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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
Answer: Positive regulation -- Activator yellow binds and get transcription
26
Genes in Dropshilla sex determination
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
General Structure of Euk mRNA
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
Answer: B --> Need both together to regulate translation
29
Poly A and 5' cap + amont of protein made
30
Eukaryotic gene regulation through mRNA translation and stbability
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
Preventing mRNA from leaving nucleus
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
Gebe regulation through RNA switches
Riboswitch
33
Riboswitch
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
Example of regulation through RNA swicth
Thiamine (B12) biosynthesis Thiamine binds to the mRNA preventing translation of an enzyme needed to synthesize thiamine - Reduce thiamine = opens = get translation
35
Answer: Negitive Feedback loop --> Get thiamine and stop thiamine biosynthesis
36
Ligand in Riboswitches
With riboswicthed Ligand is often the product of gene expression
37
Thermoswicth
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
What can Riboswitches do?
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
Low temp = not tranlsated = male High temp = translated = female
40
RNAi
Gene regulation through ncRNAs
41
dsRNA in cells
dsRNA are targeted for degradation - Regulate gene expression by getting rid of RNAs
42
RNAi processes
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
siRNA or miRNA
21-25 nucleotides long Important regulatore factors
44
Antisense RNA
Cuts off siRNA or miRNA -- important regultor factors
45
RNAi in cells
RNAi = natural cell process -- get rid of blue by modulating amount of Red RNA
46
RNAi in research
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
RNAi process
Synthetic gene sepcific siRNA --> siRNA delivered into cell --> siRNA enters into RISC and unzips --> complementary pairing --> target mRNA --> Target mRNA cleavage and degradation
48
RNAi in Drosphilla
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
RNAi in Dropshila process
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
Gene regualtion through ncRNA
1. RNAi 2. lncRNAs
51
Gene regulation through lncRNAs
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
Gene regualation through post translational modifications
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
Example Post-translational modifications
Ubiquitin -- targets modified proteins for degradation - Target protein for degradation by tagging with ubiquitin
54
Gene regulation tool kit
55
Gene regulation + Imagination
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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