Bio 340: Problem Set 11 Name:

TA:
1. Transcriptional regulation in eukaryotes is controlled by both cis- and trans-acting
elements. The following structure was isolated from honey bees. It shows such
elements as well as parts of a gene body indicated with relative positions. The arrow
denotes the transcription start site (the drawing is not in scale).

Figure 1

1) Indicate what the elements or segments, number 1, 2, 3 and 4, are most likely to stand for.
1: Exon, a coding sequence of the gene
2: A trans-acting factor, a transcription factor, or a TATA-binding protein (RNA
polymerase is not a good answer)
3. Promoter (TATA-box or promoter region is OK)
4: (Upstream) enhancer sequence/element; cis-acting element is acceptable

2) Which numbered segments can interact with trans-acting factors?

Enhancers (4) and Promoters (3) can interact with trans-regulatory factors

3) Which numbered segments are cis-acting elements?

3 and 4

2. Next, you create several mutated DNA sequences; each by deleting segment 1, 3 or
4. You mix each manipulated DNA fragment with RNA polymerase and other
nuclear factors isolated from honey bees, as well as nucleotides to start out the
transcription reaction in a test tube. You make sure that element number 2 is
present in the mix. You incubate each mutated DNA sequence and control DNA
(nothing mutated) in separate tubes in the laboratory. Later, you terminate the
reaction and measure the level of mRNA transcripts from the isolated gene. What
would you expect to find, relative to the control DNA reaction?

1) If segment 1 was deleted

A partial transcript

2) If segment 3 was deleted

No transcript

3) If segment 4 was deleted

Reduced amounts of transcript

1
Bio 340: Problem Set 11 Name:
TA:
4) If you forgot to add element number 2 to one of the tubes
No transcript

3. Gal4-UAS is a yeast transcriptional system that has been adopted to modulate gene
expression in eukaryotic model animals

1) Redraw figure 1, and indicate where you would insert a UAS DNA sequence to drive
increased expression of the honey bee gene in the presence of Gal4 protein
Upstream of the promoter

2) Your instructor tells you that the Gal4-UAS system would have little effect as a driver of
gene expression in bacteria. Why would that be true?
Answer must link Gal4 function to chromatin, and to that bacteria do not have chromatin.

4. You want to knock down the gene in figure 1 using RNA interference. Describe
briefly how you would do such an experiment on honey bees and why the procedure
would result in reduced mRNA and protein amounts for this gene.