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BIOL332 > Eukaryotic Gene Regulation > Flashcards

Eukaryotic Gene Regulation Flashcards

1
Q

Eukaryotic gene regulation (Overall)

A

Eukaryotes have complex gene regulatory systems because have more complex and different cell types

Reason:
1. Different genes are required in different cell types – need ways to regulate

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2
Q

Where can Eukaryotic gene regulation occur

A

Eukaryotic gene regulation can occur at each stage
- Eukaryotic gene regulation can occur at multiple levels
Nucleus:
1. Chromatin packaging/unpacking
2. Transcription
3. Intron Processing

Cytoplasm:
1. Translation
2. RNA stability
3. Post-Translation Modifications

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3
Q

Movement through Euk cell

A

DNA –> Transcribed to Pre-RNA –> Splice RNA –> Goes out of nucleus –> Translated into proteins –> modified after protein is made = post translational modications

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4
Q

Layers of regulation in Eukaryotes

A

Eukaryotic gene regulation always involves multiple layers of regulation
- Have many steps –> Hard to disect them all

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5
Q

Where does gene expression occur

A

Gene expression (transcription) occurs in uncondensed regions of the DNA
- Uncondensed Eurochromatin = RNA polymerase can get in
- Packed Heterochromatin = RNA can’t get

Need tools to open DNA

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6
Q

Eukaryotic DNA

A

Eukaryotic DNA is looped around Histones –> Need to get to DNA to transcribe

Need tools to open DNA

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7
Q

Chromatin Remodeling

A

Chromatin remodeling is the result of Histone and DNA modifications

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8
Q

Acylation Vs. Methylation

A

Histone tail Acylation – Relaxes Chromatin (high expression)
- Opens chromatin

Histone Tail Methylation – Tighter compaction (low Expression)
- Closed

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9
Q

Nucleosome

A

8 Histone protein with Histone tail –> Can tag things onto the tail
- Can Acylate tail – opens histone structure

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10
Q

Genes involved in Chromatin Remodeling

A

A biazillion Different genes are involved in chromatin remodleing

Overall:
1. Writers
2. Readers
3. Earasers

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11
Q

Writers

A

Introduce modification on DNA and histone tails
- Put groups onto histones or DNA – Add modifications that tell readers what to do

Example – Histone Acytelases + Histone Methyltransferases + Histone Kinases + DNA methylases

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12
Q

Readers

A

Recognize modifications and recruit chromatin remodeling enzymes or recruit transcription factors
- Proteins to open DNA + recurit RNA polymerase

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13
Q

Earasers

A

Remove the modifications introduced by the writers

Example – Histone Deaxetylases + Histone Demethylases

After = can add new things

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14
Q

Types of transcription regulation in Eukaryotes

A

***Types of transcriptional regulation

  1. Negative regulation – Repressors + Co-repressors + Inducer molecules
  2. Positive regulation – Activators + inducers + inhibitors

***Sinilar to prokaryotes transcriptional regulations

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15
Q

Transcriptional Regulation (Euk)

A
  1. Multiple Activators – binds to enhancer sequneces
    • Upstream activating seqeunces
  2. Insulators
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16
Q

Multiple Activators in Euk

A

Form of transcriptional regulation

Multiple activators are used in Eukaryotes gene regulatory systsems – Activators can bind to enhancer elements that are near (cis) or far (trans) from the promoter

Trans enhancer elements = upstream activating sequences

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17
Q

Cis vs. Trans

A

Cis – Near promoter

Trans – Far from promoter

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18
Q

Trans enhancer elements

A

Upstream activating sequences

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19
Q

Transcriptional Regulation Process (Euk)

A

Many Transcription Factors on the core promoter

Mediator binds – transcrioton activates from all over genome + no set active transcription

Transcriptional Activator protein – Binds to Upstream regulator sequnece

***Look at image

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20
Q

Insulators

A

Cis (near the promoter) regulator elements – recruits proteins that block the action of enhancer elements

Have enhancer upstream of promoter - where the activator would bind BUT have a protein that binds to the insulator –> prevents activator from binding to enhancer

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21
Q
A

Anser: Negative Regulation

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22
Q

Euk gene regulation + RNA processing

A

Eukaryotic can have gene regulation through mRNA processing

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23
Q

Example of Euk gene regulation through mRNA processing

A

Example – Drosphilla

Sex determination in flies:
XX:AA –> 1:1 – female – Sxl Is expressed
XY:AA –> 0.5:1 – male – sxl is not expressed

It is the ratio of X:A chromosomes that controls sex determination
- No X-inactivation in flies

Females = make more X protein = have extra after dimerization = protein can bind to SXL = get female development

24
Q

SXL gene in Drosphilla

A

SXL Express = female development

SXL not expressed = male development

sxl = a splicing factor that creates the Tra protein that leads to female development

25
Q
A

Answer: Positive regulation – Activator yellow binds and get transcription

26
Q

Genes in Dropshilla sex determination

A

Tra gene = has 2 introns –> have exon with stop codon

If have splicing factor (have sxl) = splice exon out –> Get Tra protein = get female develeopment

No Sxl = both introns removed = get mRNA with 4 coding domaines but have stop codon = get protein but early stop codon = male

27
Q

General Structure of Euk mRNA

A

Euk mRNA contains:
1 Open reaidng frame (sometimes with introns that need to be removed)

5’ cap (added after transcription)

3’ Poly A tail (part of transcription termination sequence)

Regulatory information in the 5’ and 3’ UTRs

28
Q
A

Answer: B –> Need both together to regulate translation

29
Q

Poly A and 5’ cap + amont of protein made

A
30
Q

Eukaryotic gene regulation through mRNA translation and stbability

A

Options: RNA + Splicing + PolyA tail

  1. Once mRNA is exported out of nucleus –> the 5’ cap binds to the PolyA tail – see which protein is avalable
    • If less complex is formed = translate less
  2. Can target RNA for degredation = not translated
  3. Poly A tail –> recurits proteins + CAP can recurit proteins –> regulate translation by giving different proteins on the PolY A tail so can’t leave nucleus
31
Q

Preventing mRNA from leaving nucleus

A

Poly A tail –> recurits proteins + CAP can recurit proteins –> regulate translation by giving different proteins on the PolY A tail so can’t leave nucleus

32
Q

Gebe regulation through RNA switches

A

Riboswitch

33
Q

Riboswitch

A

A secondary structure in RNAs that occur when a ligand binds that result in a change in protein Synthesis
- Influence ability of RNA to be translated
- Form a secondary structure – bind to ligand causing another secondary structure = blocks ribosome = ribosome can’t do translation

***Typically in the 5’ UTR region

34
Q

Example of regulation through RNA swicth

A

Thiamine (B12) biosynthesis

Thiamine binds to the mRNA preventing translation of an enzyme needed to synthesize thiamine
- Reduce thiamine = opens = get translation

35
Q
A

Answer: Negitive Feedback loop –> Get thiamine and stop thiamine biosynthesis

36
Q

Ligand in Riboswitches

A

With riboswicthed Ligand is often the product of gene expression

37
Q

Thermoswicth

A

A regulatory segment of mRNA that forms under certain temperatures

Example:
Low temp – Structure is more stable –> ribsome can’t get through = reduce development

High Temp –> secondary structure falls apart = get proteins = plant can develope

***Variation of riboswitch

38
Q

What can Riboswitches do?

A
  1. Block transcription by creating transcription termination sequences
  2. Recruit factors that cleave RNA – secondary structure can be bound by endonuclease
  3. Recruit splicing factors to alter intron processes
  4. Block Ribosome binding site preventing translation
39
Q
A

Low temp = not tranlsated = male

High temp = translated = female

40
Q

RNAi

A

Gene regulation through ncRNAs

41
Q

dsRNA in cells

A

dsRNA are targeted for degradation
- Regulate gene expression by getting rid of RNAs

42
Q

RNAi processes

A

Short non-coding RNAs that are complimentary to speciefic mRNA can lead to the degradation of those mRNA targets and therefore lower protein expression
- RNA product of ncRNA is complementary to blue = bind = dsRNA = targeted for degradation
- Antisense RNA – Cuts off siRNA or miRNA – important regultor factors

43
Q

siRNA or miRNA

A

21-25 nucleotides long

Important regulatore factors

44
Q

Antisense RNA

A

Cuts off siRNA or miRNA – important regultor factors

45
Q

RNAi in cells

A

RNAi = natural cell process – get rid of blue by modulating amount of Red RNA

46
Q

RNAi in research

A

RNAi has been adopted by researchers to lower the gene expression by lowering mRNA levels

Image – getting rid of green RNA by imposing complementary RNA –> binds to mRNA – want to block to target for degradation

47
Q

RNAi process

A

Synthetic gene sepcific siRNA –> siRNA delivered into cell –> siRNA enters into RISC and unzips –> complementary pairing –> target mRNA –> Target mRNA cleavage and degradation

48
Q

RNAi in Drosphilla

A

RNAi in drosphilla = Knock-down

Have activator downstream of tissue specific promoter –> binds to upstream activator sequence that is engineered to express RNA version of gene –> Make complementary gene
- Fly makes GAL4 in liver – have siRNA only in the liver –> degrade protein only in lover – easy to study if regulate level in certain places but not everywhere

have siRNA that is complementary to gene (YFG) + have a tissue specific promoter + have Upstream activating sequnece –> Tissue specific promoter activator binds to upstream activating sequence – get expression of gene –> mRNA for YFG is targeted for degration leading to less YFP protein

49
Q

RNAi in Dropshila process

A

Fly makes GAL4 in liver – have siRNA only in the liver –> degrade protein only in lover – easy to study if regulate level in certain places but not everywhere

50
Q

Gene regualtion through ncRNA

A
  1. RNAi
  2. lncRNAs
51
Q

Gene regulation through lncRNAs

A
  1. Transcriptional Regulation – binds to DNA blocking transcription
  2. Chromatin Modifications
  3. Signaling – Add signal to protein
  4. mRNA sponge – soak up RNAs
  5. Scafold – brings proteins
  6. Translational regulation
52
Q

Gene regualation through post translational modifications

A

Modifcations to proteins affects their activity

Example – Phsophorylation of an intiation factor blocks translation in the ribosome
- Translation factor = phosphorylation = no translation
- No Phosphoryltion = translation

53
Q

Example Post-translational modifications

A

Ubiquitin – targets modified proteins for degradation
- Target protein for degradation by tagging with ubiquitin

54
Q

Gene regulation tool kit

A
55
Q

Gene regulation + Imagination

A

If you can imagine it then biology has tried it – and iff it works then it will be there

***Use your tool kit of regulatory mechanisms to imagine a bazillion ways that gene expression may be regulated

BIOL332 (25 decks)

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