BIOL 3301 Dauwalder | Meisel Exam 4 V1
and V2 | Full Questions and Answers |
2026/27 Updated | 100% Correct - UH.
1. A cis-regulatory element is moved 500 bp closer to its target promoter, disrupting a
CTCF/cohesin loop boundary. Which outcome is most likely?
A. Promoter-enhancer contact becomes constitutive, causing enhancer-promoter
mispairing and ectopic activation.
B. The element is silenced because CTCF binding directly recruits transcriptional
repressors.
C. Loop extrusion stalls, but enhancer-promoter specificity is preserved by TFIIB.
D. The promoter is inactivated because CTCF is required for RNA Pol II recruitment.
Answer: A. Promoter-enhancer contact becomes constitutive, causing
enhancer-promoter mispairing and ectopic activation.
Rationale: CTCF/cohesin boundaries insulate topologically associating domains;
disrupting them allows inappropriate enhancer-promoter contacts and ectopic
transcription. CTCF is an insulator/architectural protein, not a direct repressor or Pol II
recruiter, eliminating B and D; TFIIB does not encode enhancer specificity, eliminating C.
2. In a Gal4-UAS reporter assay, a mutation in the SAGA complex subunit Gcn5
abolishes reporter activation despite normal Gal4 DNA binding. Which conclusion is
best supported?
A. Gal4 requires Gcn5-mediated H3K9 acetylation for stable promoter occupancy.
B. Transcriptional activation requires histone acetylation, not just activator recruitment.
C. Gcn5 directly recruits Mediator to the UAS independent of acetylation.
D. SAGA functions solely in preinitiation complex assembly at TATA-less promoters.
Answer: B. Transcriptional activation requires histone acetylation, not just activator
recruitment.
Rationale: Gcn5 is a histone acetyltransferase; loss of activation with intact Gal4 binding
demonstrates that acetylation is a required downstream activation step. Gal4 occupancy is
unaffected (A wrong), and Gcn5 acts catalytically rather than as a Mediator recruiter (C
wrong); SAGA is not restricted to TATA-less promoters (D wrong).
Page 1 of 80
,3. A Drosophila maternal-effect mutation causes loss of germ cell formation in
embryos from mutant mothers but not from mutant fathers. Which gene class is most
consistent?
A. Zygotic segmentation genes such as even-skipped
B. Pole plasm components such as oskar and vasa
C. Hox cluster genes such as Ultrabithorax
D. Imaginal disc patterning genes such as hedgehog
Answer: B. Pole plasm components such as oskar and vasa
Rationale: Maternal-effect genes like oskar and vasa localize to pole plasm and specify
germ cells; only the maternal genotype matters. Zygotic, Hox, and imaginal disc genes act
later and would not produce this maternal-effect pattern.
4. In a GWAS, a variant in a conserved noncoding region shows strong association
with type 2 diabetes. The variant disrupts a predicted FOXA2 binding site in a
pancreatic islet enhancer. Which experiment best tests causality?
A. CRISPRi of the nearest gene promoter in HepG2 cells
B. Allele-specific reporter assay in islet-derived cells with and without FOXA2
knockdown
C. ATAC-seq of whole blood from cases and controls
D. Overexpression of FOXA2 in fibroblasts followed by RNA-seq
Answer: B. Allele-specific reporter assay in islet-derived cells with and without
FOXA2 knockdown
Rationale: Testing a noncoding variant requires assessing allele-specific enhancer activity
in the relevant cell type and testing dependence on the predicted factor (FOXA2).
Liver/blood/fibroblast systems are the wrong tissue context, and overexpression does not
test the endogenous variant.
Page 2 of 80
,5. A zygotic mutation eliminates a miRNA's seed sequence but leaves its precursor
processing intact. Which change is most likely at target mRNAs?
A. Target mRNAs are destabilized because processing intermediates accumulate.
B. Target mRNAs are derepressed because the mature miRNA cannot bind 3' UTRs.
C. Target mRNAs are silenced more strongly due to Argonaute hyperactivation.
D. Target mRNAs undergo alternative splicing because splicing factors are sequestered.
Answer: B. Target mRNAs are derepressed because the mature miRNA cannot bind 3'
UTRs.
Rationale: The seed sequence mediates target recognition; its loss prevents RISC binding
and relieves repression. Processing intermediates do not destabilize targets (A), Argonaute
is not hyperactivated (C), and miRNAs do not sequester splicing factors (D).
6. A histone H3K27M mutation in a pediatric glioma globally reduces H3K27me3.
Which mechanistic consequence best explains oncogenesis?
A. PRC2 is sequestered and its repressive mark is lost, derepressing developmental
genes.
B. H3K27M enhances PRC2 activity, silencing tumor suppressors.
C. H3K27M blocks DNA methylation, causing global hypomethylation.
D. H3K27M recruits KDM6A to erase H3K4me3 at promoters.
Answer: A. PRC2 is sequestered and its repressive mark is lost, derepressing
developmental genes.
Rationale: The oncohistone H3K27M binds and inhibits PRC2 (EZH2), reducing
H3K27me3 and derepressing developmental loci. It does not enhance PRC2 (B), directly
block DNA methylation (C), or erase H3K4me3 (D).
Page 3 of 80
, 7. A population of 10,000 is in Hardy-Weinberg equilibrium. A recessive lethal allele
has frequency q = 0.1 at birth. What is the allele frequency in the next generation's
zygotes?
A. 0.10
B. 0.0909
C. 0.05
D. 0.009
Answer: B. 0.0909
Rationale: With recessive lethality, q' = q/(1+q) = 0.1/1.1 0.0909. The other options
reflect misapplication of selection or confusion between allele and genotype frequencies.
8. A quantitative trait has h² = 0.6 in one environment and h² = 0.1 in another. Which
statement is most accurate?
A. The trait is more genetically determined in the second environment.
B. Heritability is a property of the population and environment, not the trait alone.
C. The first population has more additive genetic variance than the second by definition.
D. Heritability estimates are invalid unless both environments are identical.
Answer: B. Heritability is a property of the population and environment, not the trait
alone.
Rationale: Heritability (h²) is population- and environment-specific; a change in
environment alters V_E and thus h². It does not directly indicate more genetic variance
(C), and estimates are valid within each context (D).
Page 4 of 80
and V2 | Full Questions and Answers |
2026/27 Updated | 100% Correct - UH.
1. A cis-regulatory element is moved 500 bp closer to its target promoter, disrupting a
CTCF/cohesin loop boundary. Which outcome is most likely?
A. Promoter-enhancer contact becomes constitutive, causing enhancer-promoter
mispairing and ectopic activation.
B. The element is silenced because CTCF binding directly recruits transcriptional
repressors.
C. Loop extrusion stalls, but enhancer-promoter specificity is preserved by TFIIB.
D. The promoter is inactivated because CTCF is required for RNA Pol II recruitment.
Answer: A. Promoter-enhancer contact becomes constitutive, causing
enhancer-promoter mispairing and ectopic activation.
Rationale: CTCF/cohesin boundaries insulate topologically associating domains;
disrupting them allows inappropriate enhancer-promoter contacts and ectopic
transcription. CTCF is an insulator/architectural protein, not a direct repressor or Pol II
recruiter, eliminating B and D; TFIIB does not encode enhancer specificity, eliminating C.
2. In a Gal4-UAS reporter assay, a mutation in the SAGA complex subunit Gcn5
abolishes reporter activation despite normal Gal4 DNA binding. Which conclusion is
best supported?
A. Gal4 requires Gcn5-mediated H3K9 acetylation for stable promoter occupancy.
B. Transcriptional activation requires histone acetylation, not just activator recruitment.
C. Gcn5 directly recruits Mediator to the UAS independent of acetylation.
D. SAGA functions solely in preinitiation complex assembly at TATA-less promoters.
Answer: B. Transcriptional activation requires histone acetylation, not just activator
recruitment.
Rationale: Gcn5 is a histone acetyltransferase; loss of activation with intact Gal4 binding
demonstrates that acetylation is a required downstream activation step. Gal4 occupancy is
unaffected (A wrong), and Gcn5 acts catalytically rather than as a Mediator recruiter (C
wrong); SAGA is not restricted to TATA-less promoters (D wrong).
Page 1 of 80
,3. A Drosophila maternal-effect mutation causes loss of germ cell formation in
embryos from mutant mothers but not from mutant fathers. Which gene class is most
consistent?
A. Zygotic segmentation genes such as even-skipped
B. Pole plasm components such as oskar and vasa
C. Hox cluster genes such as Ultrabithorax
D. Imaginal disc patterning genes such as hedgehog
Answer: B. Pole plasm components such as oskar and vasa
Rationale: Maternal-effect genes like oskar and vasa localize to pole plasm and specify
germ cells; only the maternal genotype matters. Zygotic, Hox, and imaginal disc genes act
later and would not produce this maternal-effect pattern.
4. In a GWAS, a variant in a conserved noncoding region shows strong association
with type 2 diabetes. The variant disrupts a predicted FOXA2 binding site in a
pancreatic islet enhancer. Which experiment best tests causality?
A. CRISPRi of the nearest gene promoter in HepG2 cells
B. Allele-specific reporter assay in islet-derived cells with and without FOXA2
knockdown
C. ATAC-seq of whole blood from cases and controls
D. Overexpression of FOXA2 in fibroblasts followed by RNA-seq
Answer: B. Allele-specific reporter assay in islet-derived cells with and without
FOXA2 knockdown
Rationale: Testing a noncoding variant requires assessing allele-specific enhancer activity
in the relevant cell type and testing dependence on the predicted factor (FOXA2).
Liver/blood/fibroblast systems are the wrong tissue context, and overexpression does not
test the endogenous variant.
Page 2 of 80
,5. A zygotic mutation eliminates a miRNA's seed sequence but leaves its precursor
processing intact. Which change is most likely at target mRNAs?
A. Target mRNAs are destabilized because processing intermediates accumulate.
B. Target mRNAs are derepressed because the mature miRNA cannot bind 3' UTRs.
C. Target mRNAs are silenced more strongly due to Argonaute hyperactivation.
D. Target mRNAs undergo alternative splicing because splicing factors are sequestered.
Answer: B. Target mRNAs are derepressed because the mature miRNA cannot bind 3'
UTRs.
Rationale: The seed sequence mediates target recognition; its loss prevents RISC binding
and relieves repression. Processing intermediates do not destabilize targets (A), Argonaute
is not hyperactivated (C), and miRNAs do not sequester splicing factors (D).
6. A histone H3K27M mutation in a pediatric glioma globally reduces H3K27me3.
Which mechanistic consequence best explains oncogenesis?
A. PRC2 is sequestered and its repressive mark is lost, derepressing developmental
genes.
B. H3K27M enhances PRC2 activity, silencing tumor suppressors.
C. H3K27M blocks DNA methylation, causing global hypomethylation.
D. H3K27M recruits KDM6A to erase H3K4me3 at promoters.
Answer: A. PRC2 is sequestered and its repressive mark is lost, derepressing
developmental genes.
Rationale: The oncohistone H3K27M binds and inhibits PRC2 (EZH2), reducing
H3K27me3 and derepressing developmental loci. It does not enhance PRC2 (B), directly
block DNA methylation (C), or erase H3K4me3 (D).
Page 3 of 80
, 7. A population of 10,000 is in Hardy-Weinberg equilibrium. A recessive lethal allele
has frequency q = 0.1 at birth. What is the allele frequency in the next generation's
zygotes?
A. 0.10
B. 0.0909
C. 0.05
D. 0.009
Answer: B. 0.0909
Rationale: With recessive lethality, q' = q/(1+q) = 0.1/1.1 0.0909. The other options
reflect misapplication of selection or confusion between allele and genotype frequencies.
8. A quantitative trait has h² = 0.6 in one environment and h² = 0.1 in another. Which
statement is most accurate?
A. The trait is more genetically determined in the second environment.
B. Heritability is a property of the population and environment, not the trait alone.
C. The first population has more additive genetic variance than the second by definition.
D. Heritability estimates are invalid unless both environments are identical.
Answer: B. Heritability is a property of the population and environment, not the trait
alone.
Rationale: Heritability (h²) is population- and environment-specific; a change in
environment alters V_E and thus h². It does not directly indicate more genetic variance
(C), and estimates are valid within each context (D).
Page 4 of 80
