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Biol 200 > Lecture 17 - Cytoplasmic mechanisms of post-transcriptional control of gene expression > Flashcards

Lecture 17 - Cytoplasmic mechanisms of post-transcriptional control of gene expression Flashcards

1
Q

To what extent can we regulate gene expression by regulating movement through NPC

A

Movement through NPC NOT a way of regulating gene expression

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2
Q

3 cytoplasmic mechanisms of post-transcriptional control of gene expression

A

1) Translation regulation
2) RNA degradation
3) mRNA localization

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3
Q

Translation regulation : Exemple of where it occurs

A

(Xenopus) Oocyte in prep. for embryogenesis has many transcripts but waits for fertilization to express them

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4
Q

Translation regulation : What is found ON the translationally dormant transcript (4)

A

1) 5’ cap
2) Coding-region of gene
3) CPE -> U-rich signal UUUUAU
4) Poly(A) SIGNAL (AAUAAA)

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5
Q

Translation regulation : How translationally dormant mRNAs are activated (in given example)

A

By cytoplasmic polyadenylation

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6
Q

Translation regulation : What are CPE and Poly(A) signal

A

CPE : U-rich signal

Poly(A) signal : AAUAAA downstream of CPE

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7
Q

Translation regulation : Why fully ready transcript is translationally dormant

A

eIF4E on 5’ cap is bound to maskin so can’t interact w/ other translation factors.

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8
Q

Translation regulation : What is maskin also bound to

A

CPEB, which is bound to CPE signal

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9
Q

Translation regulation : How is CPEB regulated and how is this linked to fertilization

A

By phosphorylation. After fertilization, activation of many phosphatases and kinases

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10
Q

Translation regulation : What happens to CPEB after fertilization and what this leads to (next event)

A

Is phosphorylated so maskin leaves and PAP (and CPSF) are recruited -> Poly(A) tail extended

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11
Q

Translation regulation : What elongation of Poly(A) tail allows

A

PABPC1 interacts with eIF4G which interacts with eIF4E

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12
Q

Translation regulation : What length of Poly(A) influences

A

Stability of the mRNA. More Poly(A) tail = more degradation by Poly(A) exonucleases, more contact between PAP and translation factors

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13
Q

Translation regulation : What mRNAs that don’t have CPE signal do

A

Also have enough Poly(A), depending on their stretch of Poly(A) tail to maintain contact with PABPC1 (which also interacts with translation initiation factors that recruit 40 S to 5’ cap)

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14
Q

Translation regulation : What process allows faster translation

A

Circular structure of the mRNA (due to PABPC1/eIF4G interaction)

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15
Q

Translation regulation : Why circular structure allows more translation

A

40S and 60S falling apart at 3’ end after end of 1 translation are immediately recruited at the 5’ cap -> HIGHLY EXPRESSED mRNA

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16
Q

Translation regulation : Other type of mRNA translation regulation

A

Iron-dependent regulation

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17
Q

First mRNA going through iron-dependent regulation and what its protein does

A

Ferritin mRNA. Ferritin binds iron ions so is required in high presence of iron

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18
Q

Regions on ferritin mRNA necessary for its regulation and where they are

A

Loop structures near 5’ end (on 5’ UTR) called IREs (iron responsive elements)

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19
Q

What happens to ferritin mRNA when iron level is low

A

IRE-BP (IRE binding protein) changes to an active conformation and binds to ferritin mRNA IREs -> Block ribosome scanning

20
Q

What happens to ferritin mRNA when iron level is high

A

IRE-BP is inactive so doesn’t bind IREs. Ferritin can be produced

21
Q

Second mRNA going through iron-dependent regulation and what its protein does

A

TfR mRNA. Protein is transferrin receptor, a protein required for iron intake in the cell. Required in low iron level

22
Q

Regions on TfR mRNA necessary for its regulation and where they are

A

Loops at its 3’ end with AU-rich region in their helix called IREs (again)

23
Q

What AU-rich regions in 3’ IREs helix of TfR mRNA do

A

Target the mRNA for exonucleases and endonucleases

24
Q

What happens to TfR mRNA s when iron level is high

A

IRE-BP is inactive and doesn’t bind their IREs to protect them

25
Q

What happens to TfR mRNA s when iron level is low

A

IRE-BP is active so it binds the IREs (and their AU-rich regions) on the 3’ and protects them from exo/endonucleases targeting

26
Q

3 mRNA regulated degradation pathways

A

1) Decapping pathway (Deadenylation independent)
2) Deadenylation-dependent pathway
3) Endonucleolytic pathway

27
Q

Decapping pathway (Deadenylation independent) explanation (2 steps)

A

1) mRNA is decapped before being deadenylated

2) degraded 5’->3’ by exonucleases

28
Q

Deadenylation-dependent pathway explanation (2 steps)

A

1) Poly(A) shortened to less than 20 residues

2) Decapped and exonucleolytic digestion 5’->3’ or 3’->5’ exonucleolytic decay by exosome

29
Q

Side effect of Poly(A) shortening in deadenylation-dependent pathway

A

Less interaction with PABPC1, loss of interaction with 5’ Cap and eIFs

30
Q

Endonucleolytic pathway explanation (2 steps)

A

1) Endonuclease cuts in middle

2) 3’->5’ decay with exosome

31
Q

Explanation of mRNA degradation by shortening its half-life (destabilizing it)

A

Addition of AU rich sequence AUUUA in 3’ UTR of mRNAs reduce their stability

32
Q

Example of gene where addition of AU rich sequence in 3’ UTR was shown to reduce stability

A

Beta-globin gene

33
Q

Why addition of AU rich sequence in 3’ UTR destabilizes eukaryotic mRNAs

A

AU-rich element recruits deadenylating enzyme and the exosome (3’->5’ decay) to degrade the mRNA

34
Q

2 types of regulatory RNAs length + what they do

A

21 nts approx. bind 3’ UTR sequences of certain mRNAs

1) miRNAs (micro RNAs) 2) siRNAs (silencing RNAs)

35
Q

How miRNA obtained : 2 steps

A

1) 70-nt precursor RNA forms a hairpin w/ few mismatches in stem
2) Dicer (a ribonuclease) produces mature miRNAs from precursor

36
Q

How well miRNAs base pair w/ their target mRNA+ effect of their base-pairing

A

Don’t base pair perfectly. Repress translation

37
Q

How siRNAs produced

A

From dsRNA through Dicer-mediated cleavage

38
Q

How well siRNAs base pair w/ their target mRNA + effect

A

Base pair PERFECTLY. Induce cleavage/degradation

39
Q

Which one of miRNA/siRNA has more flexibility

A

miRNA cause since it doesn’t base pair perfectly, it can base pair w/ different RNAs

40
Q

Where siRNAs come from

A

Double stranded RNA from viruses or transposable elements

41
Q

What RNAP transcribes miRNAs

A

RNAP II

42
Q

Where miRNA/siRNAs go and how many

A

In the RNA-induced silencing complex (RISC). ONE ssRNA of either miRNA or siRNA

43
Q

What RISC does to RNAs that are IMprecisely complementary to a miRNA it contains

A

DOES NOT degrade the RNA but translationally represses it. Complexes bind to 3’ to block translational machinery binding at 5’ end.

44
Q

What RISC does to RNAs that are precisely complementary to a siRNA it contains

A

Degrades the RNA : ENDOnuclease function

45
Q

REGULATION of mRNA localization principle

A

Exclude mRNA from a certain region of the cytoplasm -> Localize it at the site where proteins it encodes are required

46
Q

What often directs localization of mRNAs

A

3’ UTR elements

Biol 200 (30 decks)

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