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Cell Proliferation and Underlying diseases > Eukaryotic Transcription and Gene Regulation > Flashcards

Eukaryotic Transcription and Gene Regulation Flashcards

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1
Q

Types of gene regulation

A 
Transcription 
Translation 
RNA processing 
RNA degradation 
RNA export 
Protein degradation
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2
Q

What are the three classes of RNA polymerase

A

RNA polymerase I
RNA polymerase II
RNA polymerase III

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3
Q

Describe RNA polymerase I

A

for large, ribosomal RNA

- components of ribosomes

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4
Q

Describe RNA polymerase II

A

Transcribes mRNA

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5
Q

Describe RNA polymerase III

A

Transcribes 5S rNA, tRNA and other small RNAs

- Translation of mRNA into proteins

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6
Q

What is the largest subunit in RNA polymerase II

A

Carboxy-terminal domain (CTD) - consists of multiple repeats of heptamers

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7
Q

What does the 5’ untranslated region contain?

A

Signals for translation initiation

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8
Q

What does the 3’ untranslated region contain?

A

Signals for translation termination

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9
Q

What is the direction of transcription?

A

5’-3’

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10
Q

what are the 4 stages of transcription?

A

1) Template recognition
2) Initiation
3) Elongation
4) Termination

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11
Q

What happens in the template recognition phase?

A

RNA polymerase binds to duplex DNA

DNA is unwound at the promoter

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12
Q

What happens during initiation?

A

Chains of 2-9 bases are synthesised and released

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13
Q

What happens during elongation?

A

RNA polymerase synthesise RNA
Unwound region moves with RNA polymerase
RNA polymerase reaches the end of the gene

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14
Q

What happens during termination

A

The RNA polymerase and RNA is released

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15
Q

What are the requirements for transcription?

A

Coactivators - do not bind to DNA but required for activators to interact with basal transcription factors
Chromatin needs to be open before RNA polymerase can bind to the promoter
Basal transcription factors - required by RNA polymerase II to form initiation complex at RNA polymerase II promoters

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16
Q

What is the name of the transcription factors needed for initiation by RNA polymerases?

A

TFIIX

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17
Q

What is a TATA box

A

Common component of RNA polymerase II promoters

~25bp upstream of the startpoint

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18
Q

What is at the start of an RNA polymerase II promoter?

A

Initiator element (initiator Inr)

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19
Q

TATA binding protein (TBP)

A

Component of the positioning factor required for each type of RNA polymerase to bind to the promoter

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20
Q

What is the factor for RNA polymerase II?

A

TFIID

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21
Q

What does TFIID consist of?

A

TBP

Multiple TBP-associated factors (TAFs)

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22
Q

What needs to happen to allow elongation?

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A

TFIIE and TFIIH melt DNA to allow polymerase movement

Phosphorylation of the CTD to promote clearance

23
Q

What is upstream of the transcription start site

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A 
Enhancer region (enhancer factors)
Upstream control element (Upstream factors and inducible factors)
TATA box (general factors)
24
Q

What do enhancers form complexes with?

25
What conformation do enhancers work in?
Cis
26
What is required for enhancer function?
DNA looping
27
What is p53?
A tumour suppressor transcription factor induced by stress
28
What is p68?
An RNA helicase which acts as a co-activator of several transcription factors including p53 Induces cell cycle arrest and apoptosis p53 binds to DNA, p68 binds to p53
29
What happens to the 5' end during transcription
A 5' methylated cap is formed by adding a G to the terminal base
30
What is the function of the cap?
Recognised by protein factors and influences mRNA stability, splicing, export and translation
31
What are the splice site consensus'?
Major introns Minor introns Branch point
32
Explain the splice site consensus of the major introns
5' splice site at the 5' end of the intron which includes a consensus sequence GU 3' splice site at the 3' end of the intron which includes a consensus sequence AG
33
Process of splicing
5' exon is cleaved off Intron lariat formation 3' exon is cleaved off The two exons are ligated together
34
What are the different modes of alternative splicing
- Intron retention - Alternative 5' splice sites - Alternative 3' splice sites - Exon inclusion/ skipping - Mutually exclusive exons - Combinational exon selection - Alternative promoter/ splicing - Alternative polyadenylation/ splicing
35
Types of silencing enhancers and silencers
Intronic splicing silencer Exonic splicing enhancer Exonic splicing silencer Intronic splicing enhancer
36
What is the function of p68 in regards to H-Ras?
suppresses inclusion of the H-Ras IDX alternative exon -
37
What is the effect of suppressing inclusion of H-Ras IDX alternative exon?
Leads to formation of p19H-Ras rather than p21H-Ras
38
What is the function of p19H-Ras?
G1/S delay
39
What is RAS?
an oncogene
40
What does the protein complex contain which cleaves that RNA to generate a 3' end?
Specificity factor Endonuclease poly(A) polymerase
41
What is the function of the specificity factor and the endonuclease?
cleave RNA downstream of AAUAAA
42
What is the function of the poly(A) tails?
Controls mRNA stability and influences translation
43
How can p68 effect introns?
Increase splicing of both random and specific introns to increase cell activity
44
What does the vast majority of the genome transcribe?
Short and long non-coding RNAs (ncRNAs)
45
Describe long non-coding RNAs (lncRNAs)
Spliced and have polyadenylated signals | Tissue specific and development stage specific
46
What is the function of lncRNAs?
Epigenetic regulators of protein-coding expression - transcription - subcellular trafficking - protein degradation
47
Describe siRNA
Generated by DICER cleavage of dsRNA duplexes Incorporated into RNA-induced silencing complexes (RISC) Involved in gene regulation, transposon control and viral defence
48
Describe miRNA
Generated by DICER cleavage of imperfect RNA hairpins Encoded into long primary transcripts, often into introns Incorporated with argonaute proteins into RNA-induced silencing complex (RISC) Involved in post-translational gene regulation
49
What happens if you increase onco-miRNAs?
proliferation and inhibition of apoptosis
50
What happens if you decrease oncosuppressor miRNAs?
Metastasis and migration
51
Define onco-miRNA
If an miRNA represses transcription of a tumour suppressor
52
Define oncosuppressor miRNA
If a miRNA represses expression of an oncogene
53
What is low survival rate of breast cancer patients associated with?
High levels of intron containing p68 RNA

Cell Proliferation and Underlying diseases (12 decks)

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