Lecture 22 - Chromatin, Epigenetics, and the Histone Code Flashcards
What has been used as a model organism to study transcriptional mechanism?
Yeast
What are silenced regions in chromosome 3 associated with?
Yeast Mating Types
What mark neutralizes the charge between histones and DNA?
Acetylation
On which residues do methylations typically take place?
Lysine
What does H3K4 methylation result in?
Activation
What does H3K9 methylation result in?
Inactivation
What process condenses the chromatin to ensure that transcription doesn’t take place?
Heterochromatinization
What is dosage compensation? How is it done?
It is when female mammals have to shutdown one X chromosome to equalize the dose of gene expression of the X chromosome.
It is done by heterochromatinizing an X chromosome to form an inactive Barr body (highly condensed chromosome).
What does XIST do?
It coats the entire X chromosome and thus shuts down most of the transcription of that chromosome.
How is the initial choice made for which X chromosome should be turned into a Barr body?
There is a competition between the expression of XIST and an antisense RNA to it (TSIX).
What histone mark ensures that the appropriate X chromosome is heterochromatinized after each cell division?
H3K9 Trimethylated Histones
What is open active chromatin called?
Euchromatin
Suppose you want to activate a gene downstream of a gene that is recognized by a DNA-binding domain. What must you pair with the DNA-binding domain to make this work? Why can this work?
You must pair it with a transcriptional activation domain from any well-characterized transcription factor.
You can do this because transcription factors are modular.
What is a heterologous element?
It is a element that does not belong in the cell being tested and comes from different cells or organisms.
Suppose you introduce a lac operator (cis-regulatory sequence) and lac repressor (lacI) joined with a strong transcriptional activation domain like VP16 into a eukaryotic cell. What will happen?
LacI will interact with the lacO and then VP16 will change the chromatin region in the area and activate transcription. This will co-opt the cellular apparatus to transcribe genes at very high efficiency (particularly, viral genes).
What are SWI/SNF? What do they do?
SWI/SNF are chromatin remodelers that come from yeast genes.
One of the subunits of of the remodelers has homology to a helicase, but uses ATP hydrolysis to shift around the entire environment of the nucleosome which exposes regions of the DNA that would normally be hidden in the nucleosome or histone-bound high order complexes.
Which molecular process is very important for development? Why?
Transcriptional regulation is very important for development because it is needed to change the transcription of each precursor cell type and eventually the fully differentiated cell types.
What protein is often the first step in a multitude of steps that give rise to the differentiation of a lineage of cells?
Pioneer Transcription Factors
What do pioneer transcription factors do?
They bind to a region of exposed DNA and recruit major effectors that change the chromatin configuration around the binding site.
What is important for the termination or differentiation of an entire lineage of cells?
The initial chromatin change caused by pioneer transcription factors is important for this.
Why is chromatin “looped out” to increase efficiency?
Chromatin gets looped out so that regions far downstream and far upstream of the gene that have to be transcribed come together, potentially linked by enhancers or other things. The outcome is that you make it advantageous for these general transcription factors to access their promoters and then transcribe their downstream genes.
What is responsible for looping out chromatin?
The Mediator
How does the mediator cause looping out?
The mediator mediates the interactions between upstream or downstream cis-regulatory elements, like enhancers (or UAS in yeasts). These elements bridge together and the chromatin between them forms a loop.
Why is looping out advantageous?
Looping out enhances the interaction of key general transcription factors and RNA pol II with the promoters they should be interacting with and the genes they should be transcribing.
