Eukaryotic (Whitehouse) Flashcards
(55 cards)
In rna pol II’s CTD which 2 serines in the heptad repeat can be phosphorylated, and when do these occur?
Serine 5 - at the 5’ end of the gene for initiation
Serine 2 - later in the gene for productive elongation
When does 5’end capping occur?
Early in transcription after RNAPII has transcriber 20-25 nts
What enzymatic activities does mammalian capping enzyme (CE) have?
RNA triphosphatase
Guanylyltransferase
When is capping enzyme lost?
When pSer5 (RNAPII CTD) lost, after > 500 nts transcribed
What are the roles of the 5’ cap?
Increase RNA stability (protection from 5-3 exonucleases) Increase translation (eIF4F binds cap interacts with 40s ribosome sub)
In splicing, where does the snRNP U1 bind?
To the GU sequence at 5’ splice site along with ASF/SF2, U2AF, SF1/BBP
In splicing which snRNPs catalyse transesterification?
And what does this do?
U6/U2
Makes 5’ end of intron ligate to an A within the intron form lariat loop structure
What does the spliceosome consist of?
snRNPs U1,2,4,5 and 6 and ~125 proteins
What percentage of human multi exon genes are alternatively spliced?
Almost 95%
In SMN2 gene alternative splicing what binds in exon 7 and in the down stream intron to prevent exon 7 inclusion?
Heterogenous nuclear ribonucleoprotein particle A1 (hnRNP A1)
At what 2 stages do FOX1 & 2 inhibit the spliceosome
E’ and E
Block binding of SF to branch point
Block TRA2 and SRP55 binding to exonic splicing enhancers
How do high elongation rates lead to exon skipping
Allow simultaneous presentation of strong and suboptimal 3’ splice sites to the splicing machinery
Which 2 complexes are recruited to mRNA in a splicing dependent manner?
hTREX (CBP80, Aly, TAP, UAP56, hTHO)
And EJC
The final step of transcription is endonucleolyic cleavage but where does this occur?
10-30 nucleotides down stream or AAUAAA polyA signal
What are the core components of the 3’ processing complex?
CPSF (binds AAUAAA) CtsF (binds downstream U/GU rich DSE as a dimer) CF Im (binds UGUA as a dimer)
PAP and CF IIm associate transiently
Describe PAP addition of As initially and after PABII binding
Adds around 12 As at a slow rate to 3’ OH generated by cleavage
Then binding of PABII to short polyA tail accelerates rate of addition
After 200-250 As PABII signals PAP to stop
What are the 2 models of 3’ end processing’s role in transcription termination
And which is right?
Anti-terminator and torpedo
Combo of both
What complex binds to aberrant short polyA tailed RNAs and what does this initiate?
TRAMP
RNA digestion by the exosome
NPCs are freely permeable to what size?
<40kDa
What configuration does mRNA adopt when passing through NPCs
Dumbbell
The nucleoplasmic entrance of the pore is initially closed by what?
And what causes opening?
Basket filaments
To which the mRNP docks and initiates distal basket ring formation
What does non sense mediated decay prevent?
Production of truncated proteins that could be deleterious
How to EJCs lead to nonsense mediated decay?
If there is a premature stop codon >55 nts upstream of EJC
UPF1 and SMG1 bind to EJC associated UPF2, this triggers UPF1 phosphorylation and NMD by translational repression and RNA degradation
How could EJC enhance transaltion pioneer round?
Recruiting enhancer proteins PYM & SKAR onto newly exported mRNA, that enhance ribosome recruitment onto CBP80/20 capped RNA
