Lecture 29 - Transcriptional regulation

Question 1

What is the basic levels of transcriptional regulation:

Answer 1

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

Question 2

what is DNA methylation

Answer 2

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

Question 3

___ donates the methyl group to the DNA

Answer 3

SAM - s adenosylmethionine

is released and comes off as SAH

Question 4

from where is SAM derived?

Answer 4

predominately from the diet (folate) of through the conversion of serine

Question 5

How does the SAM know where to go on the DNA?

Answer 5

targeted DNA methylation is facilitated via a family of DNA methyl transferases:
Dnmt1, Dnmt3a and Dnmt3b

Question 6

How is targeted DNA demethylation mediated?

Answer 6

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)

Question 7

Serine, an important intermediate of glycolysis, can enter the 1 carbon cycle, which results in the production of __

Answer 7

SAM

so increased flux through the glycolytic pathways leads to an increase in serine

Question 8

increases in folate in the diet will cause

Answer 8

more SAM within the cell = more DNA methylation

Question 9

a-ketoglutarate levels (and hence succinate levels) are also dependent on the TCA cycle so _____is also tightly regulated

Answer 9

demethylation

Question 10

The expression levels of ____was increased 5-fold in proliferating satellite cells compared to quiescent SCs

Answer 10

Dnmt1

Question 11

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 ___

Answer 11

SAM

Question 12

Satellite cell activation, and entry into the cell cycle leads to …

Answer 12

increased DNA methylation

Question 13

what are the core histones and what are there tails susceptible to?

Answer 13

H2A, H2B, H3, H4

all have tails whihc are suscetible to PTMs (post-translation modifications)

• methylation*
• acetylation*
• ubiquination
• phosphorylation

*the focus

and many more

Question 14

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 _______

Answer 14

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

Question 15

Nomenclature

H3K27me =

Answer 15

histone H3, lysine 27 methylated

or ‘‘ac’ at the end for acetylation

Question 16

what facilitates histone methylation?

Answer 16

a family of histone methyl transferases (HMTs)

ezh2*, smyd2, prdm2 + many more

requires SAM (again) - represses transcription

*important

Question 17

what facilitates histone demethylation?

Answer 17

Lysine demethylases

LSD and JHDM families

Question 18

in the presence of high levels of FAD, LSD is able to release the methyl group from the histone, resulting in the production of..

Answer 18

FADH2

Question 19

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

Answer 19

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

Question 20

true or False

There are increased levels of H3K27me3 as satellite cells move from quiescence to proliferation

Answer 20

true

Question 21

true or false

there are alot of commonalities between histone methylation and DNA methylation

Answer 21

true

Question 22

what is histone acetylation what does it result in?

Answer 22

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

Question 23

what facilitates histone acetylation?

Answer 23

histone acetyl transferases (HATs)

p300, GCN5 and others

Question 24

Where is the acetyl group derived from?

Answer 24

acetyl-coA

which come from citrate

Question 25

what facilitates histone deacetylation?

Answer 25

histone deacetylases (HDACs)

HDAC and SIRT families (converts water to acetate)

Question 26

SIRT converts what to what in order to deacetylate?

Answer 26

NAD+ to NAM

requires high levels of NAD from the ETC

Question 27

A cell that is highly glycolytic is likely to have low levels of NAD, high levels of NADH whereas a highly oxidative cell…

Answer 27

will have high levels of NAD

which will lead to deacetylation

so cell metabolism has an important influence

Question 28

from quiescent to active satellite cell, what happens to acetylation?

Answer 28

it goes up - high levels of acetylation quite rapidly

Question 29

metabolic disorders have a large ability to impact on..

Answer 29

the ability to regenerate muscles