RNA Editing

Question 1

RNA editing

Answer 1

diverse mechanisms changing the sequence of RNA transcripts encoded by genes in a wide range of organisms
- only eukaryotic

Question 2

Editing vs Splicing

Answer 2

Similarities
- same RNA substrates
- generate protein diversity
- developmental regulation
Differences
- splicing removes sequences
- editing adds/changes information of sequence
- splicing is RNA catalysed/editing is protein catalysed

Question 3

Trypanosoma bruci

Answer 3

• discovery of RNA editing
• kinetoplast DNA (mitochondrial) has maxicircles and minicircles
• maxi circles encode components of oxidative phosphorylation machinery
• found the COII gene contained a unique premature stop codon
• however the RNA sequence had a shifted frame changing the codon
• minicircles contain the information to perform RNA editing

Question 4

What is RNA Editing

Answer 4

• insertion and deletion of uridines can form stop codons, create ORFs, remove stop codons, etc

Question 5

Minicircles vs Maxicircles

Answer 5

minicircles
- encode guideRNA instructin editing
- heterogenous sequences
maxicircles
- encodes mRNA/rRNA

Question 6

Guide RNA

Answer 6

• use wobble base pairing (G-U)
• guide insertions and deletions of uridines
  1. 5’ triphosphate
  2. anchor sequence (base pairs with mRNA)
  3. guiding sequence (directs editing)
  4. 3’poly U tail

Question 7

Mechanism of Trypanosome Editing

Answer 7

1. guide RNA transcribed and added a oligoU tail
2. annealing of gRNA and pre edited RNA
3. endonuclease cleavage at mismatch
4. uridine insertions (TUTase) and deletions (exonuclease)
5. ligation of cleaved RNA

Question 8

Editosome

Answer 8

• 20 proteins and accessories

- contains TUTase, exonuclease, ligase, binding domains

Question 9

Protein Diversity

Answer 9

• Trypanosome editing allows diversity in life cycle stages

- changes activity based on host/developmental stage

Question 10

COXIII Editing

Answer 10

• can generate either COXIII or AEP-1 proteins

- AEP-1 associated with flagellum structure

Question 11

Slimemold

Answer 11

• additions of cytosines/uridines
• additions of GU/CU
• deamination of C

Question 12

Plastids vs Mitochondria

Answer 12

• C to U dominate in both
• plastids only edit mRNA
• lower plastid frequency
• same post transcriptional time

Question 13

Plastid RNA Editing

Answer 13

• PPR proteins recognise sites
• modular RNA binding and mediate organelle gene expression
• deaminase activity

Question 14

Mammalian Editing

Answer 14

• C to U and A to I changes

Question 15

Apolipoprotein B

Answer 15

• lipid transport in circulatory system
• C terminal low density lipoprotein receptor domain
• unedited RNA has longer liver protein
• edited RNA creates stop codon for smaller intestinal protein
• APOBEC1 dimer binds to edit site
• ACF recruited for editing

Question 16

ADAR Enzymes

Answer 16

• class of RNA editing enzymes
• contain dsRNA binding motifs
• convert A to I
• alters specific codons to change amino acids or change stop codons
• specific secondary structure and editing complementary sequence
• ADAR1: primary editor of repetitive site
• ADAR2: non repetitive sites
• ADAR3: inactive and inhibits editing

Question 17

Serotonin Receptor Editing

Answer 17

• editing changes efficiency of signalling
• more editing reduces signalling
• can add 5 adenosines

Question 18

AMPA Glutamate Receptor

Answer 18

• ADAR2
• role in editing specific site in this receptor (GluA2Q)
• lack of editing causes calcium ion influx and mice death
• low editing levels is observed in patients with major depressive disorder

Question 19

Development and Editing

Answer 19

• ADAR1 mutants embryonic lethal

- stem cells have high editing levels

Question 20

Cancer

Answer 20

• ADAR1 down regulation leads to regression of leukemia in mice
• ADAR2 down regulation inhibits proliferation on brain tumors
• ADAR silencing in breast cancer cell lines led to more apoptosis

Question 21

RNA Editing in the Nervous System

Answer 21

• ADAR mutants in worms/flies cause brain related phenotypes
• genes recoded by RNA editing are enriched for neuronal genes
• ALU repeats enriched for neuronal genes and are also heavily edited

Question 22

Brain Evolution

Answer 22

• RNA editing could be driving force
• higher in humans than chimps
• expansion of RNA editing could have increased brain diversity, driving higher cognition

Question 23

Acclimatisation

Answer 23

• editing may be used in cold blooded organisms for temperature change response
• decreases in temperatures increases editing in octopus/flies
• A to G change often results in replacement of large -R group for small one
• smaller residues at promoters reduces activation energies: increases enzyme efficiency at lower temperature
  eg. Dinoflagellates have more editing in response to environmental stressors