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Genes, Genomes and Biomedical Implications > Post-Transcriptional Regulation > Flashcards

Post-Transcriptional Regulation Flashcards

1
Q

What is RNAPII involved in?

A

capping, splicing and polyadenylation coupled to transcription

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2
Q

What does phosphorylation of the CTD of RNAPII do?

A

release RNAPII from the promoter to start RNA elongation which allows different sets of proteins to bind for capping, splicing and polyadenylation

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3
Q

What is mRNA capping?

A

5’ to 5’ addition of GMP to the 5’ end of the RNA transcript

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4
Q

When is the capping reaction started?

A

when an RNA is synthesised to ~25nt

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5
Q

What are the roles of capping?

A
  • signals translation initiation by ribosome binding
  • ensures correct processing and export of mRNA through binding a cap binding complex
  • stabilises and protects 5’ end of mRNA from degradation
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6
Q

What are the 3 steps of capping?

A
  1. phosphatase removes a phosphate from 5’ end of primary transcript
  2. guanylyl transferase adds a GMP in a reverse linkage (5’-5’ instead of 3’-5’)
  3. methyl transferase adds a methyl group to the guanosine
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7
Q

What are all 3 enzymes for RNA capping associated with?

A

the CTD

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8
Q

What are the 3 splicing consensus sequences?

A
  • 5’ GU - donor site
  • 3’ CAG - acceptor site
  • branch point - loose consensus
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9
Q

What are the 2 basic steps of RNA splicing?

A
  1. join the 5’ end of intron to a branch point A to form a lariat loop
  2. cut the 3’ end of intron and join the 2 exons
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10
Q

What type of reaction happens in RNA splicing?

A

transesterification

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11
Q

What are the 5 snRNAs and what are their functions?

A
  • U1 - recognises 5’ splice site
  • U2 - initial binding to branch site
  • U4 - sequesters U6
  • U5 - brings 2 exons together
  • U6 - catalyses 2 transesterification reactions with U2
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12
Q

How are snRNPs formed?

A

each snRNA is complexed with more than 7 protein subunits

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13
Q

What does the spliceosome do?

A
  • recognise the intron splice sites
  • bring the two ends of the exon together
  • remove the intron
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14
Q

What are the 4 steps of RNA splicing?

A
  1. U1 forms base pairs with the 5’ specific junction and the BBP and U2AF recognises the branch-point site
  2. U2 displaces BBP and U2AF and forms base pairs with the branch-point site consensus sequence
  3. U4/U5-U6 triple snRNP enters the reaction and once the U4/U6 base pairs are separated, U6 displaces U1 at the 5’ splice junction which creates the active site that catalyses the first phosphoryl-transferase reaction
  4. additional RNA-RNA rearrangements create the active site for the second phosphoryl-transferase reaction, which then completes the splice site
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15
Q

What does U1 RNA contain?

A
  • several distinct stem-loop domains
  • 8 core Sm proteins and 3 U1-specific proteins
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16
Q

What are Sm proteins?

A

8 common proteins constituting the core structure of snRNPs

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17
Q

What is Sm binding site required for?

A

interaction with common snRNP proteins

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18
Q

What is recognition of consensus sequences important for?

A

to ensure the accuracy of the position for RNA splicing

19
Q

What are the 2 common types of splicing errors due to imperfect RNA pairing?

A
  • exon skipping
  • cryptic splice-site selection
20
Q

How can splicing errors be minimised?

A
  • coupling splicing to transcription to avoid exon skipping
  • exon definition
21
Q

What is the exon definition hypothesis?

A

the exon is bound by a group of SR proteins that serve as splice enhancers; they recruit U1 and U2 to define 3’ and 5’ exons respectively

22
Q

What are SR proteins?

A

proteins rich in Ser and Arg

23
Q

How are introns packaged into complexes?

A

by hnRNPs (heterogenous nuclear ribonucleoproteins)

24
Q

What does abnormal processing of the β-globin primary RNA transcript in humans produce?

A

aberrant β-globins causing β-thalassemia disease

25
Q

What are consequences of aberrant splicing?

A
  • deletion or addition of amino acid sequence
  • change of reading frame
  • truncated protein due to premature termination codon
26
Q

What does differential RNA splicing do?

A

increase product diversity

27
Q

What are products of differential splicing?

A
  • C-terminal truncation due to a premature termination codon
  • change of reading frame
  • missing of an internal part
  • differential translation start sites
28
Q

What are ways to generate multiple proteins from the same gene?

A
  • alternative promoters but producing the same protein
  • overlapping genes using different reading frames
  • different N-termini using alternative promoters
29
Q

Where is the polyadenylation termination signal?

A

10-30 nt before the polyA tail

30
Q

What are the 5 steps of transcriptional termination?

A
  1. CstF and CPSF travel with RNAPII during transcription
  2. CPSF binds to the polyA signal and CstF binds to GU/U rich region
  3. cleavage occurs with additional cleavage factors to create 3’ end
  4. PAP adds ~200 A nucleotides to the 3’ end
  5. poly-A binding protein to aid polyadenylation and protect RNA from degradation
31
Q

What is CstF and CPSF respectively?

A
  • CstF = cleavage stimulation factor
  • CPSF = cleavage and polyadenylation specificity factor
32
Q

What does differential polyadenylation determine?

A

if an antibody is membrane-bound or secreted

33
Q

What does increased CstF in activated B cells do?

A

cleave at the weak site to generate a short Ab without the membrane bound region

34
Q

What does nuclear export receptor do?

A

guide the RNA to nuclear pore complex for export

35
Q

What percentage of RNA is transported to the cytoplasm as a protein-RNA complex?

A

<10%

36
Q

What does nonsense-mediated mRNA decay (NMD) do?

A

degrade newly synthesised mRNAs with a premature termination codon to prevent the production of truncated proteins that could result in disease

37
Q

What happens in the first round of translation?

A

the ribosome removes EJCs to allow normal mRNA to continue onto translation

38
Q

How do exon junction complexes (EJCs) activate NMD?

A

by binding to Upf

39
Q

What are possible fates of mRNA after exportation?

A
  • translated immediately in cytosol (common)
  • directed to ER for synthesis of membrane and secreted proteins (common)
  • sequestered in specific intracellular locations prior to translation (specific to certain mRNAs)
40
Q

Where is the signal for mRNA localisation present?

A

in the 3’ UTR

41
Q

What are the 2 main types of RNA editing?

A
  • A to I affecting ~1,000 human genes
  • C to U
42
Q

What does an RNA editing complex do?

A

recognise a specific target sequence and/or secondary structure via its deaminase activity

43
Q

What does RNA editing affect?

A
  • protein sequence
  • RNA splicing
  • transport
  • translation efficiency

Genes, Genomes and Biomedical Implications (15 decks)

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