Chromatin organization

Reyes AA, Marcum RD, He Y. Structure and Function of Chromatin Remodelers. Journal of Molecular Biology. 2021 Jul;433(14):166929. doi: 10.1016/j.jmb.2021.166929.; Morgan MAJ, Shilatifard A. Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat Genet. 2020 Dec;52(12):1271–81. doi: 10.1038/s41588-020-00736-4. PMID: 33257899.; Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016 Aug;17(8):487–500. doi: 10.1038/nrg.2016.59. PMID: 27346641.; DesJarlais R, Tummino PJ. Role of Histone-Modifying Enzymes and Their Complexes in Regulation of Chromatin Biology. Biochemistry. 2016 Mar 22;55(11):1584–99. doi: 10.1021/acs.biochem.5b01210. PMID: 26745824.; Andrews AJ, Luger K. Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys. 2011;40():99–117. doi: 10.1146/annurev-biophys-042910-155329. PMID: 21332355.; Li G, Reinberg D. Chromatin higher-order structures and gene regulation. Current Opinion in Genetics & Development. 2011 Apr;21(2):175–86. doi: 10.1016/j.gde.2011.01.022.; Gilbert N, Gilchrist S, Bickmore WA. Chromatin organization in the mammalian nucleus. Int Rev Cytol. 2005;242():283–336. doi: 10.1016/s0074-7696(04)42007-5. PMID: 15598472.; Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997 Sep 18;389(6648):251–60. doi: 10.1038/38444. PMID: 9305837.

Metabolites

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Formaldehyde

Formula: CH2O (30.0105642)

CAS ID: 50-00-0

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

2-oxoglutarate(2-)

Formula: C5H4O5 (144.00587339999998)

CAS ID: 64-15-3

succinate(2-)

Formula: C4H4O4 (116.01095839999999)

CAS ID: 56-14-4



Enzyme

EC Number name full name note
1.14.11.-
1.14.11.66 [histone H3]-trimethyl-L-lysine9 demethylase [histone H3]-N6,N6,N6-trimethyl-L-lysine9,2-oxoglutarate:oxygen oxidoreductase
1.14.11.67 [histone H3]-trimethyl-L-lysine4 demethylase [histone H3]-N6,N6,N6-trimethyl-L-lysine4,2-oxoglutarate:oxygen oxidoreductase
1.14.11.69 [histone H3]-trimethyl-L-lysine36 demethylase [histone H3]-N6,N6,N6-trimethyl-L-lysine36,2-oxoglutarate:oxygen oxidoreductase
2.1.1.319 type I protein arginine methyltransferase S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega-dimethyl-L-arginine-forming)
2.1.1.320 type II protein arginine methyltransferase S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega'-dimethyl-L-arginine-forming)
2.1.1.360 [histone H3]-lysine79 N-trimethyltransferase S-adenosyl-L-methionine:[histone H3]-L-lysine79 N6-trimethyltransferase
2.1.1.361 [histone H4]-lysine20 N-methyltransferase S-adenosyl-L-methionine:[histone H4]-L-lysine20 N6-methyltransferase
2.3.1.48 histone acetyltransferase acetyl-CoA:[protein]-L-lysine acetyltransferase
2.7.11.22 cyclin-dependent kinase ATP:cyclin phosphotransferase


Proteins

Protein ID name full name