Non Coding RNAs

Question 1

Describe in details the biogenesis and maturation of miRNAs, including the genomic localization of miRNA genes and the characteristics of the processing complexes!

Answer 1

• From a miRNA gene to the mature, single-stranded miRNA. Definition of -5p and -3p miRNA.
• Copy number and genomic localization of miRNA genes, relative to each other and to other genes
• Characteristics of the Microprocessor complex: cellular localization, protein components and their functions; the catalyzed reaction, the structural requirements of the RNA substrate.
• Characteristics of Dicer: main domains and their functions. Cellular localization, the catalyzed reaction, the structural requirements of the RNA substrate.
• RISC: role and activities of the Argonaute proteins. How is the miRNA duplex transferred from Dicer to the RISC? What determines the fate of the miRNA strands: guide or passenger?

Question 2

Describe in details the interaction between miRNAs and mRNAs, and the possible consequences! How can this interaction be regulated and altered by the cell?

Answer 2

• How does the Argonaute protein help the miRNA-mRNA hybrid formation?
• What characterizes the miRNA-mRNA interaction, what are the essential interactions and what are the stabilizing, variable interactions? What are the differences between
  plant and animal miRNA-mRNA interactions and their consequences?
• How many miRNA binding sites can be on a mRNA for the same miRNA? Which
  region of the mRNA usually contains the miRNA binding sites?
• What are the characteristics of the P-bodies and the stress-granules? How is
  translation inhibited by the miRNA-mRNA interaction?
• Through what processes can the quantity of miRNAs be regulated? How can the
  sequence of mature miRNAs can be regulated/altered by the cell? How can the cell alter/regulate the miRNA binding sites of a mRNA?

Question 3

Mechanism of X-chromosome inactivation in humans. What are the similarities and differences with the molecular mechanism of HOTAIR-based regulation?

Answer 3

• When is the X-chromosome inactivated during human embryonic development, and what is the difference between the embryonic and extraembryonic tissues? Why is X-chromosome inactivation needed?
• Describe the X-inactivating center (XIC)! Characterize the Tsix, Xist and RepA genes: their genomic localization relative to each other, when they are active, how they are activated and inactivated, characteristics of their gene products, effects, functions.
• What are the similarities and differences with the molecular mechanism of HOTAIR- based regulation?