RNAi, PTGS, siRNA, miRNA, shRNA, but not piRNA…that was last time

Biotechnology Chapter 5 Day 2 Questions

  1. What are morpholinos? What would happen if you injected morpholinos into a frog egg?
  2. Discuss how siRNAs can “spread” systemically through a plant.
  3. What is PTGS?
  4. Describe miRNA maturation starting with transcription and ending with binding of an Argonaute protein to the target mRNA(s).
  5. A new category of RNA types is circular RNA. What is the purpose of at least some of these circRNAs?  Describe artificial constructs that can behave functionally similar to circRNAs invented in Phillip Sharp’s lab at MIT before the discovery of circRNA.
  6. Discuss RNA granules. What types of activities are most likely to occur in stress granules and processing bodies (P bodies)?  How can the activities be inferred from protein components of the RNA granules?
  7. Compare the origins of bulged and perfect Argonaute gRNAs. What is the most common functional outcome of these two types of miRNAs?  What is the “seed” region of a miRNA?
  8. Why is using RNAi in elegans so easy compared to D. melanogaster?
  9. Many publications describing siRNA-mediated knockdown of specific genes show the results of experiments using more than one custom siRNA. Why?  How can creating dsRNA from a plasmid in vitro help?
  10. Draw a picture showing the design of a custom shRNA when starting with a miRNA sequence.
  11. Why would the construct shown in figure 5.18 cause long-term knock-down of a target gene’s expression.

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