9: epigenetics in metabolism

Question 1

what is ChIRP?

Answer 1

chromatin isolation by RNA purification
can identify:
- part of chromatin that RNA is bound to
- part of RNA that is bound to protein
- proteins bound to RNA

Question 2

through what ways can the metabolic state affect gene regulation?

Answer 2

• TFs (eg SREBP) and nuclear receptors
• mTOR kinase
• AMP-activated protein kinase (AMPK)

Question 3

what is SREBP?

Answer 3

sterol regulatory element-binding protein
a TF anchored to the ER
low sterol -> SREBP is cleaved -> N terminus translocates into nucleus, binds to SRE -> activates sterol synthesis -> sterol makes cholesterol, FAs, triglycerides
- controlled by mTOR signalling pathway

Question 4

what does mTORC1 do?

Answer 4

1. promotes de novo lipid synthesis through SREBP transcription factors -> fatty acid and cholesterol synthesis
2. promotes synthesis of nucleotides (needed for DNA replication and ribosome biogenesis)
3. facilitates growth (promotes a shift in glucose metabolism from oxphos to glycolysis)

Question 5

what does AMPK do?

Answer 5

it senses the energy status of the cell (ATP:AMP level)
AMPK regulates physiological processes through phosphorylation of TFs and co-activators
- modulates protein-DNA interactions
- affects protein-protein interactions
- activates stress-promoted transcription via histone H2B Ser36 phosphorylation

Question 6

what are some metabolites that are cofactors for epigenetic machineries?

Answer 6

UDP-GlcNac
acetyl CoA
NAD+
SAM
a-KG
ATP

Question 7

how does acetyl CoA affect epigenetics

Answer 7

acetyl CoA is a cosubstrate of HATs (histone acetyltransferases)

Question 8

how does NAD+ affect epigenetics?

Answer 8

NAD+ is a co-factor of Class III HDACs
- consumes NAD+, produces NAM and O-ac-ADP ribose

Question 9

how are different pools of acetyl-CoA formed?

Answer 9

citrate that is not used in the TCA cycle transported from mito to cytosol -> converted back to acetyl-CoA

Question 10

what effects does histone acetylation have?

Answer 10

• neutralises + charge of lysine residues -> more open, accessible structure
• creates binding sites recognized by bromodomain-containing regulators

Question 11

what is ACSS2 and what does it do

Answer 11

ACSS2 is an acetyl-CoA synthetase (enzyme that produces acetyl CoA)
ACSS2 and CBP (a HAT) interact -> in close proximity to CBP, the production of acetyl CoA is used for acetylation

Question 12

what is SAM?

Answer 12

S-adenosyl methionine
SAM is a cosubstrate of lysine methyltransferases and DNMTs
is a universal methyl donor

Question 13

how does a DNMT inhibitor work?

Answer 13

inhibitor competes with SAM for the SAM binding pocket on the DNMT -> SAM cannot bind -> reduced methylation
- not specific since targets SAM binding pocket

Question 14

how is SAM synthesised?

Answer 14

methionine -> (methionine adenosyl-transferase (MAT)) -> SAM

Question 15

what is the methyl group, aminopropyl group and sulfur group of SAM used for?

Answer 15

methyl group: methylation reactions
aminopropyl group: synthesis of polyamines
sulfur group: synthesis of glutathione

Question 16

what is a-kg and how does it affect epigenetics?

Answer 16

a-ketoglutarate is a co-substrate of DNA demethylases

Question 17

what is the one-carbon pathway?

Answer 17

methionine cycle + folate cycle
carbon units cycled from aa
outcomes includes epigenetics

Question 18

what happens if SAM is depleted through methionine deprivation?

Answer 18

reduced methylations
some methylations are reduced faster than others (eg H3K4me3), could be due to different half lives of diff modifications

Question 19

what is IDH1/2 and how do they affect epigenetics?

Answer 19

isocitrate dehydrogenase, converts isocitrate into a-KG
in cancer, IDH1&2 are mutated -> gives a diff version of a-KG (2-HG)
2-HG is an inhibitory metabolite -> competes with a-kg for binding to histone demethylases -> increased histone and DNA methylation, de-differentiation of gene expression