mRNA in the cytoplasm (localisation, RNA edit)

Question 1

what happens to mRNA in cytoplasm

Answer 1

the mRNA is posttranscriptionally regulated by a variety of

ribonucleoprotein complexes

which can influence the fate of mRNA

Question 2

what is the fate of mRNA

Answer 2

refers to the localisation, stability and translation of a mRNA molecule

all three of these things can be regulated

Question 3

what is a key feature of RNA-BP

Answer 3

they are versatile, able to regulate many aspects of mRNA molecule so are multifunctional

and the RNP complexes are dynamic!! they act to coordinate a response

Question 4

for what process would mRNA localisation be important for?

Answer 4

around 71% genes have localised mRNAs

really important in development to create functional polarised cells like neurons, epithelial, t-cells

Question 5

describe how molecularly mRNA can be localised?

Answer 5

protected from degradation - mRNA associates with cytoskeleton

local entrapment - as the cytoplasm is dymamic RNP complexes move and trapped at a site

RNP active transport by transport protein (actin, motorprotein, myosin) so moves to specific locations

Question 6

how did we discover oskar mRNA LOACALISATION is important for fly oocyte patterning?

Answer 6

oskar KO resulted in complete loss of posterior structure

whilst ectopic oskar expression led to posterior duplication and complete abscence of anterior structure

therefore oskar needs to be localised correctly to pattern the embryo

Question 7

what is a key feature of oskar mRNA (in relation to mRNA localisation?

Answer 7

mRNA is expressed all over the cell

but only when its LOCALISED to the posterior pole is mRNA actually transcribed!!

Question 8

what is nuclear history?

Answer 8

as splicing of first exon and assembly of RNP complexes occur in the nucleus
this can affect the localisation of mRNA in cytoplasm

Question 9

why is alternative polyadenylation an important process with regards to cytoplasmic mRNA

Answer 9

APA results in different 3’UTR lengths being created

3’ UTR contain many interaction sites for RNA-BP and so length of UTR influences mRNA location,stabiltiy and translation

Question 10

how is rate of translation affected by UTR length

Answer 10

short 3’UTR has high rate of translation/protein synthesis

as there is less likely to be inhibition by RNA-BP

Question 11

what is the exon junction complex?

Answer 11

protein complex deposited by the spliceosome marking where 2 exons have been ligated together following splicing out of the intron

informs the cell that the mRNA molecule is mature/it has been spliced

Question 12

why is the EJC important?

Answer 12

it was found for oskar mRNA, EJC was essential for correct localisation of the mRNA molecule`

Question 13

what is nonsense mediated decay?

Answer 13

quality control/surveillance process in which abnormal mRNA molecules can be detected and degraded

Question 14

how is NMD (faulty mRNA molecule) recognised?

Answer 14

if there is an premature stop codon

stop codon occurs before a Exon junction complex

Question 15

how are mRNA molecules in cytoplasm naturally degraded (are not abnormal)

Answer 15

they undergo degradation by deadenylation-dependent pathway and decapping machinery

this takes place in P-bodies, cytoplasmic foci

Question 16

how do circular RNAs emerge? What is their function?

Answer 16

emerge from backsplicing event

they can sequester miRNAs or RNA-BP and involved in cell cycle and diseases

Question 17

what is adenosine methylation? what is its purpose?

Answer 17

another RNA processing mechanism in eukaryotic cells

acts to regulate development can destabilise mRNA or promote its translation

Question 18

what is RNA editing

Answer 18

RNA post-transcriptional modification in which RNA bases can be added, removed or substituted

Question 19

what are the main RNA edits?

Answer 19

+ or - of Uracil residues
C -> U sub = quite rate
A -> I sub = most common

Question 20

how can RNA editing affect a mRNA molecule?

Answer 20

can alter or create cryptic splice sites
can affect the 3’UTR signals so affect mRNA localisation + stability

Question 21

what are ADAR1/2? What is their function?

Answer 21

adenosine deaminases catalysing A->I RNA substituion

ADAR1 responsible for non-specific editing on long ds RNA
ADAR2 alters short d.s RNA but this is rare

Question 22

why is ADAR1 mediated RNA editing so common?

??isit adar 1 or adar 2

Answer 22

because of the prevelence of ALU sequences in the genome, many d.sRNA regions form

proving a platform for ADAR1 to perform its function

Question 23

where on the gene body does most RNA editing occur?
A exon
B intron
C 5’UTR
D 3’UTR

Answer 23

3’UTR and introns

Question 24

what biological process is RNA editing useful for?

Answer 24

good for immune defence to identify d.s VIRAL RNA which are unedited

this then triggers the interferon response

Question 25

is RNA editing functionally significant?

Answer 25

No… seems to be important for only 2 purposes
1. interferon response
2. correct glutamate receptor subunit (AMPA receptor)

but no other known functions

Question 26

describe the epitranscriptome?

Answer 26

dynamic and reversible chemical modifications present on all (nc + coding) RNA transcripts

Question 27

what did epitranscriptome analysis reveal? (bases)

Answer 27

pseudouracil was an identified base

and many other modified bases (methylated ribose or nitrogen) were identified on tRNA molecules

Question 28

what are some possible functions of epitranscriptome modifications?

Answer 28

influence tRNA localisation, its loading onto ribosomal site hence rate of translation

also quality control for tRNA biogenesis

Question 29

where do most rRNA modifications take place?

Answer 29

occur in the CORE of ribosome so affects tRNA interactions and decoding activity

but interactions with Ribosomal proteins are NOT affected

Question 30

what molecules can epitranscript modifications take place?

Answer 30

all RNA molecules

mainly tRNA molecules
but also ribosRNA and mRNA too

Question 31

how are mRNA molecules modified

Answer 31

instead of pseudouracil, mRNAs can be adenosine methylated
> 5’ cap methylated
> 3’ poly A tail modified

Question 32

how can adenosine methylation regulate trannslation?

Answer 32

can alter protein-RNA interactions by changing 2nd structure of mRNA which can expose or mask RNA-Binding site

some RNA-BP have high affinity for methylatedA so activity of demethylases can influence this selective interaction

Question 33

what are epitranscriptome changes?

Answer 33

changes to 3’UTR by APA

methylation of RNA bases

alterations of RNA bases like pseudouracil

Question 34

why is methylation an important regulator of transcription?

Answer 34

demethylases are found in the nucleus

so the nuclear history can influence the fate of mRNA in the cytoplasm

Question 35

what is the fate of mRNA

Answer 35

before it becomes traslated

its stability, localisation, transport, interaction with RNA-BP to expose or mask key translation sites/ribosome recruitment, if it becomes degraded or nah