Lkelly9 Week 9

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• Lauren M. Kelly
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Questions

• Also revisit model for extra credit, see feedback

1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
   • Graph of Change in Transcription Over Time
2. (Question 6b, p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)

Gene X
1 hour: black
3 hour: dim red
5 hour: black
9 hour: medium green
Gene Y
1 hour: black
3 hour: bright red
5 hour: dim green
9 hour: bright green
Gene Z
1 hour: black
3 hour: dim red
5 hour: medium red
9 hour: medium red

1. (Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
   • Gene X and Gene Y seem to be transcribed similarly. The ratios at each hour are close to each other.
2. (Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
   • Most spots would be yellow at the first time point because the genes are neither being strongly expressed nor strongly repressed. It is not strongly leaning in either direction.
3. (Question 10, p. 118) Go to the Saccharomyces Genome Database and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
   • The color appears to be a light green, therefore it was slightly repressed. As a result of the reduction in available glucose, cell repressed the expression of TEF4 in order reduce the translation of genes that break down glucose.
4. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
   • Instead of glucose, the cell would use ethanol as a source of carbons for the TCA cycle, thus the need for the increase of TCA cycle genes.
5. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
   • In order to ensure that genes for enzymes in a common pathway are induced or repressed simultaneously, the genome could use similar repressors and activators on the genes. In this way, they would react to the environment in similar fashions and be induced or repressed simultanously.
6. (Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
   • TUP1 has been deleted, therefore the cells will not repress the genes that break down glucose. Even as glucose is depleted, the cells will be labeled red, as there is no TUP1 to repress the genes.
7. (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?

3*With Yap1p being over-expressed, the spots will continue to turn red in the later time points of this experiment.

1. (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?
   • You could verify that you had truly deleted/overexpressed these genes by looking at the colors of the chips. The chip for TUP1 would be black, as there is no expression because the gene is deleted. The chip for YAP1 would be red, as the gene continues to be expressed.

Acknowledgements

• Worked with Cameron M. Rehmani Seraji in Seaver 120 on March 22nd.
• Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Lauren M. Kelly 13:34, 14 March 2017 (EDT)

References

• Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124.
• Dahlquist, Kam D. (2017) BIOL398-05/S17:Week 9. Retrieved from http://www.openwetware.org/wiki/BIOL398-05/S17:Week_9 on 14 March 2017.