In Figure 12-4, certain mutations decrease the relative transcription rate of the β-globin gene. Where are these mutations located, and how do they exert their effects on transcription?

Based on the information in Figure 12-6, how does Gal4 regulate four different GAL genes at the same time? Contrast this mechanism with how the Lac repressor controls the expression of three genes.

In any experiment, controls are essential in order to determine the specific effect of changing some parameter. In Figure 12-7, which constructs are the “controls” that serve to establish the principle that activation domains are modular and interchangeable?

Contrast the role of the MCM1 protein in different yeast cell types shown in Figure 12-10. How are the a-specific genes controlled differently in different cell types?

In Figure 12-11b, in what chromosomal region are you likely to find the most H1 histone protein?

What is the conceptual connection between Figures 12-12 and 12-19?

In Figure 12-19, where is the TATA box located before the enhanceosome forms at the top of the figure?

Let’s say that you have incredible skill and can isolate the white and red patches of tissue from the Drosophila eyes shown in Figure 12-24 in order to isolate mRNA from each tissue preparation. Using your knowledge of DNA techniques from Chapter 10, design an experiment that would allow you to determine whether RNA is transcribed from the white gene in the red tissue or the white tissue or both. If you need it, you have access to radioactive white-gene DNA.

In Figure 12-26, provide a biochemical mechanism for why HP-1 can bind to the DNA only on the left side of the barrier insulator. Similarly, why can HMTase bind only to the DNA on the left of the barrier insulator?

In reference to Figure 12-28, draw the outcome if there is a mutation in gene B.

What analogies can you draw between transcriptional trans-acting factors that activate gene expression in eukaryotes and the corresponding factors in bacteria? Give an example.

Contrast how the ground states of genes within DNA in bacteria and eukaryotes differ with respect to gene activation (see Figure 12-2).

Predict and explain the effect on GAL1 transcription, in the presence of galactose alone, of the following mutations:

How is the activation of the GAL1 gene prevented in the presence of galactose and glucose?

What are the roles of histone deacetylation and histone acetylation in gene regulation, respectively?

An α strain of yeast that cannot switch mating type is isolated. What mutations might it carry that would explain this phenotype?

What genes are regulated by the α1 and α2 proteins in an α cell?

What are Sir proteins? How do mutations in SIR genes affect the expression of mating-type cassettes?

What is meant by the term epigenetic inheritance? What are two examples of such inheritance?

What is an enhanceosome? Why could a mutation in any one of the enhanceosome proteins severely reduce the transcription rate?

Usually, the deletion of a gene results in a recessive mutation. Explain how the deletion of an imprinted gene can be a dominant mutation.

What has to happen for the expression of two different genes on two different chromosomes to be regulated by the same miRNA?

What mechanisms are thought to be responsible for the inheritance of epigenetic information?

What is the fundamental difference in how bacterial and eukaryotic genes are regulated?

Why is it said that transcriptional regulation in eukaryotes is characterized by combinatorial interactions?

Which of the following statements about histones is true?

Nucleosomes are

The regions of chromosomes that form heterochromatin

Dosage compensation is necessary because

Which of the following is true of chromatin in prokaryotes?

Which of the following statements is/are true of the variegated eye color phenotype in Figure 12-23?

Which of the following are epigenetic marks?

The transcription of a gene called YFG (your favorite gene) is activated when three transcription factors (TFA, TFB, TFC) interact to recruit the co-activator CRX. TFA, TFB, TFC, and CRX and their respective binding sites constitute an enhanceosome located 10 kb from the transcription start site. Draw a diagram showing how you think the enhanceosome functions to recruit RNA polymerase to the promoter of YFG.

A single mutation in one of the transcription factors in Problem 33 results in a drastic reduction in YFG transcription. Diagram what this mutant interaction might look like.

Diagram the effect of a mutation in the binding site for one of the transcription factors in Problem 33.

Null alleles (mutant genes) produce no protein product. This is a genetic change. However, epigenetically silenced genes also produce no protein product. How does one determine experimentally whether a gene has been silenced by mutation or has been silenced epigenetically?

What are epigenetic marks? Which are associated with heterochromatin? How are epigenetic marks thought to be responsible for determining chromatin structure?

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You receive four strains of yeast in the mail, and the accompanying instructions state that each strain contains a single copy of transgene A. You grow the four strains and determine that only three strains express the protein product of transgene A. Further analysis reveals that transgene A is located at a different position in the yeast genome in each of the four strains. Provide a hypothesis to explain this result.

You wish to find the cis-acting regulatory DNA elements responsible for the transcriptional responses of two genes, c-fos and globin. Transcription of the c-fos gene is activated in response to fibroblast growth factor (FGF), but it is inhibited by cortisol (Cort). On the other hand, transcription of the globin gene is not affected by either FGF or cortisol, but it is stimulated by the hormone erythropoietin (EP). To find the cis-acting regulatory DNA elements responsible for these transcriptional responses, you use the following clones of the c-fos and globin genes, as well as two “hybrid” combinations (fusion genes), as shown in the diagram below. The letter A represents the intact c-fos gene, D represents the intact globin gene, and B and C represent the c-fos-globin gene fusions. The c-fos and globin exons (E) and introns (I) are numbered. For example, E3(f) is the third exon of the c-fos gene and I2(g) is the second intron of the globin gene. (These labels are provided to help you make your answer clear.) The transcription start sites (black arrows) and polyadenylation sites (red arrows) are indicated.

You introduce all four of these clones simultaneously into tissue-culture cells and then stimulate individual aliquots of these cells with one of the three factors. Gel analysis of the RNA isolated from the cells gives the following results.

The levels of transcripts produced from the introduced genes in response to various treatments are shown; the intensity of these bands is proportional to the amount of transcript made from a particular clone. (The failure of a band to appear indicates that the level of transcript is undetectable.)

Using the experimental system shown in Figure 12-26, a geneticist is able to insert a barrier insulator between the white gene and the heterochromatin. The eye phenotype of the transgenic Drosophila would most likely be

Which of the following is an example of post-transcriptional gene repression?