Lecture 3: Gene activation through transcription factors Flashcards
What are the different types of enhancers?
Both developmental and housekeeping genes are regulated through core promoters and enhancers.
• Enhancers have specificity for different types of promoter (housekeeping and development).
• Housekeeping genes are normally activated by proximal enhancers (like SV40).
• Developmental genes tend to be activated by distal enhancers.
How can we use DNA footprinting?
DNA footprinting is a method for showing where DNA-protein interactions occur in the genome.
• DNase I cuts DNA where protein does not bind.
• This can be used to show sites that are in open, accessible chromatin (hypersensitive sites).
• DNase I HSS coincides with enhancer activation.
• TFs bind to DNA and can displace chromatin.
What are enhancers?
Enhancers are sequences of DNA which can bind to TFs and cause an enhancement in the expression of a gene upstream or downstream.
• Activation leads to HSS sites.
• Enhancers can also lead to PTMs of nucleosomes.
• 400,000 – 1.4 million supposed enhancers have been found in the mammalian genome (consider there’s only 30,000 genes). We don’t know if they’re all functional though.
• Clusters of enhancers are known as super-enhancers.
• LCRs are super-enhancers which control major developmental switches.
• We also don’t know which genes are targeted by which enhancers and how specificity is ensured.
How is the mammalian genome divided into domains?
The genome can is divided into domains and sub-domains.
• This division is performed by insulators and boundaries.
• Insulator and insulator binding proteins are used to create a domain.
• CTCF is an example of an insulator binding protein.
• Enhancer-promoter interactions are limited by the insulators/boundaries, they can only occur within a subdomain. This partially accounts for specificity.
What are TADs?
TADs are topologically associating domains.
• TADs are formed from the looping of DNA.
• They are self-interacting regions, DNA sequences within a TAD interact more frequently than sequences outside.
• TADs are formed through loop extrusion with cohesion and CTCF in chromatin.
How does CTCF work?
CTCF is an insulator binding protein.
• It helps form TADs.
• It interacts with cohesin.
• It can’t bind to methylated DNA.
How can problems in domains lead to disease?
Issues with insulators, boundaries and enhancers can lead to diseases such as Beckwith-Wiedemann syndrome.
• Methylation of DNA occurs during the production of sperm and gametes.
• There is one section of the DNA which is supposed to be methylated in sperm but not eggs.
• If the egg DNA is methylated, then CTCF protein cannot bind.
• This is an example of an imprint control region, which ensures that the gene of only one parent is produced.
• If the ICR is methylated in the egg, overgrowth syndromes such as BWS occur.
What are co-activators?
Activators are proteins which aid the binding of enhancer bound TFs to TFs by RNA pol II.
• Cohesin loops may help to stabilise these interactions (loop within loop domains).
• Co-activators can include ATP-dependent chromatin remodelling factors, histone modifying factors, mediator and cell-specific co-factors.
• Activation domains on TFs work through protein-protein interaction domains.
• Mediator is a well characterised co-activator. One component of it: Cdk8 phosphorylates Ser2 of the CTD of RNA pol II. It facilitates elongation.
