Dramir36 Week 6

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Purpose

1. To learn about how DNA microarray experiments work.
2. To reason through some DNA microarray analysis problems.
3. To discuss a case where standards of research ethics were violated.

Questions

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.

Dramir36 Change in Transcription2.jpg

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: medium 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

3. (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?

Genes Y and Z were transcribed similarly.

4. (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?

There is no previous time period for the genes to compare to at the first time point. The genes have no effect at the first time point since the genes have not had a chance to either be induced or repressed, which is why most spots are yellow, indicating no change of gene expression.

5. (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).

TEF4 was repressed because the spot became more of a green color. TEF4's change in expression is repressed because glucose may be needed by TEF4 to begin the transcription process, and when the glucose was being reduced, less TEF4 was not being used as often.

6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?

When glocose is running out, there is an increase in products of alcohol dehydrogenase which are converted into acetyl-CoA, which enters the TCA cycle.

7. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

Transcription factors regulates a large amounts of genes, so when the TFs is induced, the genes are induced as well, and the same happens when TFs are repressed. Genes change their expression levels as a group, and when energy metabolism genes are induced, protein production genes are repressed.

8. (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?

The glucose-repressed genes would be induced resulting in red spots because there is no presence of TUP1 to repress those genes, letting them activate.

9. (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?

Since Yap1p is overexpressed, there is an increased resistance to environmental stresses. This will result to red spots in the target genes because they have a resistance to a glucose depleted environment.

10. (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?

If there are is an activation of glucose-repressed genes early on in the experiment, then that shows that TUP1 has truly been depleted because there is no repression for those glucose-repressed genes. Having a continuous or increased presence of genes that are supposed to be repressed in a glucose depleted environment will indicate that YAP1 is truly overexpressed.

Acknowledgments

  • I would like to thank Dr. Dahlquist for assisting me in answering any questions I had about the format of this web page.
  • I communicated with my homework partner Michael Armas after class and through text outside of class to discuss any questions we had about the assignment questions.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Dramir36 (talk) 23:46, 9 October 2019 (PDT)

References

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