3: Gene Expression & Mechanisms of Gene Regulation II Flashcards
What are 2 ways TFs can activate transcription?
By making protein-protein interactions with:
* Basal TFs
* Co-activators
How might a basal TF help a TF to activate transcription?
Helping RNA polymerase bind to the promoter
How might co-activators help TFs activate transcription?
Bind to RNA polymerase II, and/or have enzymatic activity that modifies histones or other TFs
How do CRFs help activate transcription?
Remodels nucleosome so TFs can bind
How does histone acetylation help activate transcription?
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
Which TF has histone acetyl transferase activity?
TFIID
Describe the structure of a histone protein and its tails
- 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.
What function do histone tails have?
They have sites where enzymes can modify activity
What are a few examples of post-translational modifications that can be made to histone tails?
- Acetylation
- Phosphorylation
- Methylation
- Ubiquitination
Why are post-translation modifications in histone tails significant?
They can affect how nucleosomes stick together and, therefore may have an effect on gene regulation
Why is DNA negatively charged?
Due to its phosphate backbone
Describe the action of histone acetyltransferases (HATs)
- Add an acetyl group to the positively charged amino acid, lysine.
- Removes positive charge
What do histone deacetylases do?
removes acetyl groups from Acetyl-lysine
Why is histone acetylation significant in gene regulation?
- 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
What is an example of a protein and its CoAct that is recruited by acetylation of lysine?
What is its significance in gene regulation?
Protein: bromodomain
CoAct: Gcn5
Coactivators prevent nucleosomes from forming heterochromatin, meaning the genes are activated.
What does RAR bind to in the absence of retinoic acid?
RPD3 (a histone deacetylase)
What does RAR bind to in the presence of retinoic acid?
CBP/p300 (a histone acetylase)
Describe the action of Retinoic acid receptor
- 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.
What are some examples of co-repressors?
- Histone deacetylases
- Histone methyltransferases
- (ATP-dependent) CRFs
- DNA methyltransferases
How can non-coding RNA molecules regulate gene expression?
eRNA recruits RNA polymerase to its own promoter to transcribe its own code to produce more enhancer RNA.
What are some classes of non-coding RNA?
- enhancer (eRNA)
- transfer (tRNA)
- ribosomal (rRNA)
- micro (microRNA)
- long non-coding (lncRNA)
What property does the transcription factor YY1 have?
It can bind to both RNA and DNA, acting as a “bridge” that link them together.
What is an integrator?
- 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.
How can integrators affect gene regulation?
They bind to eRNAs and RNA polymerase, promoting interaction between enhancers and promoters.
These interactions result in the activation of transcription.
How is microRNA important in gene regulation?
- 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.
Where does miRNA get processed?
In the nucleus and cytoplasm.
How does miRNA inhibit translation of mRNA?
- 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.
How can we utilize the mechanisms of mRNA synthetically in medicine?
Synthetic siRNA or shRNA (short hairpin RNA) can be used to repress any gene of interest.
How can siRNA silence genes?
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.
What is RITS and what does it do?
RNAi-induced initiation of transcriptional gene silencing.
It helps guide siRNA to the nascent RNA
What is nascent RNA?
Newly synthesised, RNA that hasn’t been processed > mRNA (still containing introns.)
What is Swi6?
Heterochromatin protein
What does Swi6 do?
Spreads Heterochromatin, turns gene off (silences/represses)
What is CLRC?
A histone methyltransferase complex
What is a corepressor
a corepressor is a molecule that represses the expression of genes
What is RNA endonuclease, what does it do
An enzyme that cleaves the phosphodiester bond within a polynucleotide chain.
Can be specific to the RNA sequence or non specific
