Lecture 6 Flashcards
Ch.3 regulation in gene expression (53 cards)
How do transcription factors work?
They bind to response elements to recognise the binding site
What is the function of RNA polymerase II?
It starts the transcription by binding to the TATA box
How does transcription factor link to RNA polymerase?
Via co-activators or co-suppressors
Where are co-activators/-suppressors located?
Up or downstream of the gene
How can TF activity be regulated?
By dimerization, ligand binding, expression restricted to specific cell types, covalent modification, cellular localisation (eg keep away from the nucleus until specific conditions are met)
What is needed in TF domains?
DNA-binding domain and transcriptional activation domain
What TF domains are additional?
Ligand and dimerizing domains
How does the DNA-binding domain work?
It wraps around DNA, has base specificity. Can be a zinc-finger, helix-loop-helix, helix-turn-helix, leucine zipper
How does the Ligand-binding domain work?
Retinoic acid receptor comes in contact with retinoic acid, which will activate the complex (steroid hormone). Glucocorticoid is activated in the cytosol
How can the dimerization domain be activated?
By either hetero- or homodimerization
Do the domains function independently?
Yes, they do
How can the TF binding be examined using EMSA?
A radioactive label is used (DNA probe), add a TF in the DNA and if the DNA has response factors the TF will bind. The bound DNA runs slower. Can also add serum to activate TF
How can the TF binding be examined using DNAse footprinting?
Bound DNA (to TF) is protected from degradation by DNAse, so will be bigger pieces
How can the TF binding be examined using ChIP-seq?
The proteins bind to DNA via crosslinks, degrade DNA, antibody binds to protein of interest (this is called immunoprecipitation), release the DNA and put it in a sequencer
How can the TF binding be examined using luciferase reporter assay?
The promoter is used to measure transcriptional activity. Luciferase chops the promoter to see which parts are essential for activation.
Is epigenetics inheritable?
It is inheritable within the organism but not between organisms
What ways of histone modification are there?
Acetylation, methylation, phosphorylation, ubiquitination
What ways of DNA modification are there?
Methylation
What is the function of chromatin modifying enzymes?
To add or remove methylation
What is the function of HAT?
It adds acetyl to a histone to activate it
What is the function of HDAC?
It remove acetyl from a histone for repression
How does adding acetyl activate that part of the DNA?
The negatively charged is linked to the positively charged Lysine in normal circumstances. However, when acetyl is added, the positive charge from Lysine is removed, which opens up the DNA (remove the tight binding)
What is the function of HAT/HDAC in tumors?
Their activity is altered in tumors, or HDAC is recruited to the wrong gene promoters
What is the function of DNA methyltransferase?
To add or remove methyl from the DNA. It is also needed to copy methylation (DNMT1)
