Epigenetic regulation of gene expression

Almeida MV, Vernaz G, Putman ALK, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet. 2022 Jun;38(6):529–53. doi: 10.1016/j.tig.2022.02.009. PMID: 35307201.; Guarnaccia AD, Tansey WP. Moonlighting with WDR5: A Cellular Multitasker. J Clin Med. 2018 Jan 30;7(2). PMID: 29385767; PMCID: PMC5852437.; Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003 Mar;33 Suppl():245–54. doi: 10.1038/ng1089. PMID: 12610534.

Metabolites

Acetate

Formula: C2H4O2 (60.0211284)

CAS ID: 64-19-7

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Fe2+

Formula: Fe (55.934939)

CAS ID: 15438-31-0

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Nicotinamide

Formula: C6H6N2O (122.0480106)

CAS ID: 98-92-0

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

Cytosine-5-carboxylic acid

Formula: C5H5N3O3 (155.03309000000002)

CAS ID: 3650-93-9

5-Formylcytosine

Formula: C5H5N3O2 (139.03817500000002)

CAS ID: 4425-59-6

2-oxoglutarate(2-)

Formula: C5H4O5 (144.00587339999998)

CAS ID: 64-15-3

succinate(2-)

Formula: C4H4O4 (116.01095839999999)

CAS ID: 56-14-4

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

2''-O-acetyl-ADP-D-ribose(2-)

Formula: C17H23N5O15P2 (599.0665868000001)

CAS ID:

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:



Enzyme

EC Number name full name note
2.1.1.-
1.14.11.68 [histone H3]-trimethyl-L-lysine27 demethylase [histone H3]-N6,N6,N6-trimethyl-L-lysine27,2-oxoglutarate:oxygen oxidoreductase
1.14.11.80 methylcytosine dioxygenase 5-methylcytosine in DNA,2-oxoglutarate:oxygen oxidoreductase
1.14.19.1 stearoyl-CoA 9-desaturase stearoyl-CoA,ferrocytochrome-b5:oxygen oxidoreductase (9,10-dehydrogenating)
2.1.1.356 [histone H3]-lysine27 N-trimethyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine27 N6-methyltransferase
2.1.1.364 [histone H3]-lysine4 N-methyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase
2.1.1.366 [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase S-adenosyl-L-methionine:[histone H3]-N6,N6-dimethyl-L-lysine9 N6-methyltransferase
2.1.1.367 [histone H3]-lysine9 N-methyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine9 N6-methyltransferase
2.1.1.37 DNA (cytosine-5-)-methyltransferase S-adenosyl-L-methionine:DNA (cytosine-5-)-methyltransferase
2.3.1.15 glycerol-3-phosphate 1-O-acyltransferase acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase
2.3.1.199 very-long-chain 3-oxoacyl-CoA synthase malonyl-CoA:very-long-chain acyl-CoA malonyltransferase (decarboxylating and thioester-hydrolysing)
2.3.1.20 diacylglycerol O-acyltransferase acyl-CoA:1,2-diacyl-sn-glycerol O-acyltransferase
2.3.1.286 protein acetyllysine N-acetyltransferase [protein]-N6-acetyl-L-lysine:NAD+ N-acetyltransferase (NAD+-hydrolysing; 2''-O-acetyl-ADP-D-ribose-forming)
2.3.1.48 histone acetyltransferase acetyl-CoA:[protein]-L-lysine acetyltransferase
2.3.1.51 1-acylglycerol-3-phosphate O-acyltransferase acyl-CoA:1-acyl-sn-glycerol-3-phosphate 2-O-acyltransferase
2.3.1.57 diamine N-acetyltransferase acetyl-CoA:alkane-alpha,omega-diamine N-acetyltransferase
2.3.1.76 retinol O-fatty-acyltransferase acyl-CoA:retinol O-acyltransferase
2.3.2.27 RING-type E3 ubiquitin transferase [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type)
2.4.1.255 protein O-GlcNAc transferase UDP-N-acetyl-D-glucosamine:protein-O-beta-N-acetyl-D-glucosaminyl transferase
2.7.10.2 non-specific protein-tyrosine kinase ATP:[protein]-L-tyrosine O-phosphotransferase (non-specific)
2.7.11.1 non-specific serine/threonine protein kinase ATP:protein phosphotransferase (non-specific)
2.7.11.2 [pyruvate dehydrogenase (acetyl-transferring)] kinase ATP:[pyruvate dehydrogenase (acetyl-transferring)] phosphotransferase
2.7.11.22 cyclin-dependent kinase ATP:cyclin phosphotransferase
2.7.11.23 [RNA-polymerase]-subunit kinase ATP:[DNA-directed RNA polymerase] phosphotransferase
2.7.11.26 tau-protein kinase ATP:[tau-protein] O-phosphotransferase
2.7.7.6 DNA-directed RNA polymerase nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
3.1.1.23 acylglycerol lipase glycerol-ester acylhydrolase
3.1.1.3 triacylglycerol lipase triacylglycerol acylhydrolase
3.1.1.32 phospholipase A1 phosphatidylcholine 1-acylhydrolase
3.1.1.34 lipoprotein lipase triacylglycero-protein acylhydrolase
3.1.1.4 phospholipase A2 phosphatidylcholine 2-acylhydrolase
3.1.1.79 hormone-sensitive lipase diacylglycerol acylhydrolase
3.1.3.4 phosphatidate phosphatase diacylglycerol-3-phosphate phosphohydrolase
3.2.2.29 thymine-DNA glycosylase thymine-DNA deoxyribohydrolase (thymine-releasing)
3.5.1.98 histone deacetylase histone amidohydrolase
3.6.4.13 RNA helicase
5.6.2.3 DNA 5'-3' helicase DNA 5'-3' helicase (ATP-hydrolysing)
5.6.2.4 DNA 3'-5' helicase DNA 3'-5' helicase (ATP-hydrolysing)
6.2.1.1 acetate-CoA ligase acetate:CoA ligase (AMP-forming)
6.2.1.15 arachidonate-CoA ligase arachidonate:CoA ligase (AMP-forming)
6.2.1.17 propionate-CoA ligase propanoate:CoA ligase (AMP-forming)
6.2.1.24 phytanate-CoA ligase phytanate:CoA ligase (AMP-forming)
6.2.1.3 long-chain-fatty-acid-CoA ligase long-chain fatty acid:CoA ligase (AMP-forming)


Proteins

Protein ID name full name