Deck 15: Regulation of Gene Expression in Eukaryotes

Question 1

Regulatory regions of a eukaryotic gene all contain which of the following sequences, which regulate transcription of genes located on the same chromosome as the sequences?

A)zinc fingers
B)cis-acting regulatory sequences
C)homeodomains
D)trans-acting regulatory sequences
E)leucine zippers

Answer 1

B

Question 2

In yeast in the presence of galactose, you unexpectedly find that transcription is still blocked. Assuming Gal80 is present and functional, which other protein may be mutated to prevent transcriptional activation?

A)Gal2
B)Gal3
C)Gal4
D)Mig1
E)Gal10

Answer 2

B

Question 3

Galactose is absent, but you find active transcription of the GAL genes. Which protein is likely mutated or absent to allow for constitutive transcription of the GAL genes?

A)Gal2
B)Mig1
C)Gal4
D)Gal10
E)Gal80

Answer 3

E

Question 4

If a mouse inherits a deletion in the SHH enhancer, what effect would you expect to see?

A)enhanced limb development
B)abnormal limb development
C)position effect variegation
D)increased β-globin production
E)abnormal β-globin production (thalassemia)

Question 5

Chromatin remodeling involves both sliding and relocating of the nucleosomes. Which eukaryotic chromatin remodeling complex is likely involved?

A)ISWI complex
B)SWR1 complex
C)SWI/SNF complex
D)SHH complex
E)Mig1 complex

Question 6

In yeast, if you want to prevent the Gal4 regulatory protein from binding near each of the GAL genes, which sequence element would you target?

A)core promoter
B)proximal elements
C)enhancer sequence
D)homeodomain motif
E)upstream activator sequence

Question 7

The imprinting control region (ICR)involved in genomic imprinting on chromosome 15 is what type of sequence?

A)enhancer
B)insulator
C)silencer
D)promoter
E)intronic

Question 8

Inherited mutations in the Xist promoter lead to defects in which epigenetic process?

A)RNAi
B)X-inactivation
C)genomic imprinting
D)position effect variegation
E)methylation of CpG islands

Question 9

You have identified a mutation in a gene that also seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance?

A)core promoter
B)proximal elements
C)enhancer sequence
D)homeodomain motif
E)upstream activator sequence

Question 10

Prader-Willi syndrome is a genetic disorder involving a partial deletion of chromosome 15q on the paternal chromosome. When both copies of a gene (or chromosome)are functional but only one is expressed, this is an example of __________.

A)position effect variegation
B)X-inactivation
C)genomic imprinting
D)histone acetylation
E)chromatin modifications

Question 11

Which protein binds to the silencer sequence and promotes transcriptional silencing in the presence of glucose?

A)Gal2
B)Mig1
C)Gal4
D)Gal10
E)Gal80

Question 12

For the following gene, MspI and HpaII restriction sites and their positions are indicated here. Recall that HpaII is methylation sensitive, while MspI is not. If this gene is being actively transcribed, how many fragments would you expect from this restriction digest?

A)1
B)3
C)4
D)5
E)6

Question 13

Which sequences would likely have both a nucleosome-depleted region (NDR)and a poly A/T tract to attract transcriptional activators to a transcription start sequence?

A)chromatin modifiers
B)enhancers
C)open promoters
D)closed promoters
E)insulators

Question 14

Typically, methylation of nucleosome N-terminal tails leads to __________.

A)removal of the protein components of the chromatin from the DNA
B)relaxed packaging of the chromatin and increased transcription
C)tighter packaging of the chromatin and reduced transcription
D)increased amounts of euchromatin relative to heterochromatin
E)activation of topoisomerase

Question 15

For the following gene, MspI and HpaII restriction sites and their positions are indicated here. Recall that HpaII is methylation sensitive, while MspI is not. If this gene is methylated, which of the following combinations of DNA fragments would you expect from this restriction digest?

A)5 bands = 100 bp, 200 bp, 1000 bp, 1500 bp, and 1800 bp.
B)4 bands = 100 bp, 200 bp, 800 bp, and 900 bp.
C)3 bands = 200 bp, 500 bp, and 1300 bp.
D)1 band = 2000 bp.
E)No bands = DNA will be completely digested.

Question 16

If you want to affect chromatin packaging, which amino acid could you mutate to affect both histone acetylation and methylation patterns?

A)arginine
B)methionine
C)histidine
D)lysine
E)asparagine

Question 17

Molecular biologists can determine experimentally whether a region of DNA contains closed chromatin or open chromatin by assessing the sensitivity of the region to __________.

A)nucleosomes
B)histone deacetylase
C)RNA polymerase II
D)methyltransferase
E)DNAse

Question 18

Typically, acetylation of histone tails leads to __________.

A)removal of the protein components of the chromatin from the DNA
B)relaxed packaging of the chromatin and increased transcription
C)tighter packaging of the chromatin and reduced transcription
D)increased amounts of euchromatin relative to heterochromatin
E)activation of topoisomerase

Question 19

A region of chromatin has recently become DNAse I hypersensitive. Which enzyme has been activated to cause this change in chromatin structure?

A)histone methyltransferase
B)histone acetylase
C)histone deacetylase
D)phosphatase
E)kinase

Question 20

When CpG islands are unmethylated, __________.

A)chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase
B)chromatin in the promoter region is closed, preventing transcription factors and RNA polymerase from binding
C)chromatin in the enhancer region is closed, so they are unable to bind regulatory proteins to initiate transcription
D)DNAse hypersensitivity in that region of the chromosome is lost
E)genes downstream of the CpG islands cannot be expressed, because the promoter region is blocked by histones

Question 21

In vertebrates and plants, what types of modifications to the N-terminal tails of histones lead to heterochromatin formation?

Question 22

In the GAL gene system, which protein acts as an activator protein through its transcription-initiating effect?

Question 23

What are the three mechanisms by which chromatin remodelers can move nucleosomes?

Question 24

Eukaryotes use these highly specialized enhancer elements, which regulate the transcription of multiple genes packaged in complexes of closely related genes (e.g., β-globin).

Question 25

Which molecules bind regulatory sequences of DNA to encourage positive regulation of transcription?

Question 26

What are three proteins or groups of proteins you would expect to find bound to the core promoter region in eukaryotes?

Question 27

Which protein complex directs DNA bending into loops that contact RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements?

Question 28

What are the protein-binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and other promoters?

Question 29

During RNAi, what do miRNAs target for destruction?

A)heterochromatic regions of DNA
B)CpG islands
C)mRNAs
D)histones
E)ribosomes

Question 30

In gal+ yeast, what is the product of the galactose utilization pathway?

Question 31

For the following gene, which mutant likely has lost its enhancer?
Mutant # Deletion Region % Transcription
WT None 100%
1 1-200 150%
2 250-400 100%
3 500-800 50%
4 950-1100 0%

Question 32

For the following gene, you notice the following results.
Mutant # Deletion Region % Transcription (lungs)% Transcription (kidneys)
WT None 100% 100%
1 1-200 150% 150%
2 250-400 100% 100%
3 500-800 50% 50%
4 950-1100 0% 100%
What type of sequence has been mutated in mutant 4?

Question 33

In yeast, which gene would you expect to be activated during phosphate starvation?

Question 34

Gal4 is mutated such that it still binds to the DNA but cannot interact with Gal80. What effect would you expect to see in the absence of galactose?

Question 35

For the following gene, which type of regulatory sequence has likely been deleted in mutant 1?
Mutant # Deletion Region % Transcription
WT None 100%
1 1-200 150%
2 250-400 100%
3 500-800 50%
4 950-1100 0%

Question 36

Many types of cancer are known to overexpress the receptor protein tyrosine kinase. Which molecular technique can be used to reduce expression of an oncogene in vitro?

A)PCR
B)DNAse sensitivity assay
C)RNAi
D)Southern blotting
E)western blotting

Question 37

In the GAL gene system, which protein binds to the activation domain of the activator protein, ultimately blocking transcription in the absence of galactose?

Question 38

Which of the four nucleotides are typically methylated in "islands," resulting in closed chromatin structure?

Question 39

Gal80 is mutated such that it cannot interact with Gal3. What effect would you expect to see in the presence of galactose?

Question 40

If you block histone deacetylase, what effect would you expect to see on transcriptional activity?

Question 41

Tortoiseshell cats have a coat-color gene on their X chromosome. What process in eukaryotes explains why males can have solid orange or black fur, and only females can have the tortoiseshell pattern of fur?

Question 42

________ in Drosophila results from the movement of the transcriptionally active w⁺ allele into the centromeric heterochromatin region of the fruit-fly X chromosome.

Question 43

Histone deacetylase (HDAC)inhibitors are commonly used as mood stabilizers or in the treatment of neurodegenerative diseases. What effect would a HDAC inhibitor have on the target cells?

Question 44

Both cis-acting sequences and trans-acting proteins affect gene expression in eukaryotic chromosomes. What are the three basic mechanisms by which trans-acting proteins access specific regulatory DNA sequences in eukaryotic chromosomes? Describe how chromatin is altered in each of these processes.

Question 45

Which protein complex binds dsRNA fragments to generate ssRNAs for RNAi?

Question 46

Which enzyme cuts dsRNA into 21-25 bp fragments during RNAi?

Question 47

What gene is critical for establishment of X-inactivation in mammals?

Question 48

Explain what effect histone deacetylase inhibitors would have on gene expression and why they may be an effective anticancer therapeutic because of their impact on tumor suppressor genes.

Question 49

Demethylation and acetylation lead to open chromatin structure and are associated with ________ regions of genomes.

Question 50

Gal4 binding leads to the formation of a multiprotein complex known as the ________, which is an enhanceosome that forms after the activator protein binds.

Question 51

The gene encoding coat color is X-linked, and male cats have a single copy of the X chromosome. They can therefore express either the O or o allele, resulting in orange or black coat, respectively. Female cats, on the other hand, have two copies of the X chromosome. Thus, they can be heterozygous and express either orange or black. Using this information, list the possible genotypes for these individuals:
• orange male
• orange female
• black male
• black female
• tortoiseshell

Question 52

How does transcription inhibition differ between prokaryotes and eukaryotes? Describe the two mechanisms used by eukaryotes to direct the enhancers toward certain promoters and away from others.

Question 53

What are the common types of epigenetic modifications? Describe how epigenetic modifications can assist in predicting whether a gene is active or inactive in a cell.

Question 54

In the GAL gene system, ________ are cis-acting regulatory elements, and ________ protein is a trans-acting regulatory protein.

Question 55

In animals, the ________ enzyme cuts pri-miRNA to produce miRNA.

Question 56

What effect does methylation of CpG islands have on human promoters?