17: Regulation of transcription in Eukaryotes Flashcards
What is specific transcription factors?
- Respond to a stimulus which signals that one or more genes should be turned on.
- Capable of entering the nucleus.
- Recognize and bind to specific seq on DNA.
- Make contact with the transcription apparatus, directly or indirectly.
What are the two domains of TFs?
DNA binding
Activation: interacts with transcription apparatus.
What is the function of the mediator complex?
Eukaryotes: Recognition and binding to promoter by general TFs.
Not sufficient with activators as in prokaryotes.
Mediator: protein complex that transmits the signal from TFs to the RNA pol in eukaryotic cells. Provides a site of contact for activators, especially those bound to enhancers.
=> combines the signals of multiple activators and/or repressors -> RNA pol II.
Constant core unit and variable subunits.
Removal of CDK8 enz => stationary scaffold complex -> transcriptional activator.
What are enhancers and insulator sequences? How do they function in the regulation of transcription?
Enhancers:
- May be found several kb upstream/ downstream from promoter
- Loops DNA so the activator proteins bound at enhancer can contact transcription apparatus via mediator complex.
Insulators (boundary elements):
- DNA seq that shields promoters from the action of enhancers and also prevents the spread of heterochromatin.
- Form loops in the DNA
- Binds zinc-finger insulator-binding proteins (IBPs, i.e., CTCF). Require assistance by condensin complex to hold DNA in correct conformation.
=> Prevent enhancers from interfering with the wrong genes.
- GC-rich => can be methylated => no binding to IBPs => inactivation
What are matrix attachment regions, MARs?
Nuclear matrix appears on the inside of nuclear membrane (interphase).
DNA attached to proteins of matrix by MARs / scaffold attachment regions (SARs).
200-1000 bp
AT rich (70%), no consensus
Multiple A’s on DNA => bending.
Nuclear proteins that bind MAR recognize bends.
Topoisomerase II recognition sites often next to MAR sites => supercoiling of each loop adjusted independently.
Enhancers often associated with MAR sites.
How is transcription negatively regulated in eukaryotes?
Often act by interfering with activators (rather than obstructing the movement of RNA pol, as in prokaryotes).
- Occupy the recognition site of an activator => no binding => no assembly of transcription apparatus.
- CAAT-binding factor (CTF) can be prevented from binding the CAAT box (a
small DNA motif), by the CAAT-displacement protein (CDP).
Heterodimerization:
- Basic helix-loop-helix proteins (bHLH) has one helix containing basic amino
acid residues that facilitate DNA binding. bHLH proteins binds DNA as dimers, but can only bind DNA if both proteins contain the basic helix region.
- TF MyoD can form heterodimers with bHLH protein E12 (can bind DNA). Heterodimerization with ID protein (lacks basic region) => dimer that can not bind DNA.
How can heterochromatin block access to DNA in eukaryotes?
Key words: histones, acetylation, remodeling, Swi/Snf, ISWI
DNA coiled around histones -> nucleosomes.
Acetylation of lysine groups on histone tails (H2A, H2B, H3, H4) controls access of regulatory proteins to the DNA.
Histone acetyl transferases (HATs) and histone deacetylases (HDACs) add (from Ac-CoA) and remove acetyl gr., respectively.
No acetylation => highly condensed heterochromatin.
Chromatin remodeling:
- Rearrangement of histones in chromatin (by ATP) => looser structures of nucleosomes
- Slide nucleosomes along DNA molecule.
- Swi/Snf family: binds DNA strongly. Can slide and remodel nucleosomes.
- ISWI family: smaller. Can slide, but not rearrange. Binds to histones.
What are co-activators and co-repressors?
Co-activators (i.e., HATs) and co-repressors (HDACs) does not bind DNA directly, but bind to TFs on DNA.
What is the sequence of events for activating a typical eukaryotic gene?
(7 steps)
- TF binds to DNA
- HAT binds to TF
- HAT acetylates the histones in the vicinity and the association of the nucleosome is loosened.
- Chromatin-remodeling complex slides or rearranges the nucleosomes, allowing access to the DNA.
- Further TFs bind.
- RNA pol binds to DNA
- Initiation requires a positive signal to be transmitted via the mediator complex from one or more specific TFs.
What is the histone code? Which modifications can be made to histones?
N-terminal tails of histones projects outward. Exposed on surface of nucleosomes.
Modifications:
- Acetylation: opens up chromatin
- Deacetylation: promotes aggregation of chromatin.
- Methylation: of Lys residues at position 4 and 36 of histone H3 => transcriptional activation. Of Lys residues at 9 and 27 => repression.
- Phosphorylation: activation/ deactivation depending on location.
- Ubiquitination: induced by DNA damage. Activation/deactivation depending on location => binding of DNA repair proteins.
- Rare: ADP-ribosylation, sumoylation, biotinylation
How can methylation control eukaryotic gene expression?
Key words: methylases, GC islands
Prokaryotes use methylation to distinguish newly synthetized DNA.
Higher animals methylate up to 10% of cytosines, and higher plants methylate up to 30%.
Methylation often used as a marker for genes whose expression is involved in tissue differentiation.
Epigenetic changes.
Maintenance methylases:
- Add methyl gr. to newly made DNA at locations opposite methyl gr. on the old, parental strand => inheritance of methylation patterns.
Changing the methylation patterns: - de novo methylases: add new methyl gr. - demethylases: remove methyl gr.
GC islands:
- Region of DNA in eukaryotes that contains many clustered GC seq that are used as targets of cytosine methylation.
- Common on housekeeping genes.
What is gene silencing, and what can be the cause?
Switching off (repression) genes in a relatively nonspecific manner.
In eukaryotes: covalent modification of DNA and histones.
May affect a single gene, a cluster of genes, regions of a chromosome, or a whole chromosome.
Cause:
Methylation of cytosine in5’-CG-3’ (5’-CNG-3’) seq.
Methylated CG recognized by methyl-cytosine binding proteins (MeCPs). Recognized by proteins that remove acetyl groups.
=> heterochromatin => “silenced” DNA.
What is genetic imprinting?
When the expression of a particular allele depends on whether it originally came from the father or the mother.
Only one of a pair of gene in diploid cell is expressed. The other copy is silenced by methylation.
Rare exception to the normal rules of genetic dominance.
