mRNA in the cytoplasm (localisation, RNA edit) Flashcards
what happens to mRNA in cytoplasm
the mRNA is posttranscriptionally regulated by a variety of
ribonucleoprotein complexes
which can influence the fate of mRNA
what is the fate of mRNA
refers to the localisation, stability and translation of a mRNA molecule
all three of these things can be regulated
what is a key feature of RNA-BP
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
for what process would mRNA localisation be important for?
around 71% genes have localised mRNAs
really important in development to create functional polarised cells like neurons, epithelial, t-cells
describe how molecularly mRNA can be localised?
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
how did we discover oskar mRNA LOACALISATION is important for fly oocyte patterning?
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
what is a key feature of oskar mRNA (in relation to mRNA localisation?
mRNA is expressed all over the cell
but only when its LOCALISED to the posterior pole is mRNA actually transcribed!!
what is nuclear history?
as splicing of first exon and assembly of RNP complexes occur in the nucleus
this can affect the localisation of mRNA in cytoplasm
why is alternative polyadenylation an important process with regards to cytoplasmic mRNA
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
how is rate of translation affected by UTR length
short 3’UTR has high rate of translation/protein synthesis
as there is less likely to be inhibition by RNA-BP
what is the exon junction complex?
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
why is the EJC important?
it was found for oskar mRNA, EJC was essential for correct localisation of the mRNA molecule`
what is nonsense mediated decay?
quality control/surveillance process in which abnormal mRNA molecules can be detected and degraded
how is NMD (faulty mRNA molecule) recognised?
if there is an premature stop codon
stop codon occurs before a Exon junction complex
how are mRNA molecules in cytoplasm naturally degraded (are not abnormal)
they undergo degradation by deadenylation-dependent pathway and decapping machinery
this takes place in P-bodies, cytoplasmic foci
how do circular RNAs emerge? What is their function?
emerge from backsplicing event
they can sequester miRNAs or RNA-BP and involved in cell cycle and diseases
what is adenosine methylation? what is its purpose?
another RNA processing mechanism in eukaryotic cells
acts to regulate development can destabilise mRNA or promote its translation
what is RNA editing
RNA post-transcriptional modification in which RNA bases can be added, removed or substituted
what are the main RNA edits?
+ or - of Uracil residues
C -> U sub = quite rate
A -> I sub = most common
how can RNA editing affect a mRNA molecule?
can alter or create cryptic splice sites
can affect the 3’UTR signals so affect mRNA localisation + stability
what are ADAR1/2? What is their function?
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
why is ADAR1 mediated RNA editing so common?
??isit adar 1 or adar 2
because of the prevelence of ALU sequences in the genome, many d.sRNA regions form
proving a platform for ADAR1 to perform its function
where on the gene body does most RNA editing occur?
A exon
B intron
C 5’UTR
D 3’UTR
3’UTR and introns
what biological process is RNA editing useful for?
good for immune defence to identify d.s VIRAL RNA which are unedited
this then triggers the interferon response
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
describe the epitranscriptome?
dynamic and reversible chemical modifications present on all (nc + coding) RNA transcripts
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
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
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
what molecules can epitranscript modifications take place?
all RNA molecules
mainly tRNA molecules
but also ribosRNA and mRNA too
how are mRNA molecules modified
instead of pseudouracil, mRNAs can be adenosine methylated
> 5’ cap methylated
> 3’ poly A tail modified
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
what are epitranscriptome changes?
changes to 3’UTR by APA
methylation of RNA bases
alterations of RNA bases like pseudouracil
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
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
