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

Eukaryotic Transcription and Gene Regulation Flashcards

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?

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

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?

A

Activators

25
Q

What conformation do enhancers work in?

A

Cis

26
Q

What is required for enhancer function?

A

DNA looping

27
Q

What is p53?

A

A tumour suppressor transcription factor induced by stress

28
Q

What is p68?

A

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
Q

What happens to the 5’ end during transcription

A

A 5’ methylated cap is formed by adding a G to the terminal base

30
Q

What is the function of the cap?

A

Recognised by protein factors and influences mRNA stability, splicing, export and translation

31
Q

What are the splice site consensus’?

A

Major introns
Minor introns
Branch point

32
Q

Explain the splice site consensus of the major introns

A

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
Q

Process of splicing

A

5’ exon is cleaved off
Intron lariat formation
3’ exon is cleaved off
The two exons are ligated together

34
Q

What are the different modes of alternative splicing

A
  • 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
Q

Types of silencing enhancers and silencers

A

Intronic splicing silencer
Exonic splicing enhancer
Exonic splicing silencer
Intronic splicing enhancer

36
Q

What is the function of p68 in regards to H-Ras?

A

suppresses inclusion of the H-Ras IDX alternative exon -

37
Q

What is the effect of suppressing inclusion of H-Ras IDX alternative exon?

A

Leads to formation of p19H-Ras rather than p21H-Ras

38
Q

What is the function of p19H-Ras?

A

G1/S delay

39
Q

What is RAS?

A

an oncogene

40
Q

What does the protein complex contain which cleaves that RNA to generate a 3’ end?

A

Specificity factor
Endonuclease
poly(A) polymerase

41
Q

What is the function of the specificity factor and the endonuclease?

A

cleave RNA downstream of AAUAAA

42
Q

What is the function of the poly(A) tails?

A

Controls mRNA stability and influences translation

43
Q

How can p68 effect introns?

A

Increase splicing of both random and specific introns to increase cell activity

44
Q

What does the vast majority of the genome transcribe?

A

Short and long non-coding RNAs (ncRNAs)

45
Q

Describe long non-coding RNAs (lncRNAs)

A

Spliced and have polyadenylated signals

Tissue specific and development stage specific

46
Q

What is the function of lncRNAs?

A

Epigenetic regulators of protein-coding expression

  • transcription
  • subcellular trafficking
  • protein degradation
47
Q

Describe siRNA

A

Generated by DICER cleavage of dsRNA duplexes
Incorporated into RNA-induced silencing complexes (RISC)
Involved in gene regulation, transposon control and viral defence

48
Q

Describe miRNA

A

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
Q

What happens if you increase onco-miRNAs?

A

proliferation and inhibition of apoptosis

50
Q

What happens if you decrease oncosuppressor miRNAs?

A

Metastasis and migration

51
Q

Define onco-miRNA

A

If an miRNA represses transcription of a tumour suppressor

52
Q

Define oncosuppressor miRNA

A

If a miRNA represses expression of an oncogene

53
Q

What is low survival rate of breast cancer patients associated with?

A

High levels of intron containing p68 RNA

Cell Proliferation and Underlying diseases (12 decks)

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