Co-Factors and Chromatin Remodelling Flashcards
Why do some TFs require co-activators to interact with the basal transcriptional apparatus directly?
they only have DNA binding and no (or weak) activation domains
What are the main roles of co-factors?
- part of core transcription machinery
- bridging TFs and PIC
- help recruit GTFs and RNAPII
- chemical modification of nucleosomes
- chromatin remodelling
What is the mediator complex?
a protein complex tightly associated with RNAPII CTD in yeast that can act as a scaffold for protein-protein interaction
What are the 5 classes of co-factors?
- I - core PIC
- II - bridging
- III - mediator
- IV - histone modification
- V - chromatin remodelling
How are nucleosomes dynamic?
they can ‘wrap-unwrap-rewrap’ in milliseconds, allowing DNA to be accessible most of the time for binding TFs
What is nucleosome positioning important for?
influencing gene transcription
What are the 4 main mechanisms by which transcriptional activators direct local alterations in chromatin structure?
- nucleosome remodelling
- nucleosome removal
- histone replacement
- histone modifications
Give examples of covalent modifications of histones
acetylation, phosphorylation and methylation
What does each nucleosome have?
8 unstructured, flexible histone tails
What is the histone code hypothesis?
covalent modifications of histone tails facilitate the binding of specific proteins to chromatin to perform distinct functions
Which histone modificaiton is most used to identify active enhancers?
H3K27Ac
How are conventional histone genes arranged?
clustered in the genome in tandem repeats with all of five histone genes in each repeat
How are histone variants encoded?
by different histone genes expressed at lower levels than regular histones
What can insertion of different histone variants into nucleosomes do?
signal different functions that can be recognised by chromatin remodelling complexes
What does acetylation do?
remove the positive charge on histone tails, which decreases the interaction between histones and the negatively charged groups of the DNA, making the condensed chromatin open for transcription
How does the acidic AD of CREB exist?
as unstructured random coils with a strong negative charge
How is CBP activated?
increased cAMP levels activate PKA to phosphorylate CREB which allows it to interact with CBP and activate its HAT activity
What gene classes are CBPs associated with?
inducible genes and those involved in cell differentiation
How does CBP increase transcription rates?
- HAT activity - acetylates histone tails to remodel chromatin
- increasing recruitment rate of RNAPII promoter
What are the 6 steps of chromatin remodelling to transcription initiation?
- gene activator protein binds to chromatin
- chromatin remodelling
- covalent histone modification
- additional activator proteins bound to gene regulatory region
- assembly of PIC at the promoter
- transcription initiation
What are possible mechanisms of transcriptional activation?
- binding of one factor facilitates binding of other factors
- activators promote assembly of IC
What are possible mechanisms of transcriptional repression?
- interaction of transcription regulators
- nucleosome remodelling
What 3 things are recruited for nucleosome remodelling for transcriptional repression?
- chromatin remodelling complexes
- histone deacetylases
- histone methyl transferase
What is the super enhancer composed of?
large clusters of enhancers densely bound with the mediator complex, TFs and chromatin regulators
What do master TFs do?
form super enhancers at key cell identity genes
What do super enhancers do?
- span large domains
- employ a large fraction of mediator
- drive cell-specific gene expression programs
How can genes be switched off through DNA methylation?
methylated nucleotides prevent DNA binding for some gene regulatory proteins or TFs
How can DNA methylation patterns be passed to daughter cells?
by maintenance methyl transferase
