reporter analyses as both show the distribution of a gene product
while the animal (or plant) continues to develop.
D. The method demonstrates cell lineage relationships.
E. The method is useful for detecting mRNAs for one or a few genes at a time.

Answer 27

E. The method is useful for detecting mRNAs for one or a few genes at a time.

Question 28

Imagine you have just started an internship at Viagen, a company that clones house pets and
horses for customers who have enough money. On your first day, you field a call from a prospective
customer who is interested in your services because their much-beloved lamprey, Smootches, is
getting old and may soon expire. They are hoping you can preserve cells from skin or blood for
deriving a Smootches clone, when she finally passes into the long dark lamprey night. Assuming you
are honest with your prospective customer, what would you say about using these cells from
Smootches for your cloning services?
A. Almost certainly feasible because clonal organisms have been made from differentiated cells of
frogs, which are only a small evolutionary step away from lamprey.
B. Should be ok, provided enough skin or blood stem cells can be isolated.
C. Not feasible because the genomes of Smootches’ skin and blood cells cannot be counted on to have all the genes that will be need for making Smootches-Two.
D. Risky but still worth a try as the cloning process would use a surrogate with a complete
genome.
E. Not a good approach because only mammary gland epithelial cells can be used for cloning and
despite all her other charms Smootches is just not a mammal.

Answer 28

C. Not feasible because the genomes of Smootches’ skin and blood cells cannot be counted on to have all the genes that will be need for making Smootches-Two.

Question 29

When a mouse knockout is made using traditional methods, selection for neomycin resistance is
important because:
A. embryos will otherwise be mosaic
B. foster mothers carry a different microbiome
C. homologous recombination is inefficient
D. stem cells will otherwise form tumors
E. chromatin marks need to be reset

Answer 29

C. homologous recombination is inefficient

Question 30

Trait distributions may appear continuous if…
A. the phenotype is affected by allelic variation at a few loci as well as environmental influences.
B. the phenotype depends on many genes and alleles, each having a small additive effect.
C. there is no allelic variation but the trait is responsive to a range of environmental effects or is
intrinsically variable in its expression.
D. all of the above
E. none of the above

Answer 30

D. all of the above