You are studying the effects of specific transcription factors on the activation of gene expression. You notice that one particular transcription factor binds far away from the promoter of its target gene. What can explain this?

Question

A.  The transcription factor transcribes small RNAs that then bind to the promoter and activate the gene's expression.
B.  The transcription factor tags the enhancer with ubiquitin to stimulate transcription.
C.  DNA looping brings the transcription factor closer to the promoter and initiates gene transcription.
D.  RNA looping brings the transcription factor closer to the promoter and initiates gene transcription.

Clarify Question
· What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

Gather Content
· What do you already know about transcriptional regulation?

Consider Possibilities
· Consider the different answer options. Which can you rule out?

Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
 Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

C.  DNA looping brings the transcription factor closer to the promoter and initiates gene transcription.

Clarify Question
· What is the key concept addressed by the question?
        o This question addresses transcriptional regulation.
· What type of thinking is required?
        o This question is asking you to weigh and judge evidence, or evaluate, to choose the best of the possible answers.
· What key words does the question contain and what do they mean?
        o Transcription factors are proteins that regulate transcription of their target genes.
        o The promoter is the region of the gene just upstream from the transcription start site.

Gather Content
· What do you already know about transcriptional regulation?
        o Transcription is regulated in eukaryotes by transcription factors.
        o Specific transcription factors can bind at the promoter, or at more distant enhancer sites.

Consider Possibilities
· Consider the different answer options. Which can you rule out?
        o Is it likely that the transcription factor transcribes small RNAs that then bind to the promoter and activate the gene's expression? No, because small RNAs would typically inhibit gene expression.
        o Is it likely that the transcription factor tags the enhancer with ubiquitin to stimulate transcription? No, because only proteins are tagged with ubiquitin, to target them for proteolysis.
        o Is it likely that RNA looping brings the transcription factor closer to the promoter and initiates gene transcription? No, because the pre-mRNA is not involved.

Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Is it likely that DNA looping brings the transcription factor closer to the promoter and initiates gene transcription? Yes! This is how distant enhancers are thought to work.
 Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked why a transcription factor might bind far from its target gene’s promoter.
        o The question required you to weigh and judge evidence, or evaluate, to choose the best of the possible answers.
        o Did you recognize that the transcription factor is likely binding an enhancer?
        o Did you know that distant enhancers are thought to work by the looping of the DNA?