Lecture 29 - Transcriptional regulation Flashcards
What is the basic levels of transcriptional regulation:
Binding of transcription factors to the 5’ promoter region - pax7, myoD, MyoG etc… (to induce transcription)
Binding of RNA polymerase to the TSS
Epigenetic regulation
what is DNA methylation
The addition of a methyl group to the cytosine base of a CpG dinucleotide
- often occurs at promotor region of genes (leading to repression)
- Generally occurs in areas rich in ‘CG’ base pairs
___ donates the methyl group to the DNA
SAM - s adenosylmethionine
is released and comes off as SAH
from where is SAM derived?
predominately from the diet (folate) of through the conversion of serine
How does the SAM know where to go on the DNA?
targeted DNA methylation is facilitated via a family of DNA methyl transferases:
Dnmt1, Dnmt3a and Dnmt3b
How is targeted DNA demethylation mediated?
a family of DNA demethylases
tet1, tet2 and tet3
This reaction is dependent on the presence of a-ketoglutarate (an intermediate of the TCA cycle)
Serine, an important intermediate of glycolysis, can enter the 1 carbon cycle, which results in the production of __
SAM
so increased flux through the glycolytic pathways leads to an increase in serine
increases in folate in the diet will cause
more SAM within the cell = more DNA methylation
a-ketoglutarate levels (and hence succinate levels) are also dependent on the TCA cycle so _____is also tightly regulated
demethylation
The expression levels of ____was increased 5-fold in proliferating satellite cells compared to quiescent SCs
Dnmt1
In activated satellite cells, there are elevated levels on DNMT, increased expression of all the genes that encode for the enzymes necessary to produce high levels of ___
SAM
Satellite cell activation, and entry into the cell cycle leads to …
increased DNA methylation
what are the core histones and what are there tails susceptible to?
H2A, H2B, H3, H4
all have tails whihc are suscetible to PTMs (post-translation modifications)
- methylation*
- acetylation*
- ubiquination
- phosphorylation
*the focus
and many more
histone methylation invlves the addition of ___group to a specific ___(or ______) AA in the histone ___
It often results in the formation of tightly packed ________, which prevents transcription factor binding and inhibits _______
histone methylation invlves the addition of amthyl group to a specific lysine (or arginine) AA in the histone tail
It often results in the formation of tightly packed chromatin, which prevents transcription factor binding and inhibits transcription
Nomenclature
H3K27me =
histone H3, lysine 27 methylated
or ‘‘ac’ at the end for acetylation
what facilitates histone methylation?
a family of histone methyl transferases (HMTs)
ezh2*, smyd2, prdm2 + many more
requires SAM (again) - represses transcription
*important
what facilitates histone demethylation?
Lysine demethylases
LSD and JHDM families
in the presence of high levels of FAD, LSD is able to release the methyl group from the histone, resulting in the production of..
FADH2
FAD is a metabolite used by TCA cycle and ETC - so when there is excessive movement of h+ ion along the ETC you can get increased production of FAD which can be exported and use by ___ to _______the histones
FAD is a metabolite used by TCA cycle and ETC - so when there is excessive movement of h+ ion along the ETC you can get increased production of FAD which can be exported and use by LSD to demethylate the histones
true or False
There are increased levels of H3K27me3 as satellite cells move from quiescence to proliferation
true
true or false
there are alot of commonalities between histone methylation and DNA methylation
true
what is histone acetylation what does it result in?
the addition of an acetyl group to a specific lysine AA in the histone tail
- often results in the formation of loosely packed chromatin, which allows transcription factor binding and promotes transcription
what facilitates histone acetylation?
histone acetyl transferases (HATs)
p300, GCN5 and others
Where is the acetyl group derived from?
acetyl-coA
which come from citrate
what facilitates histone deacetylation?
histone deacetylases (HDACs)
HDAC and SIRT families (converts water to acetate)
SIRT converts what to what in order to deacetylate?
NAD+ to NAM
requires high levels of NAD from the ETC
A cell that is highly glycolytic is likely to have low levels of NAD, high levels of NADH whereas a highly oxidative cell…
will have high levels of NAD
which will lead to deacetylation
so cell metabolism has an important influence
from quiescent to active satellite cell, what happens to acetylation?
it goes up - high levels of acetylation quite rapidly
metabolic disorders have a large ability to impact on..
the ability to regenerate muscles
