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BMB > Post-transcriptional control of gene expression > Flashcards

Post-transcriptional control of gene expression Flashcards

1
Q

RNA purification for RNA:protein ints

A
  • synthesise biotinyllated oligo
  • incubate with proteins
  • recover RNA:protein complexes with streptavidin beads
  • detect bound proteins by WB
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2
Q

Protein purification for for RNA:protein ints

A
  • analogous to ChIP: purify protein with RNAs using antibodies
  • generate cDNAs from mRNAs using reverse transcriptase
  • detect cDNA of interest by PCR
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3
Q

Cross-linking RNA and proteins for RNA:protein ints

A

stabilise ints by crosslinking with UV light

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4
Q

3 parts of eukaryotic mRNA processing

A

5’ capping
removal of introns (splicing)
3’ polyadenylation

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5
Q

function of mRNA 5’ cap

A

increase splicing efficiency
need for export to cytoplasm
need for efficient translation initiation
protect mRNA from 5’ exonucleases

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6
Q

5’ cap formation

A
  • remove terminal phosphate from DNA 5’ end by RTPase (RNA terminal phosphatase)
  • GMP transferred from GTP by RNA guanylyl transferase (RGTase), gives G5’ppp5’N
  • guanine is methylated by RNA-(guanine-N-7)-methyltransferase. = cap 0. further mods in mammals
  • RTPase and RGTase are part of same polypeptide in multicellular orgs

early, cotranscriptional event
nuclear cap bound by CBC, cap-binding complex

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7
Q

specificity of 5’ capping

A
  • all and only pol II transcripts
  • only di-/ tri- phosphate ends
  • cotranscr, by factors associated w pol II CTD
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8
Q

pol II a CTD

A
  • heptad tandem repeats
  • residues that can be phosphorylated
  • close to RNA exit channel of pol II
  • initiation: dephosph
  • elongation: early S5 phosph, later S2 phosph
    CTD = landing platform for cotranscriptional factors
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9
Q

experiment that shows pol II CTD needed for capping

A
  • cells transfected witha version of amanitin resistant RNAP II
  • one version has normal length CTD, one version has fewer repeats
  • inhibit endogenous RNAP II with amanitin (so see activity of mutant only)
  • quantify capped and uncapped mRNAs
  • fewer capped mRNAs produced with mutant CTD than WT
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10
Q

2 experiments to show capping enzymes associate w phosphorylated pol II CTD

A

1
pass nuclear extract thr affinity column, WT CTD/ mutant CTD/ phosphorylated CTD
- measure capping act in each of samples retained
- only retained in column w phosph CTD

2
fission yeast: make CTD that cannot be phosph at S5, replace endogenous gene w mutant - no cell growth
fuse mammalian capping enzyme to CTD - rescues mutation

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11
Q

5’ cap structure

A

N7 methyl guanosine, attached to mRNA 5’ through 5’-5’ triphosphate bond

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12
Q

pol II transcription termination

A

doesn’t terminate at precise positions

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13
Q

evidence for run-on transcription

A

incubate nuclei with NTPs + radioactive UTP. RNAs are completed, cleaved and hybridised to DNA probes spaced along the gene and downstream regions
==> radioactive signal continues downstream of mature 3’ mRNA end, signal decreases in 5’ to 3’ direction

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14
Q

structure of polyA tail

A

many A residues, shortened as mRNA ages so linked to RNA decay

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15
Q

functions of polyA tail

A

protection from 3’ exonucleases, control degradation rate, need for transcr initiation

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16
Q

cis sequences needed for polyadenylation

A

AAUAAA upstream of cleavage site

U// GU rich DSE downstream of cleavage site

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17
Q

how was polyadenylation shown to occur in 2 stages

A
  • cleavage needs AAUAAA, 10 As are added

- polyA doesn’t need AAUAAA but does need 10 As, longer polyA tail added

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18
Q

2 stages of polyadenylation

A
  • cleavage

- polyadenylation

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19
Q

trans factors needed for polyadenylation

A
  • CPSF = cleavage polyadenylation specificity factor, binds AAUAAA and CStF, need for both cleavage and polyadenylation
  • CStF = cleavage stimulation factor, binds GU/ U, need for cleavage only
  • polyA polymerase adds A residues, also need for cleavage
    (identified by MS)
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20
Q

evidence that 3’ end processing is cotranscriptional

A

mutant CTD cells are defective in 3’ end processing

CPSF and CStFbind CTD in affinity columns

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21
Q

example of alternative polyadenylation

A

Sex-Lethal (SXL) in drosophila: RBP expressed only in females, regulates polyadenylation

target: e(r), has 2 alternative polyadenylation sites. males use first site, females use second
females: SXL binds e(r) premRNA and competes w CStF for binding first GU element - so second site used. in males, CStF binds proximal site.
importance: female specific 3’ UTR has transcriptional repression sequences so e(r) not produced.

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22
Q

genome-wide view of polyadenylation

A
  • high throughput seq: fragment RNAs, purify fragments w polyA, sequence and identify those w boundary betw polyA and gene sequence
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23
Q

3’ end processing assay

A

incubate RNA substrate with nuclear extracts and ATP

  • presence of ATP:cleavage, polyA
  • ddATP: cleavage but not polyA
  • RNA that mimics cleaved substrate is polyAed.
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24
Q

discovery of splicing: R loop analysis

A
  • hybridise mRNA to dsDNA in conditions that favour RNA:DNA interactions, 1 DNA strand displaced = R loop
  • visualise by EM: can distinguish single vs double strands by width
  • use on adenovirus DNA: mRNA had tails protruding on both ends. 3’: polyA, 5’ unexplained
  • 5’ anneals the mRNA from a separate part of the genome, mRNA=composite
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25
Q

cis elements for splicing

A
  • 5’ splice site consensus
  • most introns start w GU and end with AG (GU/AG rule)
  • 3’ end: branch point consensus with conserved adenine, polypyrinidine tract downstream of branchpoint
    3’ splice site = YAG
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26
Q

trans factors for splicing

A

snRNPs = smalll nuclear RiboNucleoProteins: RNA associated w protein, RNA = functional
U1 snRNP: basepairs with 5’ splice site
U2 snRNP: basepairs with branchpoint
U2AF: U2 auxiliary factor (protein). large 65 subunit binds polypyrimidine tract, 35 subunit binds 3’ splice site.

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27
Q

splicing: mutations

A

mutation within consensus sequence can inactivate splicing/ use cryptic splice sites
mutation outside of consensus - no effect
5’ SS/ branchpoint mutations can be reversed by complementary mutations in U1/ U2 = evidence for base pairing

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28
Q

in vitro analysis of splicing

A
  • synthesise splicing substrate (2 exons, 1 intron)
  • incubate radiolabelled RNA w nuclear extracts, ATP
  • take samples at intervals, analyse RNA by denaturing electrophoresis, autoradiography
    debranching - normal migration of previously circular intermediates
    see product acc over time
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29
Q

chemistry of splicing

A

2x transesterification

  • 2’ hydroxyl of A of branchpoint attacks phosphate at 5’ of intron, 5’ exon released and lariat formed
  • 3’ hydroxyl of 5’’ exon attacks phosphate at 3’ of intron. exons are ligated, intron released as lariat. lariat then degraded.
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30
Q

splicing code

will a splice site be used?

A

splicing enhancers and repressors form splicing code, regulates efficiency of splice site usage

introns often contain regulatory sequences as well as core splice sites

will a splice site be used?

  • strength - similarity to consensus
  • enhancers/ repressors with bound proteins
  • RNA secondary str
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31
Q

alternative splicing - why?

A

pairing dif combos of splice sites - tissue specific/ developmental specific differences
- regulation of gene expr
- different protein isoforms
most human genes

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32
Q

alternative splicing: drosophila SXL

A

SXL expressed in females but not males: include exon 3 in males, includes a stop codon so no SXL produced.
skip exon 3 in females so can produce ful length protein
exon 3 = ‘poison exon’
so control gene expression

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33
Q

alternative splicing: drosophila DSCAM

A

many mutually exclusive exons
38k possible isoforsm (more than drosophila genes!)
protein variability for recognition of specific neurones

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34
Q

splicing and genetic disease

A

many genetic conditions causes by mutations affecting splice sites, eg inactivation/ generating new, regulatory regions
eg HGPS: a silent point mutation activates a cryptic splice site, creates a protein with a deletion lacking a protease cleavage site, incorrectly processed.

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35
Q

splicing: ATP

A

actual chemistry: no ATP needed as number of phosphodiester bonds conserved.
ATP needed for spliceosome assembly

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36
Q

translation cycle - what happens in each stage

A

initiation - recognise initiation codon … up to first peptide bond formation
elongation - formation of all peptide bonds
termination - release of polypeptide, ribosome dissociation

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37
Q

stages of translation cycle

A
  • small subunit then large associates with mRNA
  • can associate without mRNA, dissociation factor binds and prevents this reassociation to form an inactive complex. (IF3/ e-IF3) - released in initiation
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38
Q

tRNA binding sites of ribosome

A

A: aminoacyl-tRNA
P: peptidyl-tRNA
E: exit from ribosome

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39
Q

what is needed for prokaryotic translation initiation (7)

A
  • mRNA with RBS
  • ribosomes
  • initiator tRNA
    3 IFs:
  • IF1: bind A site, prevent tRNA access
  • IF2: complexes with initiator tRNA and GTP
  • IF3: dissociation factor
  • GTP
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40
Q

prokaryotic translation initiation

A
  • IF1 and IF3 bind the 30S subunit, this then binds mRNA at the RBS
  • IF2 forms a ternary complex with GTP and charged initiator tRNA. joins the 30S, forming 30S initiation complex
  • 50S joins, GTP hydrolysis by IF2 and all IFs released. 70S initiation complex
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41
Q

prokaryotes - initiator tRNA

A

formyl methionine tRNA

42
Q

experiment to identify translation initiation sites - prokaryotes

A
  • bind ribosomes to mRNAs, elongation inhibited
  • digest unprotected mRNA with RNase
  • isolate and sequence the protected fragments
43
Q

in vitro evidence for base pairing between the SD and 16S rRNA

A
  • radiolabel an RNA fragment containing initiation codon , incubate with ribosomes, initiation factors, initiator, with initiation allowed but elongation inhibited.
  • treat with SDS (denatures proteins but doesn’t affect RNA:RNA ints)
  • non denaturing gel electrophoresis
    labelled RNA comigrates with 16S rRNA
44
Q

in vivo evidence for base pairing between the SD and 16S rRNA

A

compensatory mutations in 16S rRNA suppress mutant SD
eg: hGH gene under constitutive promoter w mutant SD
E coli 16S pre-rRNA gene under control of heat shock promoter, with complementary mutation and resistant to spectinomycin.
- 37C: no hGH, mutated SD nonfunctional
- 42C: get hGH, must be due to mutant 16S rRNA
spec: inhibits WT 16S rRNA

45
Q

polycistronic mRNAs: prokaryotes

A

possible to recognise multiple RBS on a simgle mRNA as recruitment is direct

46
Q

locations of factors - early initiation translation

A

P site: initiator

A site: blocked by IF1

47
Q

locations of factors - late initiation translation

A

P site: initiator

A site: empty, ready to accept first aa-tRNA

48
Q

locations of factors - elongation translation

A

P site: peptidyl-tRNA
A site: next aminoacyl-tRNA, tRNA paired to next codon to be translated
initiator is only aminoacyl-tRNA to enter P site

49
Q

basic steps of translation elongation - prokaryotes

A
  • aminoacyl-tRNA binds A site
  • peptide bond formed as polypeptide transferred from P site to aminoacyl-tRNA of A site
  • ribosome translocation
    deacylated tRNA ejected through E site
50
Q

translation factors - prokaryotic elongation

A

EF-Tu - brings aa-tRNA to A site
EF-G - need for translocation
EF-Ts - recycling of EF-Tu

51
Q

binding of aminoacyl-tRNA to A site

A
  • EF-Tu binds GTP and aa-tRNA, gives ternary complex
    this binding masks aa-tRNA, prevents from reacting with peptidyl-tRNA
  • ternary complex into A site. incorrect codon-anticodon match: release ternary complex w/o GTP hydrolysis
    correct match: GTP hydrolysis and release of EF-Tu GDP. aminoacyl can now move towards peptidyl-transferase centre (accomodation)
52
Q

peptide bond formation - translation

A

accomodation - aminoacyl and peptidyl ends brought together, catalysed by 50S peptidyl transferase activity

53
Q

translocation - prokaryotic translation

A

ribosome moves 3 nts along - needs EF-G-GTP. can only bind if the ternary complex has been ejected ie the peptide bond has been formed
GTPase needed for translocation

54
Q

translation termination prokaryotes

A 
release factors recognise termination codons, induce hydrolysis of peptide chain
class I: direct recognition of term codon (RFI, RF2)
class 2: RF3, binds ribosome with GDP, GTP replaces GDP, conformational change, relase of RFs (?)
55
Q

importance of GTP hydrolysis for translation

A

GTP hydrolysis needed for correct order/ fidelity of process, rather than being coupled to chemical modifications
eg EF-Tu conformation changes between GTP and GDP bound forms, only the GTP-bound form can bind aa-tRNAs and mask the amino acid.

56
Q

Ribosome structure

A

Core = RNA, stabilise through ints with peripheral proteins and base pairing
A, P, E located between both subunits
23S: peptidyl transferase = ribozyme

57
Q

structural view of translation termination

A

RFs mimic tRNA shape, one domain induces peptidyl-tRNA hydrolysis, one domain recognises termination codon, via a tripeptide called the peptide anticodon.

58
Q

translation initiation site consensus features

A
  • AUG start codon

- Shile-Dalgarno seq = RBS = AGGAGG, complementary to 3’ of 16S rRNA

59
Q

translation initiation - prokaryotes - model

A

SD pairs with complementaryregion of 16S rRNA, identify initiation codon. fMet-tRNA anticodon pairs with AUG

60
Q

regulating translation initiation - prokaryotes (6)

A
  • similarity of SD to consensus
  • translational coupling
  • proteins
  • temp (thermosensors)
  • small ncRNAs
  • small molecules (riboswitches)
61
Q

regulating translation initiation - prokaryotes - repressor proteins, MS2 example
experiment

A

MS2 coat protein binds replicase gene initiation site w high affinity, stabilising a stem loop which represses initiation of translation
so replicase only translated during early infection, not once coat protein accumulated.

62
Q

regulating translation initiation - prokaryotes - translational coupling
eg MS2

A
  • polycistronic mRNAs: sometimes ribosome initiation of a downstream codon is dependent on translation of an upstream cistron.
    eg MS2 - secondary str around SD of replicase gene needs to be unwound by ribosomes translating the coat protein gene (upstream) for accessibility
63
Q

regulating translation initiation - prokaryotes - secondary structures

A

bacteriophage MS2 mRNA

  • coat protein gene: SD folded into secondary str
  • mutations carried out which stabilised or destabilised the secondary structure without changing SD
  • fraction of unfolded mRNA corrleates with translation efficiency, so SD accessibility important
64
Q

thermosensors

A

secondary structures which block SD access and are temp sensitive

65
Q

2 types of transcription termination - prokaryotes

A

rho dependent, rho independent

66
Q

rho dependent transcr term

A

Rho binds a C rich region, translocates along RNA until it reaches the polymerase and induces dissociation.
a hairpin delays RNAP so rho can reach it.

67
Q

rho independent transcr term

A

GC rich hairpin, 6xUs

hairpin causes polymerase pausing, U-A RNA:DNA pairing is weak so dissociate

68
Q

attenuation

eg?

A

way to repress gene expression with premature termination of transcription
relies on transcription and translation being coupled
eg for amino acid biosynthetic operons
trp operon

69
Q

riboswitches

guanine-binding riboswitch

A
  • control gene expression in response to small molecules via attenuation or translational control
  • eg guanine binding riboswitch - highly specific binding of guanine, controls attenuation: w guanine, a terminator is formed, so there is premature termination of transcription.
70
Q

at which stage is translation in bacteria mostly regulated

A

initiation

71
Q

eukaryotic vs prokaryotic translation (6) 3 similarities, 3 differences

A

generally similar

  • start codon
  • initiator tRNA
  • small ribo subunit binds first
  • euk - larger ribosomes
  • initiation very different, more complex in euk
  • eukaryotes need both GTP and ATP, prok only need GTP
72
Q

eukaryotic vs prokaryotic translation initiation

A

prok: small subunit binds SD and initiation codon
euk: small subunit binds cap, scans mRNA until first initiation codon

73
Q

initiation in eukaryotes - scanning model

A

43S binds methylated cap, scans to 3’ and first AUG is initiation codon. 60S joins, elongation starts

74
Q

evidence for scanning model - eukaryotes

A
  • initiation at new AUGs inserted betw cap and actual
  • stable secondary str between cap and AUG inhibit translation
  • cap needed: low efficiency of uncapped/ cap analogue mRNAs
75
Q

mechanism of translation initiation - eukaryotes

A

cap binding complex on 5’ end of mRNA
joined by 43S initiation complex
forms 48S initiation complex

76
Q

43S initiation complex

A

40S ribosome subunit, initiation factors, initiator tRNA

77
Q

cap binding complex

A

eIF4F - cap recognition. contains eIF4A, a helicase, and eIF4E, recognises cap. eIF4G
eIF4B then joins cap and stimulates eIF4A activity

78
Q

scanning - eukaryotic translation initiation

A
  • ribosome translocation
  • unwinding of RNA secondary structure - by helicase, needs ATP
    GTP is hydrolysed once the AUG is recognised, eIFs are released.
79
Q

role of polyA in translation

A

polyA coated in PABP: polyA Binding Protein

interacts with eIF4G, causes mRNA to have a circular conformation which stimulates translation

80
Q

internal initiation

A

picornaviruses - uncapped mRNA with many AUGs and secondary str - mRNA translated by direct ribosome binding to an internal ribosome entry site, IRES

some picornaviruses inactivate host cap-dependent protein synthesis

81
Q

evidence for internal initiation

A

dicistronic reporter experiment - insert part of viral 5’ UTR (contains IRES) between 2 cistrons, can drive internal initiation of downstream cistron

82
Q

why must eukaryotic mRNAs be monocistronic?

A

since ribosomes scan from 5’ cap and detach at termination, cannot access downstream cistrons.

83
Q

global regulation of translation in eukaryotes: eIF2a phosphorylation

A

eIF2-GDP needs recycling to the GTP bound form by a GEF, eIF2B
phosphorylation of eIF2a sequesters eIF2B in a comlex, so eIF2 cannot be recycled, translation initiation is blocked globally

84
Q

global regulation of translation in eukaryotes: eIF4E-eIF4G interaction

A

eIF4E binds cap, recruits eIF4G - interaction modulated by 4E-binding proteins - compete with 4G
their binding affinities are regulated by phosphorylation

85
Q

gene specific regulation of translation in eukaryotes: RNA binding proteins

A

one protein binds 3’ UTR: specificity. one protein binds the cap and one bridges the others. this forms a loop which blocks translation by inhibiting eIF4F recruitment.

86
Q

RNA degradation - how

A
  • cap and polyA tail normally protective from exonucleases - start by removing one of these
    eg polyA nucleases shorten polyA.
    then can get decapping and 5’-3’ degr, or 3’-5’ degr

3’-5’ - degradation by the exosome
redundancy of pathways

87
Q

RNA degradation - why

A

keeping mRNA levels constant requires a balance between transcription and decay
removal of defective RNAs

88
Q

transcript specific regulation of RNA decay - factors

A

cis elements often in 3’ UTRs

trans factors - sequence specific RBPs/ miRNAs

89
Q

how to measure the half life of an mRNA

A
  • block transcription - changes in mRNA levels are due to degradation only
  • follow mRNA changes with a time course
90
Q

mRNA localisation - why/ how

A

to specific subcellular compartments, causing asymmetric localisation of encoded proteins. eg need for embryogenesis, yeast differentiation

91
Q

determining mRNA localisation with FISH: ASH1

A
  • incubate fixed cells with flourescently labelled probe complementary to the mRNA, observe by fluorescence microscopy
92
Q

determining mRNA localisation with cis elements: ASH1

A
  • make reporter with ASH1/ control 3’ UTR

- folow localisation by FISH and probe complementary to reporter seq

93
Q

localisation of B-actin mRNA: in vivo tagging

A
  • tag mRNAs by adding MS2 coat protein binding site

- MS2 protein fused to GFP expressed, binds MS2 binding site on mRNA, follow in vivo by fluorescence microscopy

94
Q

3 types of eukaryotic small regulatory RNAs

what protein do they work with?

A

miRNA
siRNA
piRNA

argonaute family

95
Q

biogenesis of miRNA

A
  • transcribed as long precursors by pol II
  • cleaved by nuclease drosha
  • export to cytoplasm, further cleavage by dicer
  • miRNA loaded onto RISC (contains argonaute proteins), passenger strand is degraded and guide kept
96
Q

biogenesis of siRNA

A
  • from dsRNA precursors, eg generated from viral infection, also when exogenous RNA introduced in RNAi
  • cleaved by Dicer and loaded onto RISC
97
Q

regulation of gene expression by miRNA and siRNA

A

siRNA: base pairs with target mRNA, leads to endonucleolytic cleavage and decay of target
miRNA: causes translational repression

98
Q

genome wide view of translational control - ribosome profiling

A
  • measuring translational rates for every mRNA in the cell
  • mRNAs can be translated by multiple ribosomes at a time, the number of ribosomes estimates efficiency of translation
  • purify mRNA with ribosomes
  • use a ribonuclease which degrades all mRNA except fragments protected by ribosome binding
  • sequence protected fragments, map to genome
  • number of protected fragments corresponding to an mRNA reflects how many ribosomes are bound, so how efficiently mRNA is being translated
99
Q

identifying RBP binding sites: CLIP

A

analogous to ChIP, RNA and proteins are crosslinked using UV light, purify the protein of interest with antibody, analyse by deepseq and map to genome

100
Q

functional stidies of RBPs (splicing)

A

splicing sensitive DNA microarrays: have probes for exon-exon and exon-intron junctions so can quantify frequency of each splicing event.

101
Q

exonucleases vs endonucleases

A

exo - decreade from ends

endo - cut in the middle

102
Q

how to block transcription

A
  • RNAP II inhibitor
  • ts mutants of RNAP II components
  • clone gene of interest in with regulateable promoter

BMB (5 decks)

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