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Cell and Molecular > L15 - Control of Gene Expression - RNA > Flashcards

L15 - Control of Gene Expression - RNA Flashcards

1
Q

What 3 things can achieve different isoforms?

A

Alternative splice sites
Start sites
Poly-adenylation sites

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2
Q

What is subcellular localisation used for?

A

Used to target translation to the part of the cell its needed

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3
Q

What 2 things can translation be regulated by?

A

Directly by sequences in untranslated regions

Globally by regulation of eIFs

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4
Q

Some mRNAs have a second open reading frame that can be?

A

Regulated independently

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5
Q

What % of Drosophilla and human genes are alternatively spliced?

A

40% Drosophila

75% human

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6
Q

What are the 4 types of alternative splicing?

A

Optional exon
Optional intron
Mutually exclusive exon
Internal splice site

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7
Q

Why are splice donor and acceptor sequences found so frequently?

A

They are only two bases

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8
Q

What is a cryptic splice site?

A

A site that is favoured over neighbouring splice sites

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9
Q

What else effects the choice of splice site in RNA?

A

Other sequences

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10
Q

Regulation of alternative splicing - sex determination in Drosophila genes

A

Sxl – sex lethal
Tra – transformer
Dsx – double sex

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11
Q

Sex determination in Drosophila males method

A

Transcripts for sxl and tra are spliced to produce inactive isoforms
Transcripts for dsx are active and spliced to produce a male specific repressor protein
- Represses transcription of genes required for female development

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12
Q

Sex determination in Drosophila females method

A

Two X chromosomes allow a small amount of active Sxl protein - alternative promoter
Sxl represses splicing by blocking binding by U2AF
This feeds back on the sxl transcript to make more of itself and also binds to tra transcripts
Results in a female specific isoform of Dsx

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13
Q

Site of polyadenylation on mRNA - B lymphocytes

A

They produce two antibody isoforms

Antibody gene has two positions for cleavage and polyadenylation of RNA transcript

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14
Q

Site of polyadenylation - when the cell produces the long transcript

A

First stop codon is spliced out

Results in the translation of a transmembrane domain

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15
Q

Site of polyadenylation - when the cell produces the short transcript

A

Splice acceptor is lost and first stop codon isn’t lost

Results in the antibody being secreted

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16
Q

Alternative start sites - optimal sequence

A

Kozak sequence - ACCAUGG

17
Q

What happens if the start sequence is not perfect - leaking scanning

A

Small ribosome can scan past the first AUG
- Stops at a second or third AUG
All in the same reading frame, so isoforms differ only by the sequence of there N-terminus

18
Q

What favours the first AUG?

A

High levels of eIF-4F in a cell

19
Q

Regulated nuclear transport - regulating mRNA - HIV small genome integration

A

HIV has a small genome that is integrated into the host genome
After integration the entire genome is transcribed in one piece
- Alternative splicing allows for many different protein products to be made

20
Q

Regulated nuclear transport- why is full length RNA needed to make new virons?

A

Un-spliced RNAs cannot leave the nucleus
Rev protein binds to HIV introns and interacts with nuclear pore to allow unspliced RNA to leave
Rev levels distinguish two phases of infection

21
Q

What is Rev protein involved in?

A

Involved in binding to HIV introns to allow unspliced RNA to leave

22
Q

Signals in the untranslated region of mRNA can target it to part of the cell – regulating mRNA

A

Intermolecular base pairing within the 3’ UTR forms stem loops
These are recognized by cellular proteins
Gives rise to localised translation

23
Q

Translated control elements in mRNA - regulating mRNA - ferritin

A

Stores iron in the cell - reducing the available Fe

24
Q

Translated control elements in mRNA - regulating mRNA - transferrin

A

Receptor imports iron into the cell - increasing the available Fe

25
Q

Aconitase if low Fe in cytoplasm method

A

Binds to stem loops in the 5’ UTR of ferritin mRNA and blocks translation
Binds to stem loops in the 3’ UTR of transferrin mRNA and blocks its degradation

26
Q

Aconitase if high Fe in cytoplasm method

A 
Binds to iron in the cytoplasm and goes through a conformational change
Releases the mRNAs
- Ferritin mRNA translated 
- Transferrin mRNA degraded 
Rapid and strong regulation
27
Q

Global regulation by eIF2 and eIF2B – regulating translation

A

If the cell is…. it turns down global translation by phosphorylating eIF-2
o Entering G0
o Infected by a virus
o Lacking nutrition
This causes eIF-2b to bind to eIF-2 very tightly, blocking its recycling

28
Q

eIF-2 and GTP

A

Active - binds to Met tRNA to start ribosome scanning

29
Q

eIF-2 and GDP

A

Inactive

30
Q

What is eIF-2b required for?

A

The dissociation of GDP from eIF-2 to activate it

31
Q

What are IRES?

A

Internal ribosome entry sites are stem loops in RNA

32
Q

IRES allow more than one gene to be present on mRNA – regulating translation

A

They can initiate formation of the ribosome independent of the cap/polyA initiation complex

33
Q

eIF-4G

A

Is required for IRES based initiation

Binds to the IRES stem loop

34
Q

Where are IRES often found?

A

In viral transcripts
Viruses favour translation of their transcripts by cleaving eIF-4G into a form that cannot bind eIF-4E but still binds IRES

35
Q

What happens to eIG-4G during apoptosis?

A

Cleaved into a form that cannot bind eIF-4E but still binds IRES
Certain genes required during cell death utilize IRES and they continue to be translated

36
Q

RNA stability - regulating transcription - RNA degradation

A

The half-life of different mRNAs varies greatly
Poly A tails start at 200 in length, but an exonuclease cuts them down to 30nt
- At this point they are decapped and degraded

37
Q

What is re-adenylation?

A

Some mRNAs are re-adenylated in the cytoplasm to activate them or to extend half-life

38
Q

Which factors promote translation but block degradation?

A

DAN competes with eIF-4E for binding to the cap

Cell and Molecular (24 decks)

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