mRNA in the cytoplasm (localisation, RNA edit) Flashcards

1
Q

what happens to mRNA in cytoplasm

A

the mRNA is posttranscriptionally regulated by a variety of

ribonucleoprotein complexes

which can influence the fate of mRNA

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2
Q

what is the fate of mRNA

A

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

all three of these things can be regulated

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3
Q

what is a key feature of RNA-BP

A

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

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4
Q

for what process would mRNA localisation be important for?

A

around 71% genes have localised mRNAs

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

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5
Q

describe how molecularly mRNA can be localised?

A

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

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6
Q

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

A

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

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7
Q

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

A

mRNA is expressed all over the cell

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

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8
Q

what is nuclear history?

A

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

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9
Q

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

A

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

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10
Q

how is rate of translation affected by UTR length

A

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

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

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11
Q

what is the exon junction complex?

A

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

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12
Q

why is the EJC important?

A

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

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13
Q

what is nonsense mediated decay?

A

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

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14
Q

how is NMD (faulty mRNA molecule) recognised?

A

if there is an premature stop codon

stop codon occurs before a Exon junction complex

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15
Q

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

A

they undergo degradation by deadenylation-dependent pathway and decapping machinery

this takes place in P-bodies, cytoplasmic foci

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16
Q

how do circular RNAs emerge? What is their function?

A

emerge from backsplicing event

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

17
Q

what is adenosine methylation? what is its purpose?

A

another RNA processing mechanism in eukaryotic cells

acts to regulate development can destabilise mRNA or promote its translation

18
Q

what is RNA editing

A

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

19
Q

what are the main RNA edits?

A

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

20
Q

how can RNA editing affect a mRNA molecule?

A

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

21
Q

what are ADAR1/2? What is their function?

A

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

22
Q

why is ADAR1 mediated RNA editing so common?

??isit adar 1 or adar 2

A

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

proving a platform for ADAR1 to perform its function

23
Q

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

A

3’UTR and introns

24
Q

what biological process is RNA editing useful for?

A

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

this then triggers the interferon response

25
is RNA editing functionally significant?
No... seems to be important for only 2 purposes 1. interferon response 2. correct glutamate receptor subunit (AMPA receptor) but no other known functions
26
describe the epitranscriptome?
dynamic and reversible chemical modifications present on all (nc + coding) RNA transcripts
27
what did epitranscriptome analysis reveal? (bases)
pseudouracil was an identified base and many other modified bases (methylated ribose or nitrogen) were identified on tRNA molecules
28
what are some possible functions of epitranscriptome modifications?
influence tRNA localisation, its loading onto ribosomal site hence rate of translation also quality control for tRNA biogenesis
29
where do most rRNA modifications take place?
occur in the CORE of ribosome so affects tRNA interactions and decoding activity but interactions with Ribosomal proteins are NOT affected
30
what molecules can epitranscript modifications take place?
all RNA molecules mainly tRNA molecules but also ribosRNA and mRNA too
31
how are mRNA molecules modified
instead of pseudouracil, mRNAs can be adenosine methylated > 5' cap methylated > 3' poly A tail modified
32
how can adenosine methylation regulate trannslation?
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
33
what are epitranscriptome changes?
changes to 3'UTR by APA methylation of RNA bases alterations of RNA bases like pseudouracil
34
why is methylation an important regulator of transcription?
demethylases are found in the nucleus so the *nuclear history* can influence the fate of mRNA in the cytoplasm
35
what is the fate of mRNA
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