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#*TUP1p is one of the several repressor proteins that down-regulate glucose-repressed genes in the presence of glucose. In a ∆TUP1 mutant, the TUP1 gene would never be translated, and therefore no TUP1p would be present in the cell. In the absence of this repressor protein, the glucose-repressed genes it impacts would be less dramatically down-regulated, or simply not down-regulated at all if they were solely repressed by TUP1p, in the presence of glucose. Therefore, glucose-repressed genes would be translated at higher than normal rates at t0 and subsequently become exceedingly induced as any lingering repression subsided over the course of the experiment. Thus, glucose-repressed genes that are repressed only by TUP1p would have yellow spots, and glucose-repressed genes that were repressed by other proteins as well would have red spots at the later time points.

#*TUP1p is one of the several repressor proteins that down-regulate glucose-repressed genes in the presence of glucose. In a ∆TUP1 mutant, the TUP1 gene would never be translated, and therefore no TUP1p would be present in the cell. In the absence of this repressor protein, the glucose-repressed genes it impacts would be less dramatically down-regulated, or simply not down-regulated at all if they were solely repressed by TUP1p, in the presence of glucose. Therefore, glucose-repressed genes would be translated at higher than normal rates at t0 and subsequently become exceedingly induced as any lingering repression subsided over the course of the experiment. Thus, glucose-repressed genes that are repressed only by TUP1p would have yellow spots, and glucose-repressed genes that were repressed by other proteins as well would have red spots at the later time points.

# (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?

# (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?

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#*YAP1p is a transcription factor that is known to confer resistance to environmental stress. Therefore, this transcription factor must induce the transcription of genes that confer resistance to environmental stress such as glucose depletion. In a mutant where YAP1 is overexpressed, yeast cells will have abnormally high levels of YAP1p, which in turn will activate the target genes of YAP1 that confer environmental resistance. Thus, genes that respond to glucose-depletion will be active already at t0. In early stages of glucose depletion, the cell will be largely resistant to this stress and up-regulation of YAP1's target genes will occur little if at all, resulting in yellow and red spots. At later time points, the cell will begin to be stressed by the glucose-limited environment and express YAP1 at high rates. This in turn will induce YAP1's target genes, resulting in red spots.

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#*YAP1p is a transcription factor that is known to confer resistance to environmental stress. Therefore, this transcription factor must induce the transcription of genes that confer resistance to environmental stress such as glucose depletion. In a mutant where YAP1 is overexpressed, yeast cells will have abnormally high levels of YAP1p, which in turn will activate the target genes of YAP1 that confer environmental resistance. Thus, genes that respond to glucose-depletion will be active already at t0. In early stages of glucose depletion, the cell will be largely resistant to this stress and up-regulation of YAP1's target genes will occur little if at all, resulting in yellow and red spots. At later time points, the cell will begin to be stressed by the glucose-limited environment and express YAP1 at high rates. This in turn will dramatically induce YAP1's target genes, resulting in relatively bright red spots.

# (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?

# (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?

#*In the case of the ∆TUP1 mutant, successful deletion of TUP1 would result in the absence of any TUP1 transcription products in the cell. Therefore, no cDNA would be created in the experiment that would bind to the TUP1 spot. This spot would consequentially be black, the sign of an inactive gene (as it was deleted).

#*In the case of the ∆TUP1 mutant, successful deletion of TUP1 would result in the absence of any TUP1 transcription products in the cell. Therefore, no cDNA would be created in the experiment that would bind to the TUP1 spot. This spot would consequentially be black, the sign of an inactive gene (as it was deleted).

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#*In the case of the YAP1 overexpression mutant, the expression of YAP1 in response to environmental stress over the course of the experiment would be amplified. Consequentially, YAP1 would be induced at a very high rate by the end of the experiment, resulting in the YAP1 spot being bright red during later time points.

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#*In the case of the YAP1 overexpression mutant, the expression of YAP1 in response to environmental stress over the course of the experiment would be amplified. Consequentially, YAP1 would be induced at a very high rate by the end of the experiment, resulting in the YAP1 spot being bright red during later time points. A different way to verify that YAP1 was overexpressed would be to assess the transcription rates of YAP1's target genes over the course of the experiment. If they remained yellow after initial glucose depletion, then YAP1p was present in higher than normal rates in the cell, indicating an overexpression mutant. If the spots immediately turned red after the initial glucose depletion, this would indicate the normal response of YAP1 (i.e. that a mutant was not created).

==Links==

==Links==

Bklein7 Week 7 - Revision history

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