Abstract
Lysine and arginine methylations are among the most abundant posttranslational modifications found on histone proteins. The recognition of methylated lysine and arginine residues by epigenetic reader proteins provides an important molecular requirement for regulation of human genes. Recent structural and mechanistic studies importantly advanced our basic understanding of biomolecular recognition of methylated histones by diverse classes of epigenetic readers. In this chapter, we describe chemical biological studies on the recognition of methylated histones by the aromatic cage-containing reader proteins.
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References
Al Temimi AHK, Belle R, Kumar K et al (2018) Recognition of shorter and longer trimethyllysine analogues by epigenetic reader proteins. Chem Commun 54:2409–2412
Andrews FH, Strahl BD, Kutateladze TG (2016) Insights into newly discovered marks and readers of epigenetic information. Nat Chem Biol 12:662–668
Baril SA, Koenig AL, Krone MW et al (2017) Investigation of trimethyllysine binding by the HP1 chromodomain via unnatural amino acid mutagenesis. J Am Chem Soc 139:17253–17256
Belle R, Al Temimi AHK, Kumar K et al (2017) Investigating d-lysine stereochemistry for epigenetic methylation, demethylation and recognition. Chem Commun 53:13264–13267
Bhushan B, Erdmann A, Zhang Y et al (2018) Investigations on small molecule inhibitors targeting the histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorganic Med Chem 26:2984–2991
Blus BJ, Wiggins K, Khorasanizadeh S (2011) Epigenetic virtues of chromodomains. Crit Rev Biochem Mol Biol 46:507–526
Bonasio R, Lecona E, Reinberg D (2010) MBT domain proteins in development and disease. Semin Cell Dev Biol 21:221–230
Boswell RE, Mahowald AP (1985) tudor, a gene required for assembly of the germ plasm in Drosophila melanogaster. Cell 43:97–104
Botuyan MV, Lee J, Ward IM et al (2006) Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 127:1361–1373
Champagne KS, Kutateladze TG (2009) Structural insight into histone recognition by the ING PHD fingers. Curr Drug Targets 10:432–441
Chen Z, Notti RQ, Ueberheide B et al (2018) Quantitative and structural assessment of histone methyllysine analogue engagement by cognate binding proteins reveals affinity decrements relative to those of native counterparts. Biochemistry 57:300–304
Collins RE, Northrop JP, Horton JR et al (2008) The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol 15:245–250
Côté J, Richard S (2005) Tudor domains bind symmetrical dimethylated arginines. J Biol Chem 280:28476–28483
Dawson MA, Kouzarides T (2012) Cancer epigenetics: from mechanism to therapy. Cell 150:21–27
Daze KD, Pinter T, Beshara CS et al (2012) Supramolecular hosts that recognize methyllysines and disrupt the interaction between a modified histone tail and its epigenetic reader protein. Chem Sci 3:2695–2699
Eisert RJ, Waters ML (2011) Tuning HP1α chromodomain selectivity for di- and trimethyllysine. ChemBioChem 12:2786–2790
Eustermann S, Yang JC, Law MJ et al (2011) Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nat Struct Mol Biol 18:777–783
Gamal-Eldin MA, Macartney DH (2013) Selective molecular recognition of methylated lysines and arginines by cucurbit[6]uril and cucurbit[7]uril in aqueous solution. Org Biomol Chem 11:488–495
Gayatri S, Bedford MT (2014) Readers of histone methlyarginine marks. Biochim Biophys Acta 1839:702–710
Greer EL, Shi Y (2012) Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13:343–357
Hanauer T, Hopkinson RJ, Patel K et al (2017) Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor. Org Biomol Chem 15:1100–1105
Hof F (2016) Host-guest chemistry that directly targets lysine methylation: synthetic host molecules as alternatives to bio-reagents. Chem Commun 52:10093–10108
Hughes RM, Wiggins KR, Khorasanizadeh S et al (2007) Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect. Proc Natl Acad Sci U S A 104:11184–11188
Iwase S, Xiang B, Ghosh S et al (2011) ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nat Struct Mol Biol 18:769–777
Jahan S, Davie JR (2015) Protein arginine methyltransferases (PRMTs): role in chromatin organization. Adv Biol Regul 57:173–184
James LI, Beaver JE, Rice NW et al (2013) A synthetic receptor for asymmetric dimethyl arginine. J Am Chem Soc 135:6450–6455
Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080
Kamps JJAG, Huang J, Poater J et al (2015) Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins. Nat Commun 6:8911
Kuo AJ, Song J, Cheung P et al (2012) The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature 484:115–121
Le DD, Cortesi AT, Myers SA et al (2013) Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc 135:2879–2882
Lee YJ, Schmidt MJ, Tharp JM et al (2016) Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader. Chem Commun 52:12606–12609
Li H, Fischle W, Wang W et al (2007) Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Mol Cell 28:677–691
Liu K, Chen C, Guo Y et al (2010) Structural basis for recognition of arginine methylated Piwi proteins by the extended tudor domain. Proc Natl Acad Sci U S A 107:18398–18403
Liu K, Guo Y, Liu H et al (2012) Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30. PLoS One 7:e30375
Liu J, Zhang S, Liu M et al (2018a) Structural plasticity of the TDRD3 tudor domain probed by a fragment screening hit. FEBS J 285:2091–2103
Liu R, Gao J, Yang Y et al (2018b) PHD finger protein 1 (PHF1) is a novel reader for histone H4R3 symmetric dimethylation and coordinates with PRMT5–WDR77/CRL4B complex to promote tumorigenesis. Nucleic Acids Res 46:6608–6626
Lu R, Wang GG (2013) Tudor: a versatile family of histone methylation “readers”. Trends Biochem Sci 38:546–555
Maurer-Stroh S, Dickens NJ, Hughes-Davies L et al (2003) The tudor domain “Royal Family”: tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci 28:69–74
McGovern RE, Snarr BD, Lyons JA et al (2015) Structural study of a small molecule receptor bound to dimethyllysine in lysozyme. Chem Sci 6:442–449
Migliori V, Müller J, Phalke S et al (2012) Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol 19:136–145
Min J, Allali-Hassani A, Nady N et al (2007) L3MBTL1 recognition of mono- and dimethylated histones. Nat Struct Mol Biol 14:1229–1230
Mosammaparast N, Shi Y (2010) Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem 79:155–179
Patel DJ, Wang Z (2013) Readout of epigenetic modifications. Annu Rev Biochem 82:81–118
Pieters B, Belle R, Mecinovic J (2013) The effect of the length of histone H3K4me3 on recognition by reader proteins. ChemBioChem 14:2408–2412
Pieters BJGE, Meulenbroeks E, Belle R et al (2015) The role of electrostatic interactions in binding of histone H3K4me2/3 to the Sgf29 tandem tudor domain. PLoS One 10:e0139205
Pinkin NK, Waters ML (2014) Development and mechanistic studies of an optimized receptor for trimethyllysine using iterative redesign by dynamic combinatorial chemistry. Org Biomol Chem 12:7059–7067
Qin S, Min J (2014) Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci 39:536–547
Sanchez R, Zhou MM (2011) The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36:364–372
Seeliger D, Soeroes S, Klingberg R et al (2012) Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches. ACS Chem Biol 7:150–154
Sikorsky T, Hobor F, Krizanova E et al (2012) Recognition of asymmetrically dimethylated arginine by TDRD3. Nucleic Acids Res 40:11748–11755
Simon MD, Chu F, Racki LR et al (2007) The site-specific installation of methyl-lysine analogs into recombinant histones. Cell 128:1003–1012
Sims RJ, Reinberg D (2006) Histone H3 Lys 4 methylation: caught in a bind? Genes Dev 20:2779–2786
Smith BC, Denu JM (2009) Chemical mechanisms of histone lysine and arginine modifications. Biochim Biophys Acta 1789:45–57
Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45
Su X, Zhu G, Ding X et al (2014) Molecular basis underlying histone H3 lysine – arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev 28:622–636
Supekar S, Papageorgiou AC, Gemmecker G et al (2018) Conformational selection of dimethylarginine recognition by the survival motor neuron tudor domain. Angew Chemie Int Ed 57:486–490
Taverna SD, Li H, Ruthenburg AJ et al (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14:1025–1040
Teske KA, Hadden MK (2017) Methyllysine binding domains: structural insight and small molecule probe development. Eur J Med Chem 136:14–35
Tripsianes K, Madl T, MacHyna M et al (2011) Structural basis for dimethylarginine recognition by the tudor domains of human SMN and SPF30 proteins. Nat Struct Mol Biol 18:1414–1420
Wagner EK, Nath N, Flemming R et al (2012) Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 51:8293–8306
Yang Y, Lu Y, Espejo A et al (2010) TDRD3 is an effector molecule for arginine methylated histone marks. Mol Cell 40:1016–1023
Yun M, Wu J, Workman JL et al (2011) Readers of histone modifications. Cell Res 21:564–578
Zhou MM (2015) Histone recognition. Springer, Cham
Acknowledgement
We thank the European Research Council for financial support (ERC Starting Grant to J.M., ChemEpigen-715691).
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Porzberg, M.R.B., Pieters, B.J.G.E., Mecinović, J. (2019). Biomolecular Recognition of Methylated Histones. In: Jurga, S., Barciszewski, J. (eds) The DNA, RNA, and Histone Methylomes. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-030-14792-1_17
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DOI: https://doi.org/10.1007/978-3-030-14792-1_17
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