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4.E: Genetic Toolkit Exercises

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    Journal Club

    This week's reading is Three Habits of Highly Effective Signaling Pathways

    Reading Guide Questions

    Signaling flips a switch

    1. What are the three habits of signaling pathways?

    2. What is an SPRE and what is it's significance in signaling pathways?

    3. What might be the purpose of experimentally activating a signaling pathway?

    Activator Insufficiency

    4. Define activator insufficiency and zones of competence

    5. How do the authors explain the finding that SPREs are insufficient in vitro, but sufficient in cultured cells?

    Cooperative Activation

    6. What is a signal-independent activator?

    7. What is the purpose of co-activators?

    Default Repression

    8. How do developing organisms solve the problem of leaky expression?

    9. Compare two types of default repression and how signaling releases the repression

    Functional/mechanistic/evolutionary considerations

    10. What role does chromatin modification play in develpmental signal transduction cascades?

    Class Discussion Questions

    Signaling flips a switch

    1. Chose one habit to illustrate with a drawing.

    2. Explain how Notch, Wnt and Hh accomplish transcriptional switching.

    Activator Insufficiency

    3. What do the authors mean when they say that signaling pathways exhibit "selective transcriptional responsiveness of target genes to pathway activity."?

    4. What ways can cells limit the activation of a target gene by an activated signaling pathway?

    Cooperative Activation

    5. What is a potential drawback to cooperative activation?

    Default Repression

    6. Illustrate the different types of default repression

    7. Illustrate one example of default repression

    Functional/mechanistic/evolutionary considerations

    8. Explain Figure 5: how is it a summary of the output of signaling pathway habits?

    9. Explain how Koide et al tested whether default repression is separate from activator insufficiency.

    Group exercise

    This HHMI activity explores the evolution of cis-regulatory elements. You can complete the exercise without watching the suggested movie (available on YouTube and the HHMI website).

    Modeling the Regulatory Switches of the Pitx1 gene in Stickleback Fish

    This page titled 4.E: Genetic Toolkit Exercises is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Ajna Rivera.

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