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Life And Times Of An RNA > Eukaryotic (Whitehouse) > Flashcards

Eukaryotic (Whitehouse) Flashcards

1
Q

In rna pol II’s CTD which 2 serines in the heptad repeat can be phosphorylated, and when do these occur?

A

Serine 5 - at the 5’ end of the gene for initiation

Serine 2 - later in the gene for productive elongation

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2
Q

When does 5’end capping occur?

A

Early in transcription after RNAPII has transcriber 20-25 nts

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3
Q

What enzymatic activities does mammalian capping enzyme (CE) have?

A

RNA triphosphatase

Guanylyltransferase

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4
Q

When is capping enzyme lost?

A

When pSer5 (RNAPII CTD) lost, after > 500 nts transcribed

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5
Q

What are the roles of the 5’ cap?

A 
Increase RNA stability (protection from 5-3 exonucleases)
Increase translation (eIF4F binds cap interacts with 40s ribosome sub)
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6
Q

In splicing, where does the snRNP U1 bind?

A

To the GU sequence at 5’ splice site along with ASF/SF2, U2AF, SF1/BBP

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7
Q

In splicing which snRNPs catalyse transesterification?

And what does this do?

A

U6/U2

Makes 5’ end of intron ligate to an A within the intron form lariat loop structure

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8
Q

What does the spliceosome consist of?

A

snRNPs U1,2,4,5 and 6 and ~125 proteins

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9
Q

What percentage of human multi exon genes are alternatively spliced?

A

Almost 95%

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10
Q

In SMN2 gene alternative splicing what binds in exon 7 and in the down stream intron to prevent exon 7 inclusion?

A

Heterogenous nuclear ribonucleoprotein particle A1 (hnRNP A1)

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11
Q

At what 2 stages do FOX1 & 2 inhibit the spliceosome

A

E’ and E
Block binding of SF to branch point
Block TRA2 and SRP55 binding to exonic splicing enhancers

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12
Q

How do high elongation rates lead to exon skipping

A

Allow simultaneous presentation of strong and suboptimal 3’ splice sites to the splicing machinery

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13
Q

Which 2 complexes are recruited to mRNA in a splicing dependent manner?

A

hTREX (CBP80, Aly, TAP, UAP56, hTHO)

And EJC

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14
Q

The final step of transcription is endonucleolyic cleavage but where does this occur?

A

10-30 nucleotides down stream or AAUAAA polyA signal

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15
Q

What are the core components of the 3’ processing complex?

A 
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

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16
Q

Describe PAP addition of As initially and after PABII binding

A

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

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17
Q

What are the 2 models of 3’ end processing’s role in transcription termination
And which is right?

A

Anti-terminator and torpedo

Combo of both

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18
Q

What complex binds to aberrant short polyA tailed RNAs and what does this initiate?

A

TRAMP

RNA digestion by the exosome

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19
Q

NPCs are freely permeable to what size?

A

<40kDa

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20
Q

What configuration does mRNA adopt when passing through NPCs

A

Dumbbell

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21
Q

The nucleoplasmic entrance of the pore is initially closed by what?
And what causes opening?

A

Basket filaments

To which the mRNP docks and initiates distal basket ring formation

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22
Q

What does non sense mediated decay prevent?

A

Production of truncated proteins that could be deleterious

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23
Q

How to EJCs lead to nonsense mediated decay?

A

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

24
Q

How could EJC enhance transaltion pioneer round?

A

Recruiting enhancer proteins PYM & SKAR onto newly exported mRNA, that enhance ribosome recruitment onto CBP80/20 capped RNA

25
Q

What do the decapping enzymes Dcp1p/Dcp2p lead to?

A

5’-3’ degradation by Xrn1p exonuclease

And removal of cap inhibits eIF4E binding therefore translation

26
Q

What are Pbodies ?

A

RNA-protein granules in which mRNAs complexed with decapping machinery assemble

27
Q

What are the 2 outcomes for mRNA In Pbodies?

A

Degradation by Xrn1p

Re-enter translation

28
Q

What are stress granules?

A

Contain mRNAs and subset of translation initiation factors (eIF4E, 4G,4A) 40S ribosome and PABP.
Also contain RBPs to self aggregate to form granules

29
Q

Where is m6A methylation enriched?

A

Around stop codons 3’UTR and 5’ cap

30
Q

What causes retininis pigementosa?

A

Loss of cones and rosa in retinal pigment epithelium linked to mutations in splicing factor PRP31

31
Q

FTBP-17 is caused by mutations in tau exon 10 that…?

A

Disrupt an exonic splicing enhancer, leads to mis-splicing that leads to aggregation

32
Q

Mutations in PABPN1 cause what?

A

Oculopharnygeal muscular dystrophy

33
Q

The gene linked to ataxia telangiectasia, ATM, encodes what type of enzyme? And what is this essential for?

A

Kinase, essential for p53 activity

34
Q

Where are mutations in beta-globin gene that cause to thalalassemia?

A

Intron 2

35
Q

How can AOs be used to treat thalassemia

A

Block 5’ cryptic splice sites in intron 2 to restore normal splicing pattern

36
Q

What’s the difference between SMN1 gene product and SMN2?

A

SMN2 doesn’t include exon 7 due to a silent mutation that disrupts and exonic splicing enhancer

37
Q

How are KSHV encoded proteins exported if they are not spliced? (They wouldn’t have hTREX)

A

KSHV encodes SR protein ORF57 that recruits hTREX components UAP56, Aly and CIP29

38
Q

How long are miRNAs

A

~22 nt

39
Q

What region of mRNA contains complimentary miRNA targets?

A

3’UTR

Usually in multiple copies

40
Q

What does Lin-4 in c.elegans do?

A

Complimentary to Lin-14 leads to its degradation which is key for larval development

41
Q

What enzyme transcribes miRNA?

A

RNAPII

42
Q

Primary miRNA is cleaved by Drosha but requires what other enzyme?

A

DiGeorfe syndrome critical region in gene 8 protein (DGCR8)

43
Q

Where does drosha cleave ?

A

11bps away from ssRNA stem loop junction on primiRNA

44
Q

What does exportin 5 recognise ?

A

> 14bp dsRNA stem loop with 3’ overhang

45
Q

What does exportin 5 recruit and how does this aid miRNA export?

A

RanGTP, hydrolysis of GTP in cytoplasm releases pre-miRNA

46
Q

What activity does DICER have and what does it do?

A

RNase III

Cleaves 22nt away from pre existing terminus of pre-miR

47
Q

TRBP and PRKRA are associated with what?

A

DICER

48
Q

If there are few mismatches in miRNA: target mRNA what does this cause

A

mRNA cleavage

49
Q

miR-223 roles in myeloid cell development?

A

Expression promoted by PU1 and CEBPB
promotes differentiation of neurotrophils and monocytes by repressing NFA-1
Represses ELF like factor 2 modulate neutrophil differentiation

50
Q

In CLL a region of Chr 13 is deleted, it contains which miRs? And what function do these have?

A

miR-15a and miR-16

Regulate BCL2

51
Q

PTEN and BIM are tumour suppressor and targets of which miR?

A

miR-17-92

52
Q

What orientation to ICP0-a is HIV miR-H2-3p transcribed?

A

Antisense

53
Q

KSHV encodes how many miRs from how many pre-miRs?

A

17 from 12

54
Q

BCLAF1 is targeted by what virus and which miR?

A

KSHV’s miR-K5

55
Q

What type of cancer does miR-let-7 have an effect on and what is the effect?

A

Lung tumours, reduces tumour burdens in mice models

Life And Times Of An RNA (3 decks)

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