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[ONCG2002] Cancer Cell Genetics > 3: Gene Expression & Mechanisms of Gene Regulation II > Flashcards

3: Gene Expression & Mechanisms of Gene Regulation II Flashcards

1
Q

What are 2 ways TFs can activate transcription?

A

By making protein-protein interactions with:
* Basal TFs
* Co-activators

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2
Q

How might a basal TF help a TF to activate transcription?

A

Helping RNA polymerase bind to the promoter

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3
Q

How might co-activators help TFs activate transcription?

A

Bind to RNA polymerase II, and/or have enzymatic activity that modifies histones or other TFs

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4
Q

How do CRFs help activate transcription?

A

Remodels nucleosome so TFs can bind

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5
Q

How does histone acetylation help activate transcription?

A

Attaching an acetyl group to a histone protein means histone proteins don’t form heterochromatin
This means the DNA is wound less tight, so RNA polymerase II can attach easier

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6
Q

Which TF has histone acetyl transferase activity?

A

TFIID

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7
Q

Describe the structure of a histone protein and its tails

A
  • A core region where 8 histone proteins are held tightly
  • 8 tail regions that extend from the core. These are highly mobile and have no regular structure.
  • Histone proteins are positively charged and are attracted to negatively charged DNA.
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8
Q

What function do histone tails have?

A

They have sites where enzymes can modify activity

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9
Q

What are a few examples of post-translational modifications that can be made to histone tails?

A
  • Acetylation
  • Phosphorylation
  • Methylation
  • Ubiquitination
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10
Q

Why are post-translation modifications in histone tails significant?

A

They can affect how nucleosomes stick together and, therefore may have an effect on gene regulation

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11
Q

Why is DNA negatively charged?

A

Due to its phosphate backbone

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12
Q

Describe the action of histone acetyltransferases (HATs)

A
  • Add an acetyl group to the positively charged amino acid, lysine.
  • Removes positive charge
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13
Q

What do histone deacetylases do?

A

removes acetyl groups from Acetyl-lysine

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14
Q

Why is histone acetylation significant in gene regulation?

A
  • DNA is wound less tightly due to the loss of charge in the lysine amino acid.
  • acetylated nucleosomes form bead-on-string structure but not a higher-order chromatin structure
  • therefore DNA is more accessible to transcription
  • acetylation can also recruit transcription-activating remodeling protein
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15
Q

What is an example of a protein and its CoAct that is recruited by acetylation of lysine?
What is its significance in gene regulation?

A

Protein: bromodomain
CoAct: Gcn5

Coactivators prevent nucleosomes from forming heterochromatin, meaning the genes are activated.

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16
Q

What does RAR bind to in the absence of retinoic acid?

A

RPD3 (a histone deacetylase)

17
Q

What does RAR bind to in the presence of retinoic acid?

A

CBP/p300 (a histone acetylase)

18
Q

Describe the action of Retinoic acid receptor

A
  • RAR is a TF, it binds to DNA all of the time.
  • Its interaction with the DNA changes in depending on the presence/absence of retinoic acid.
  • In the absence of retinoic acid, it binds to RDP3, which is a histone deacetylase
    > This means there is no acetyl group attached, so lysine remains positive, and heterochromatin can be formed. This gene is inactive.

-In the presence of retinoic acid, it binds to CBP/p300, which is a histone acetyltransferase.
> The acetyl group is attached to lysine, nucleosomes are not packaged tightly, forming euchromatin. The gene is active.

19
Q

What are some examples of co-repressors?

A
  • Histone deacetylases
  • Histone methyltransferases
  • (ATP-dependent) CRFs
  • DNA methyltransferases
20
Q

How can non-coding RNA molecules regulate gene expression?

A

eRNA recruits RNA polymerase to its own promoter to transcribe its own code to produce more enhancer RNA.

21
Q

What are some classes of non-coding RNA?

A
  • enhancer (eRNA)
  • transfer (tRNA)
  • ribosomal (rRNA)
  • micro (microRNA)
  • long non-coding (lncRNA)
22
Q

What property does the transcription factor YY1 have?

A

It can bind to both RNA and DNA, acting as a “bridge” that link them together.

23
Q

What is an integrator?

A
  • Multiprotein complex with RNA endonuclease activity required for 3’-end processing of non-polyadenylated RNAs.
  • Binds to eRNA and RNA polymerase facilitating enhancer-promoter interactions.
24
Q

How can integrators affect gene regulation?

A

They bind to eRNAs and RNA polymerase, promoting interaction between enhancers and promoters.

These interactions result in the activation of transcription.

25
Q

How is microRNA important in gene regulation?

A
  • Around half all human genes are controlled (in part) by miRNA
  • They can regulate genes by binding to matching sequences to control transcription/translation of the gene, turning it on/off.
26
Q

Where does miRNA get processed?

A

In the nucleus and cytoplasm.

27
Q

How does miRNA inhibit translation of mRNA?

A
  • It can recruit RISC (RNA-induced silencing complex) to mRNA that have complementary sequences.
  • Results in the degradation/down-regulation of gene expression.
  • If the miRNA has a complete match, the mRNA is degraded. If it is an incomplete match, the processes is halted, but not completely stopped.
28
Q

How can we utilize the mechanisms of mRNA synthetically in medicine?

A

Synthetic siRNA or shRNA (short hairpin RNA) can be used to repress any gene of interest.

29
Q

How can siRNA silence genes?

A

SiRNA binds to complementary sequences in nascent (newly synthesised, before it is turned into mRNA) RNA.

SiRNA binds with the RITS (RNAi-induced initiation of transcriptional gene silencing) complex

This leads to methylation of lysine in histones, forming Heterochromatin, leading to gene silencing as genes can no longer be transcribed.

30
Q

What is RITS and what does it do?

A

RNAi-induced initiation of transcriptional gene silencing.

It helps guide siRNA to the nascent RNA

31
Q

What is nascent RNA?

A

Newly synthesised, RNA that hasn’t been processed > mRNA (still containing introns.)

32
Q

What is Swi6?

A

Heterochromatin protein

33
Q

What does Swi6 do?

A

Spreads Heterochromatin, turns gene off (silences/represses)

34
Q

What is CLRC?

A

A histone methyltransferase complex

35
Q

What is a corepressor

A

a corepressor is a molecule that represses the expression of genes

36
Q

What is RNA endonuclease, what does it do

A

An enzyme that cleaves the phosphodiester bond within a polynucleotide chain.
Can be specific to the RNA sequence or non specific

[ONCG2002] Cancer Cell Genetics (6 decks)

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