Ribosome profiling (lect 10)

Question 1

What are the advantages of ribosome profiling?

Answer 1

-cells don’t need to be genetically manipulated
-sensitive (can identify low levels of translation)
-quantifiable results
-directly detects changes in protein expression
-gives precise info about positions

Question 2

What are the disadvantages of ribosome profiling?

Answer 2

-difficult to freeze ribosomes in place
-antibiotics can cause artefacts to arise (only inhibits one step!)
-fragments are short in length, making it difficult to identify and map similar sequences
-elongation rate is assumed to be constant (which it is not!)
-assumed that ribosome association will lead to protein (not true either!)

Question 3

Antibiotic that targets translation elongation (used in ribosome profiling)

Answer 3

cycloheximide

Question 4

Antibiotic that targets transition from translation initiation to elongation (used in GTI-seq)

Answer 4

lactimidomycin

Question 5

What assumptions are made in ribosome profiling?

Answer 5

-translation elongation rate is constant
-ribosome association to RNA leads to polypeptide formation