Lecture 4 and 5 - transcription regulation in eukaryotes Flashcards
What is a transcription factor?
a protein that influences some aspect of the transcription of DNA into RNA
What are general transcription factors required for?
to initiate basal transcription at the core promoter
What do regulatory transcription factors do?
bind to a regulatory element and influence the rate of transcription initiation at a core promoter
What can eukaryotic transcription be controlled by?
activator proteins, repressor proteins, small molecule effectors, accessibility of the core promoter, chromatin packing and dna methylation
What does the coactivator protein do?
when the activator protein binds to the enhancer and recruits TFIID to the core promoter, the coactivator protein (that does NOT bind DNA itself), bridges the activator protein and TFIID by using a transactivation domain
*the end result is that the rate of transcription increases
What are the two main strategies that some repressors use to inhibit the ability of TFIID to initiate transcription?
block TFIID recruitment and to block TFIID from recruiting RNA polymerase II
*with both these strategies the outcome is that the rate of transcription decreases
What is a mediator?
a multiprotein complex that interacts with regulatory transcription factors and RNA polymerase II to control transcription
What is the mediator required for?
for the regulation of the expression of most genes
What happens when the mediator is inactivated?
mRNA synthesis is abolished
How do activator proteins affect the mediator?
they stimulate the mediators ability to promote CTD phosphorylation
How do repressor proteins affect the mediator?
they can inhibit the mediators ability to promote ctd phosphorylation
What are glucocorticoids and what do they do?
a class of steroid hormones that influence the metabolism of carbohydrates
How do glucocorticoids regulate gene expression?
by influencing glucocorticoid receptor protein (GCR)
What is released when GCR binds to glucocorticoid?
HSP90 is released and a nuclear localization signal is exposed
What do nucleosomes contain?
they contain a segment of double-stranded DNA wrapped around on an octamer of histone proteins
What does the CCCTC binding factor bind to?
repeats of the sequence CCCTC to fold chromatin into a loop by dimerizing
What are the two types of chromatin?
euchromatin and heterochromatin
What is the structure and composition of euchromatin?
euchromatin is less compact (more open)
Why is open chromatin good?
it is more accessible to transcription factors and RNA polymerase
What is the structure and composition of heterochromatin?
it is more compact or “closed”
Why is closed chromatin not so good?
closed chromatin is not accessible to transcription factors and rna polymerase
What can chromatin remodeling do?
it can alter the positions and composition of nucleosomes
What are the 3 examples of chromatin remodeling?
rearrangement of nucleosomes, removal of nucleosomes and formation of nucleosome variants
what is dna methylation?
its a regulatory mechanism in which dna bases are covalently modified so that they contain a methyl group
What can methylation effect?
whether a protein is able to bind dna
*it is heritable
What do Methyl-CpG-binding proteins bind to?
methylated DNA
What is the definition of epigenetics?
the study of heritable phenotype changes that do not involve alterations in the DNA sequence
What are the 5 common mechanisms for epigenetic inheritance?
*chromatin remodeling
*histone modifications
*localization of histone events
*dna methylation
*feedback loop
What are the 2 types of heterochromatin?
constitutive heterochromatin and facultative chromatin
What are the differences between constitutive heterochromatin and facultative chromatin?
constitutive - regions of dna that are in ALL cell types
facultative - regions of dna that are in SOME cell types
