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1
Q

What does the lncRNA HOTAIR do?

A

Reprograms chromatin state to promote cancer metastasis

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2
Q

Outline the B-DNA structure

A 
Bases are inside with a phosphate backbone
Near perfect symmetry
10bp per turn
3.4nm wide
DNA is normally in this form
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3
Q

Outline the A-DNA structure

A

Found under dehydrating conditions
Larger and wider than B-DNA
11.6bp per turn
3.4nm

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4
Q

What is the RNA World Hypothesis?

A

Developed by Gilbert in 1989, it imagines a world with just RNA, as they can catalyse reactions, self-replicate are involved in important cellular responses and they are required for DNA replication, indicating that RNA came first.

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5
Q

What are the key functions of mRNA?

A

transports genetic information from DNA –> Ribosome
Regulates gene expression
Base Pairing with other NTs thus providing a guide for proteins

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6
Q

What are the key finctions of ncRNA`?

A

Scaffolding and interaction platforms for proteins
RNAs cna be catalytically active
Riboswitches

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7
Q

Name some RNA bindind proteins linked to cancer

A

Sam68, eIF4E, QKI

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8
Q

Name an RNA binding protein that is linked to neurological disorders

A

FMRPI

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9
Q

Which RNA binding proteins are mutated in ALS?

A

FUS and TDP-43

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10
Q

What are RNA recognition motifs made up of?

A

RNP1 and RNP2 folding units which lie on 2 anti-parallel B-sheets.

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11
Q

What is the KH domain?

A

A region in an RNA binding protien which has hnRNP K homology. It consists of about 70 amino acids, alpha helices and beta sheets and interacts with RNA mainly through H bonding

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12
Q

What structural form does dsRNA take?

A

the A form

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13
Q

Do dsRNA binding proteins have a sequence dependent reaction?

A

No

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14
Q

What method did Castello use to identify over 300 RNA binding proteins?

A

He cross-linked the RNA and proteins using UV

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15
Q

What method did they use to identify Pum and Brat co-.activity?

A

They radiolabelled RNA and icnubated it with increasing levels of protein. Which was used to determine the Kd of each. They found that when both Brat and Pum are applied, this gives a higher Kd.

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16
Q

What is the mechanism of Pum/Brat binding?

A

Pum binds removing the secondary structures so that Brat can bind more easily.

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17
Q

What are the advantages of mRNA vaccinations over proteins?

A

Easier to manufacture
Stable over greater temperature ranges
Can cross the BBB

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18
Q

What are the possible uses for mRNA vaccinations?

A 
Infectious disease vaccines
Cancer immunotherapies
Genetic reprogramming through TFs
Allergy tolerization
Genome Engineering
Protein Replaceent and supplementation
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19
Q

What are the key elements of a pol 2 promoter?

A 
Initator element
TATA box
Downstream Promoter Element
BRE
Motif 10
Distal Transcriptional enhancers
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20
Q

Describe the initiator element of pol II promoters

A

It surrounds the start to ensure correct initiation

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21
Q

What is the TATA box?

A

TATAAA sequence, 25-30bp upstream of the start site.

It is not compulsory

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22
Q

What is the BRE in pol2 promoters?

A

TFIIB recognition element

Upstram of the TATA box

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23
Q

What is the MTE in pol2 promoters?

A

Motif 10, is located downstream of the start and can compensate for mistakes in the TATA and DPE

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24
Q

What are the distal transcriptional enhancers?

A

They have a binding role for TFs

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25
Q

How many proteins is pol2 comprised of?

A

12

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26
Q

Where does the active centre lie in pol2?

A

Between the two large subunits Rpb1 and Rpb2

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27
Q

What does TBP do?

A

The TATA binding protein creates a kink in the DNA to facilitate strand melting

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28
Q

What does TFIIF do?

A

It interacts with pol2 and promoter DNA stabilizing their interaction and recruits TFIIE and TFIIH

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29
Q

What does TFIIE do?

A

It melts the DNA

It’s addition converts the PIC to the Elongation Complex

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30
Q

What does the TFIIH do?

A

The Cyclin Acitivating Complex (CAK) phosphorylates the CTD of polII and is very important for capping enzyme recruitment.
The core complex has ATPase and helicase activity for consecutive melting of the DNA and DNA repair

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31
Q

What can the mediator do?

A

Communicate between activators/represors and PolIi

Help polII get round portions of DNA which are looped out

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32
Q

How is directionality regulated in pol II initiation?

A

In the wrong direction you will find polyA close to the promoter leading to cleavage

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33
Q

What are the two models for termination of transcription?

A

The Anti-terminator model - in which the pol2 reaches the polyA stretch and falls off the RNA
The Torpedo model - in which Xrn2 chases polII, and when it catches up it cleaves after the polyA tail

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34
Q

What are the functions of the 5` cap?

A 
Splicing
Protection from exonucleases
3`end processing 
mRNA export
Translation
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35
Q

What are the three enzymes involved in the capping process?

A

Cet1 - RNA Triphosphatase
Ceg1 - Guaninemethyl transferase
Abd1 - Guanine-N7 methyl transferase

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36
Q

When are the capping enzymes recruited to the complex?

A

After synthesis of 20-30nt

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37
Q

How is interaction of the capping enzymes with the elongation complex facilitated?

A

By phosphorylation of the CTD, as Ceg1 binds phospho-Serine5 on he CTD

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38
Q

Why must capping occur so quickly?

A

To protect the mRNA

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39
Q

Which is the 1st post-transcriptional modification?

A

Capping

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40
Q

What does the Cap Binding Complex do?

A

The CBC can bind to the cap to protect it further, this also acts as another QC mechanism

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41
Q

What are the functions of polyadenylation?

A

mRNA export
mRNA stability
Stimulates translation
Gene Regulation

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42
Q

Outline the main complexes involved in poly-adenylation

A 
CPSF
CstF
CFIm
CFIIm
PAP
PABP
Symplekin
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43
Q

What are the components of the poly-adenylation machinery CPSF complex?

A

CPSF-160 - Binds the polyadenylation signal
CPSF - 100 - Binds pre-mRNA
CPSF-73 - Binds and cleaves premRNA
CPSF-30 - Binds U rich sequences
hFip1 - Directs PAP to the correct pa site

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44
Q

What are the components of the CstF complex involved in polyadenylation?

A

CstF-50 - Required for cleavage
CstF-64 - Binds G/U rich downstream elements
CstF - 77 - Required for cleavage

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45
Q

What are the components of the CFIm complex involved in polyadenylation?

A

CFIm 68kDa
CFIm 25kDa
Both help recognize the polyadaenylation signal

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46
Q

What are the components of the CFIIm complex involved in polyadenylation?

A

hClpI - Bridges CPSF with CFIm

hPcfII - Interacts with RNAP 2

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47
Q

What is the function of PAP?

A

The Poly (A) Polymerase adds A to the cleaved pre-mRNA

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48
Q

What is the function of PABP?

A

The Poly (A) Binding Proteins bind and stabilize the poly (A) tail, regulate it’s length and regulate translation.

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49
Q

What is the function of Symplekin?

A

It is a scaffold protein that bridges the individual polyadenylation complexes together

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50
Q

Why do oncogenes often have shorter poly (A) tails?

A

In order to have stronger expression due to loss of negative regulation

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51
Q

Why do mRNAs have differing lengths of poly (A) tails?

A

They act as regulatory elements

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52
Q

What does the PABP nuclear 1 do?

A

It suppresses alternative cleavage and polyadenylation sites.

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53
Q

What is CPEB?

A

The CBE binding protein binds to the cytoplasmic polyadenylation element and recruits varying machinery including CPSF, Symplekin, PARN and GLD2

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54
Q

Where is Ran GAP located?

A

In the cytoplasm

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55
Q

Where is Ran GEF located?

A

In the nucleus

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56
Q

What does the NLS consists of?

A

One or more short sequences of lysines or arginines

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57
Q

What does the NES consist of?

A

4 hydrophobic residues

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58
Q

What are the mRNA export receptors?

A

TAP/p15 and Crm1

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59
Q

What are the mRNA-export adaptors?

A

ALY/REF, SR proteins and ARE binding proteins

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60
Q

What are the factors involved in Ran independent mRNA export?

A

Dbp5/Gle1 and ALY and Tap/p15

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61
Q

Where are snRNAs commonly found?

A

In the splicing speckles of Cajal Bodies in the nucleus

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62
Q

On average how long is an snRNA?

A

about 150 nt

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63
Q

What are snRNAs transcribed by?

A

RNAPII or RNAPIII

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64
Q

What are the functions of snRNA?

A

mRNA processing
Aid in regulation of TFs e.g. 7SKRNA
Help maintain telomeres

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65
Q

What are the two major classes of snRNAs and how are they defined?

A 
Sm-class snRNA - transcribed by polII, 7methylG cap and this includes U1, U2, U4, U5, U7, U11 and U12
Lsm-class snRNA -transcribed by polIII, never leave the nucleus and these include U6 and U6atac
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66
Q

What is the function of the U1 snRNP?

A

Initial recognition of the splice site

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67
Q

What is the function of the U2 snRNP?

A

Creates a bulged A at the branch site

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68
Q

What is the function of U6 snRNP?

A

Forms an active site with U2

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69
Q

What is the function of the U5 snRNP?

A

Contacts the 5’ exon

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70
Q

What are the features of Group 1 intron splicing?

A

Self splicing
Require a guanine phosphate
2 trans-esterification reactions

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71
Q

What are the features of Group 2 intron splicing?

A

Present in all 3 kingdoms
Self splicing - some are aided by proteins
No Guanine mononucleotide required
Branch point often used

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72
Q

What are the features of group 3 intron splicing?

A

Branch point uses 2’OH to attack the phosphodiester bond

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73
Q

Outline the process of spliceosome assembly and function

A
  1. U1snRNP binds to the 5’ splice site
  2. U2 snRNPs are recruited
  3. u4/U6.U5 tri-snRNPs are recruited
  4. Spliceosome activated, U1 aand U4 dissociates
  5. 2 Transesterification reactions
  6. Spliceosome dissociates
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74
Q

What are the features of circular mRNA?

A 
Non-coding
Covalently closed loop 
Can regulate genes
Highly abundant in the brain
High in both colorectal and ovarian cancer
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75
Q

What are the features of usnRNA?

A

TATA less polII promoters
No introns
No polyadenylation
Capped with 7-methylG

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76
Q

How do usnRNAs cross the nucleus?

A

They exit the nucleus unassociated. To enter the nucleus they react with the SMN complex to get a ring of SPNs, the 5’ end is then hypermethylated by TGS, now it enters the nucleus

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77
Q

What are the types of RNA editing?

A

U insertions/deletions
C –> U deadenylation
A –> I deadenylation

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78
Q

Outline the process of Uridine insertion

A

Guide RNAs identif the editing site with the target RNA
ENdonuclease cleaves the target RNA at the editing sit4e
TUTase adds the uridines to the 3’ end of the cleaved RNA fragment
Ligase ligates the two fragments

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79
Q

Outline the process of a Uridine deletion

A

gRNA identifies the editing site in the target RNA
Endonuclease cleaves the target RNA at the editing site
Exonuclease removes the unwated uridines
Ligase ligates the two fragments

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80
Q

Which enzyme is used for C–> deamination?

A

APOBED catalyzes the deamination

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81
Q

What enzyme is used for an A –> I deamination?

A

ADAR protein faimly

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82
Q

Where is me6Adenine common?

A

In 3’ UUTRs and near stops

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83
Q

Which RNAp transcribes rRNA?

A

RNAP I

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84
Q

Which RNAP transcribes tRNA?

A

Pol III

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85
Q

Which RNAP transcribes mRNA?

A

Pol II

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86
Q

What are the 6 main factors of an RNAP I gene?

A 
Enhancer
Upstream Core Element (UCE)
Core Element
TFiB
Upstream Binding Factor (UBF)
TTF1
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87
Q

What does the TFiB do in RNAP I genes?

A

It is required for recogniiton

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88
Q

What does the UBF do in RNAP I genes?

A

It binds the upstream core element and the core element

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89
Q

What does TTF1 do in RNAP1 genes?

A

It stops RNAP

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90
Q

Outline the intiation process for pol 1

A
  1. TFiA associates with RNAP when phosphorylated
  2. UBF associates with UCE and recruits SL1 (TFiB)
  3. UBF binds DNA so SL1 and core come into contact
  4. Pol 1 binds the UBF/Sl1 through TFIA
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91
Q

Outline the three different states for rRNA genes

A

Completely Off - these can not be switched back on, as the UCE is methylated and a Nucleosome covers the core element

Off - These can be switched on, as there is no methylation at the UCE, however the Nucleosome covers the core element

On - These are transcriptionally active genes, with the nucleosome being located inbetween the UCe and core elements

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92
Q

What is the switch between different rRNA gene states?

A

TTF1 binds and recruits a chromatin remodelling enzyme which brings the nucleosome to it’s binding site thus switching genes on

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93
Q

What does the ribomotor do?

A

Facilitates release and re-initation of RNAp1

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94
Q

Outline a basic RNAPII rna

A

Enhancer
Promoter
gene
Poly A sequence

95
Q

Outline the three types of RNAP III genes

A

Type 1 - Has an A and B internal regulatory element
Type 2 - Has an A and C internal regulatory element
Type 3 - Has a distal element, a promoter specific element and a TATA box

96
Q

Which type of RNAP III genes does TFIIIA act on?

A

Type 1 genes

97
Q

Which type of RNAP III gene does TFIIIC act on?

A

Types 1 and 2

98
Q

Which types of RNAP III genes does TFIIB act on?

A

All three types

99
Q

Outline the prokaryotic RNAP structure

A

It is a crab claw shape made up of 2 alpha, beta, beta prime and omega subunits

100
Q

Can RNAP1 perform simultaneous transcription?

A

Yes you can have up to 100 on 1 gene, with ribosome assembly taking place as the rRNA is made

101
Q

Can RNAP 2 perform simultaneous transcription?

A

No only one on one gene

102
Q

What is a transcription factory?

A

An area within the nucleolus or nucleoplasm which has a high density of transcription

103
Q

Which chromosomes are (partially) located in the nucleolus?

A

Y, 1, 9, D and G

104
Q

Where are the rRNA genes located?

A

On 5 acrocentric chromosomes, 13, 14, 15, 21 and 22 known as nucleolus organising regions

105
Q

What are the three layers of the nucleolus?

A

Granular centre
Dense Fibrillar Centre
Fibrillar Centre

106
Q

Where are inactive genes located in the nucleolus?

A

The fibrillar centre

107
Q

Where are active genes located in the nucleolus?

A

Dense fibrillar centre

108
Q

Where does ribosome assembly take place in the nucleolus?

A

Granular Centre

109
Q

What is UBF?

A

An important nucleolus distinguishing factor as it is only present there

110
Q

What are the three types of mRNA decay?

A

Deadenylation dependent decay
Deadenylation independent decay
Endonuclease mediated decay

111
Q

Outline the process of deadenylation dependent decay

A
  1. The poly(A) tail is removed by PARN or CCR4/NOT
  2. The mRNA is decapped by Dcp1/2
  3. The mRNA is degraded by Xrn1
    OR
  4. The mRNA is degraded by the exosome
  5. The cap is scavenged by DcpS
112
Q

What are the two exonucleases involved in mRNA decay?

A

Xrn 1 - cytoplasmic

Xrn 2 -Nucleic

113
Q

What is the exosome?

A

A 3’ –> 5’ exoribonuclease involved in mRNA decay, QC and trimming

114
Q

What are the 6 proteins that form the ring of the Exosome?

A

Rrp 41 - Rrp 45
Rrp 46 - Rrp 43
Rrp 42 - Mtr 3

115
Q

What are the three proteins that form the exosomes cap?

A

Rrp 4
Cs 14
Rrp 40

116
Q

What are the three regulators of the exosome?

A

TRAMP Complex
SKI Complex
NEXT Complex

117
Q

What is the TRAMP complex?

A

A nuclear enzyme which guides the exosome to particular nuclear RNAs to degrade them

118
Q

Outline the structure of the TRAMp complex

A

Air 1/2 = RNA binding protein
Trf 4/5 = Poly (A) polymerase - made to attract exosome
Mtr 4 = RNA Helicase

119
Q

What is the SKI complex?

A

A cytoplasmic enzyme which guides the exosome to particular RNAs to degrade them

120
Q

What is the mechanism of the NEXT complex?

A

It binds to the CBC and takes the mRNA in the nucleus to the exosome

121
Q

Outline deadenylation independent decay

A

It starts from the 5’ end
Rare
Decaps with Dcp1/2 then degrades with Xrn1

122
Q

Outline endonuclease dependent decay

A

Endonuclease cuts it into two
Exosome and Xrn1 degrade the pieces
DcpS scavenges the cap

123
Q

What does PARN do?

A

Poly(A) ribosomal nucleasecan bind to the 5’ cap and remove the nt from the poly(a) tail

124
Q

How does translation reduce deadenylation?

A

When RNA is bound by initiation factors 4E and 4G it reduced the interaction between PARN and the mRNA

125
Q

What is he product of deadenylation?

A

5’-adenosine monophosphates

126
Q

What are the three different methods for deadenylation?

A

PAN2/3 complex binds to the PABPC
CCR4/NOT complex
PARN

127
Q

What factors protect the cap from decapping?

A

eIF4E and eiF4G

128
Q

What enzymes are required for decapping?

129
Q

What does DcpS do?

A

It scavenges gthe cap

130
Q

What are P-bodies

A

Cytoplasmic domains that contain proteins involved in the post-transcriptional process, where decapping enzymes are found

131
Q

What shape is the secondary structure of tRNA?

A

Clover leaf

132
Q

Where are the key regions on tRNA?

A 
14, 15, 16 - DHU Loop
34, 35,36 - Anticodon
37 - Hypervariable site
44, 45, 46 - Variable Arm
54, 55, 56 - TpseudoU C loop
74, 75, 76 - ACC Post transcriptional addition
133
Q

What shape is the teritary structure of tRNA?

134
Q

What are Hoogster pairs?

A

Triples that form in the tertiary structure of tRNA to stabilize the L-shape

135
Q

What helps stabilize the tertiary structure of tRNA?

A

Hoogster pairs

Co-axial stacking

136
Q

What is the Wobble Base Hypothesis?

A

That mRNA codon positions 1 and 2 undergo standard watson-crick base pairing but the third position wobbles.

137
Q

How is an aa transferre to a tRNA?

A

The aa is activated onto the aminoacyl-tRNA synthase. Then the tRNA is charged

138
Q

What is the Double Sieve model?

A

A QC mechanism performed by aminoacyl-tRNA synthase, which the aa is first checked by the activation site which discards anything to big, then the swinging arm dumps it onto the editing site which discards anything too small.

139
Q

What rRNA is in the 50S prokaryotic ribosomal subunit?

A

23S and 5S

140
Q

What rRNA is in the 30S prokaryotic ribosomal subunit?

141
Q

What rRNA is in the 60S eukaryotic ribosomal subunit?

A

28S in humans

142
Q

What rRNA is in the 40S eukaryotic ribosomal subunit?

A

18S in humans

143
Q

What do Chloramphenical, erythromycin and ricin target?

144
Q

Outline the process of eukaryotic ribosomal biosynthesis

A

rDNA is converted to 35S prerRNA which is converted to a 90S pr-ribosome along with RPs which is then converted to a 60S pre-ribosome and a 44S pre-ribosome which are then converted into the respective 60S ribosomal subunit and the 40S ribosomal subunit

145
Q

How many times roughly is the rDNA gene repeated?

A

about 150-200

146
Q

What are the RNA cleavage factors?

A

Endonucleases - Not1, 17RR, Rnt1

Exonucleases -Rat 1, XRN1, Exosome

147
Q

What are the ribosomal biogenesis factors?

A 
ATPases
DEAD Box helicases
Kinases
GTPases
RNA chaperones
Export Factors -Crm1 and Ran
148
Q

Where does ribosomal biogensis quality control occur?

A

In the nucleus

149
Q

How can ribosomal biogenesis act as a stress sensor?

A

If ribosomes can’t form then ribosomal proteins are just free, these inhibit Mdm 2 which activates p53 which causes a decrease in cell proliferation

150
Q

What do Müller Bodies show in S. cerevisae?

A

That there rRNA processing and ribosome assembly occurs co-transcriptionally

151
Q

What is the SSU?

A

the processosome of he small unit causing RNA cleavage

152
Q

What is snR30?

A

The conformational switch in pre-ribosomes

153
Q

Does ribosome assembly occur gradiently or indepedently?

A

There is evidence for both
Gradiently would mean that ribosome assembly would stop if a factor was not present, thus slowing down.
Independently means that if a factor was not presen, assembly would continue then the ribosome would need to be degraded

154
Q

What does RIcin do?

A

It is a toxin that reduced translation to 15% leading to cell death by cleaving adenine in 25/28S rRNA

155
Q

What do ribosomopathies tend to affect?

A

Cell development and proliferation

156
Q

Name two ribosomopathies

A

Diamond blackfin anaemia

Treacher Collins Syndrome

157
Q

What is the aim of nonsense mediated decay?

A

To eliminate transcripts that contain premature stop codons

158
Q

What can cause PTC?

A

Incorrect splicing, incorrect initiation, t-cell receptors and Ig

159
Q

What are the proteins involved in NMD?

A

Upf1, Upf2, Upf 3

160
Q

When phosphorylated does this activate or inactivate Upf1?

161
Q

How is the PTC detected in yeast?

A

Hrp1 recognises downstream sequence elements and associates. The Ribosome can sense if it has passed a DSE or not also the ribosome can sense the distance to Pab1 which is bound to the poly(A) tail

162
Q

How is the PTC detected in mammals?

A

The ribosome detects whethere thare are more exon-exon junction complexes (EJc), in most cases these do not exist after the true termination codon

163
Q

Outline the mammalian mechanism of NMD

A

erF1/3 associates with the ribosome, Upf 2/3 is bound to the EJc.
The SURF complex (Upf1 and Smg1) binds to erF1/3 at the PTC, if there is a further EJc it detects this by interactind with Upf2/3.
The mRNA is then degraded

164
Q

What are the three quality control pathways?

165
Q

Outline the process of NSD

A

Non-stop mRNA decay, causes the ribosome to stall when a termination codon is missing

166
Q

Outline NGD

A

When the ribosome gets stalled it is normally due to a secondary structure. Dom34 and Hbs1 recognise these structures and the mRNA is cleaved here and degraded

167
Q

What is the main function of snoRNA?

A

Guide chemical modifcations to tRNA, rRNA and snRNA

168
Q

What type of cap does snoRNA have?

A

A tri-methyl cap

169
Q

What is snoRNA transcribed by?

170
Q

Describe the three possible genomic organsizations for snoRNA?

A

Can sit in introns of genes
Can form clusters of snoRNAs
Can be individual genes

171
Q

What are the 2 classes of snoRNAs?

A

Box H/ACA snoRNA -U –>

Box C/D snoRNAs - 2’O methylation

172
Q

What are the proteins involved in a box H/ACA snoRNP?

A

NHP2, NOP10, Dyskenin, GAR

173
Q

What are the proteins involved in a box C/D snoRNP?

A

2 x 15.5K, 2x NOP 56/55, 2 x fibrallarin

174
Q

Where are snoRNAs transported after pre-assembly?

A

Cajal Bodies

175
Q

HWat are Cajal Bodies?

A

Areas within the nucleus that contain coilin.

176
Q

What are scaRNAs?

A

snoRNAs that are located in cajal bodies, they ahve a cajal body box for localization

177
Q

What are orphan snoRNAs?

A

They don’t have a specific complementary sequence therefore have no partner

178
Q

What does Df31 andorphan snoRNAs do?

A

Maintain accesible higher order structures of chromatin

179
Q

What is Prader-Willi syndrome?

A

Mental retardation caused by the loss of HBII-85 C/D box snoRNA

180
Q

What is telomerase?

A

An RNA-protein complex

181
Q

What does Teleomerase reverse transcriptase (TERT) do?

A

It can use telomerase DNA to make telomerase RNA

182
Q

What is special about the structure of TERT?

A

Half of the structure appears like a H/ACA snoRNA

183
Q

How big are lncRNAs?

184
Q

Where can you find lncRNA genes?

A

In known gene loci, inrons, a divergent promoter or itnergenic

185
Q

What are the classes of lncRNA?

A

Signal
Decoy
Guide
Scaffold

186
Q

Why do lncRNA moleules make good signals?

A

They show time and cell specific expression
They are responsive to a diverse range of stimuli
They have a tightly ontrolled expression pattern
Quick as much easier to make than a protein

187
Q

What do signalling lncRNAs do?

A

they control levels of downstream genes

188
Q

How does X-chromosome inactivation work in humans?

A

Xist lncRNA, made from the X inactivation centre interacts with the polycomb repressive complex 2 (PRC2) to cause DNA compaction of a random X chromosome

189
Q

What does Tsix doe?

A

It causes antisense repression of Xist thus keeping the X chromosome active

190
Q

How do Drosophila hyperactivate the X chromosome on a male fly?

A

roX attracts MSL protein complex which causes H4K16ac opening the DNA

191
Q

Outline the H19/Igf2 model of lncRNA gemonic imprinting

A

In the maternal gene the CTCF interacts with the unmethylated ICR, activating H19 gene
In the paternal gene the ICR is methylated so Igf2 is active

192
Q

Outline the Kcnq model of lncRNA genomic improtinting

A

In the paternal gene Kcnqot1lnc RNA is procued blocking expression
In the maternal gene, the allele is methylated thus the lncRNA is not produced and the gene is expressed

193
Q

Outline UV damage mediated activation of lncRNAs

A

Upon UV damage p53 is activated which causes transcription of linc-p21 which interacts with hnRPK to cause p53 mediated gene repression. p53 causes PANDA transcription which inhibits NF-YA causing cell apoptosis and it activated the gene CDKN1A which causees the creation of p21 which causes cell cycle arrest.

194
Q

Outline the COLDAIR model of temperature mediated lncRNA activation

A

In hot conditions the FLC gene is active, with COOLAIR RNA being produced.
When it is COLD the lncRNA COLDAIR is produced which recruits PRC2 to suppress the FLC gene.
Affter cold exposure the FLC gene continues to be repressed due to the recruited PRC2 complexes

195
Q

What is the function of 6S RNA?

A

It acts as a decoy by mimicking an open promoter thus sequestering bacterial RNAP

196
Q

How is the DHFR promoter represed?

A

By the lncRNA disrupting the PIC

197
Q

Outline the functions of HOTAIR

A

It acts as a gude by guiding the PRC2 complex to HOXD on chromosome 2, thus suprressing it by methylation on K27.
It acts as a scaffold by the 5’ end binding to the PRC2 complex and the 3’ region binding to the LSD1-CoRES-REST complex causing silencing of the target locus

198
Q

What are the cytoplasmic functions of lncRNA?

A 
miRNA decoys e.g. PTENP1
mRNA degradation e.g. guide mRNA to STAU1
mRNA stability
Translation disruption
miRNA site masking
199
Q

What is the function of TINCR?

A

It is essential for epidermis differentiaion. It forms a complex with STAU 1 to stabilize their differentaion mRNAS

200
Q

What are enhancer RNAs?

A

RNAs produced from the enhancer region which can alter gene function.

201
Q

What are the functions of enhancer RNA?

A

chromatin looping

chromatin remodelling

202
Q

Outline the Diele-Alder rreaction

A

Conjugated Diene + Alkene –> Cyclohexene system

203
Q

What are hammerhead ribozyymes?

A

They can self vleave and are common in viruses to splice their own RNA

204
Q

Describe the GlmS Ribozyme/Riboswitch

A

Found in prokaryotes it is required for glucosamin-6-P metabolism, it acts asa riboswitch to change the environment creating a ribozyme

205
Q

How long is siRNA?

A

21 nt with a 2nt 3’ overhang

206
Q

How does siRNA work?

A

It is chopped up by dicer then one strand is loaded into RISC which then links it to the complementary RNA, mRNA is the cleaves and destroyed

207
Q

How do off target effects occur with siRNA?

A

One strand is taken randomly
Inhibition of unrelated mRNAs due to complementarity
Partially complementary siRNAs can act as miRNAs

208
Q

What increases the chances of off target effects with siRNA?

A

High concentration and low sequennce specifity

209
Q

What do the argonaute proteins do?

A

Here the target RNA can be cleaved whilst the siRNA is left untouched.
They are aessential catalytic components of the RISC complex

210
Q

What are RNA dependent RNAPs?

A

They use RNA as a primer to create a complementary strand, they can create a second wave of siRNAs however they are not found in mammals, only in speicies in which long ds RNA is not toxic

211
Q

How does miRNA guided gene silencing work?

A

Dicer cleaves, asymmetry is sensed, argonaut and chaperones bind and 2 strand is removed

212
Q

Why are the 3’ UTRs of pseudogenes conserved?

A

They acts as sponges for miRNAs in cancer

213
Q

Outline the ping pong cycle

A

piRNAs recognise their target, recruit PiWi protein, cleave the target 10nt from 5’piRNA to create secondary piRNAs

214
Q

What can riboswitches and aptamers regulate?

A

mRNA stability
Translation
transcription

215
Q

What happens to activate a riboswitch?

A

A metabolite binds that changes the structure of RNA

216
Q

How do riboswitches regulate translation?

A

If the shine-dalgarno switch is located on a secondary structure it makes it difficult for the RNAP to bind, thus when a riboswitch is activated which straightens out this region it makes it easier for RNAP to bind

217
Q

What are the three main regions of a riboswitch?

A

The Aptamer domain - binds metabolite
The switching sequence
the expression platform

218
Q

What are the 2 types of riboswitches?

A

Type 1 -has a small change in structure

Type 2 - has a global change in structure

219
Q

What is the 3-state folding mechanism for riboswitches?

A

It is used in order to give robustness over a large temperature
Each stage has a different Kd

220
Q

What is the function of 7sk snRNA?

A

It binds Hexm proteins whicha re sponges for pTEF-b thus 7sk snRNA inbhibits transcription by trapping the pTEFb in a large structure

221
Q

Briefly describe the structure of 7sk snRNA

A

It has 4 extended hairpins which act as binding docks fr proteins

222
Q

Which proteins bind to 7sk snRNA?

A

Hexim 1/2, hnRNPs, LARP7

223
Q

Where does the La protein bind?

A

To all short poly (U) stretches

224
Q

What does the La protein do?

A

It binds the 3’ end of polII transcripts and supports correct folding

225
Q

How does pTEFb work?

A

It phosphorylates the 1st serine of the CTD of pol II, causing the nTEFs NELF and DSIF to dissociate

226
Q

What do Alu, B1, B2 ncRNAs do?

A

They directly inhibit RNAP II

227
Q

What is the function of 7SL RNA?

A

It is key for protein translocation

228
Q

Briefly describe the structure of 7SL snRNA

A

It has the Alu and S domain

It has extended hairpins at both ends

229
Q

Which proteins bind to eukaryotic 7SL RNA?

A

SRP9/14, SRP 68/72, Srp19 and SRP54

230
Q

What do the SRP proteins consist of?

A

A G domain which has GTPase activity and an M domain which binds to the signal peptide

231
Q

Outline the process of translocation from the cytoplasm to the ER

A
  1. SRP 54 recognises the signal peptide
  2. The other end of the 7SL snRNA binds the ribosomes binding pocket to stop further translation
  3. It binds the SRP slpha receptor which in turn binds to the docked SRPbeta receptors.
  4. The ribosome is then attached to the translocon and the RNA passed through
232
Q

What are the subunits of the eurkayrotic translocon?

A

Sec 61 beta, Sec 61 alpha and Sec61 gamma

233
Q

What proteins are involved in prokaryotic translocation?

A

the ffH protein acts similarly to SRP54
the HBsu protein acts similarly to SRP 19
The SRP receptor = Ftsy

234
Q

What are the subunits of the prokaryotic translocon?

A

SecA, Sec Y, Sec E and Sec G

RNA Biology (1 decks)

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