This is an article review and below are the instructions ( basically questions to respond after reading the article):
Answer the following questions about the article below. These questions focus on the introduction and results beginning from the bottom of page 149 (Figures 3, 4, and 5).
Pircher, A., Bakowska-Zywicka, K., Schneider, L., Zywicki, M., and Polacek, N. (2014) An mRNA-derived noncoding RNA targets and regulates the ribosome. Molecular Cell 54, 147-155. (click on reference for active hyperlink)
1. The Summary states that “an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome.” Explain the difference between an mRNA and an ncRNA in this context.
2. Figure 3A shows the overall growth of yeast in high salt conditions, each with different combinations of DNA expressed in the cell.
a. Describe each of the 4 treatment groups shown in Figure 3A. What DNA is being expressed in each? Why were each of these DNA sequences tested?
b. What is the interpretation of the results in Figure 3A? Be specific about how the sum of ALL of the data lead to this conclusion.
3. Explain how 35S-Met was used in the experiment shown in Figure 4. How is detection of this radioactive molecule used in Figure 4B?
4. Explain the purpose of including cycloheximide (CHX) in the experiments shown in Figures 4 and 5. Be specific regarding the effect of CHX and the reason it was used in terms of experimental design.
5. The authors concluded that the 18-mer ncRNA inhibited translation initiation.
a. What specific figure panel do you think is the most direct evidence of this? Explain your answer.
b. Answer this based on your own knowledge of translation initiation and not based on the paper: what is one way that you could envision a ncRNA interrupting the translation initiation process?
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