Post-transcriptional regulation of gene expression in eukaryotes

Question 1

There is a … in mRNA to proteome amplification

Answer 1

high degree of variability

Question 2

Describe the relationship between mRNA abundance and protein abundance

Answer 2

• weak
• in C. elegans: r^2 = 0.54
• in H. sapiens: r^2 = 0.13

Question 3

miRNAs - the basics

Answer 3

• microRNAs
• smal,l non-coding RNAs that bind mRNA
• trigger degradation or alter affinity for ribosome

Question 4

Describe the three “key players” in post-transcriptional regulation in eukaryotes

Answer 4

• RBPs
• codon usage bias
• miRNAs

Question 5

RBPs

Answer 5

• RNA binding proteins
• proteins that bind mRNA changing stability and affinity for ribosome

Question 6

Describe codon usage bias

Answer 6

the relative usage of iso-accepting tRNAs

Question 7

miRNAs - the specifics

Answer 7

• lin-4 first to be discovered
• 2600 miRNA genes in human genome
• bind to target mRNAs in a sequence specific manner
• fate depends on where it binds, how it binds, and what proteins get recruited

Question 8

Describe miRNA gene sequences

Answer 8

hairpin loops

Question 9

Binding of miRNAs can cause

Answer 9

degradation or translational inhibition

Question 10

Describe what happens if the miRNA is a perfect match

Answer 10

mRNA degradation

Question 11

Describe what happens if the miRNA is an imperfect match

Answer 11

Translational inhibition

Question 12

miRNAs partially explains why

Answer 12

abundant transcripts can produce little protein

Question 13

Describe the role of miRNAs in defence

Answer 13

• first line of defence against retrotransposons
• let-7
• protect cells against viral infection
  ~2000humanmiRNAstarget 400
  different human viruses
• ~120 human miRNAs predicted
  to target COVID-19

Question 14

List some viruses that miRNAs protect us against

Answer 14

• influenza viruses
• paramyxoviruses
• flaviviruses
• picornaviruses
• (alphaviruses)

Question 15

Describe RBPs - the specifics

Answer 15

• 1500 genes encoding RNA binding proteins in human genome
• least well understood of all regulatory proteins that control gene expression

Question 16

Describe the functions of the RBPs

Answer 16

• processing
• modification
• stability
• translation
• localisation

Question 17

Describe RBPs structure

Answer 17

RNA binding domain

Question 18

Which phenomenon underlies codon usage bias

Answer 18

redundancy - multiple codons encode the same amino acid

Question 19

tRNA molecule structure

Answer 19

• N terminus
• ester bond
• intramolecular base pairing
• anticodon

Question 20

Describe tRNA across species

Answer 20

• different species have different copy number of tRNA genes in genome, and therefore a different abundance in the cell
• measured by anticodon

Question 21

What allows tRNA to bind to multiple codons

Answer 21

deamination of adenine to inosine by hydrolytic deaminase

Question 22

Uracil can base pair with

Answer 22

adenine or guanine

Question 23

What is the effect of the deamination of adenine to inosine by hydrolytic deaminase

Answer 23

• loss of redundant tRNA genes
• no need for tRNA with G in 5’ position of anticodon

Question 24

What is a translationally optimal codon

Answer 24

• the one with most cognate (related) tRNAs
• genes that use a higher frequency of translationally optimal codons make more protein per transcript
• main reason why mRNA abundance is a poor predictor of protein abundance

Question 25

Describe the use of translational optimisation for vaccines

Answer 25

• codon optimising SARS-CoV-2 spike protein for mRNA vaccine
• codon de-optimising SARS-CoV-2: live attenuated vaccine

Question 26

After transcription…

Answer 26

lots of factors extrinsic and intrinsic to the mRNA can effect the abundance of the gene product.

Question 27

The inherent codon use bias of the mRNA determines the encoded gene product abundance.