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The Role of Protein Lysine Methylation in the Regulation of Protein Function: Looking Beyond the Histone Code

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The DNA, RNA, and Histone Methylomes

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Abstract

Histone proteins and their diverse array of post-translational modifications have been subject to exquisite evolutionary conservation in eukaryotes. Accordingly, the factors that control the deposition, removal, and interpretation of histone modifications are themselves deeply conserved, with many strongly impacting development and disease in humans. Of these modifications, lysine methylation has in recent years emerged as a prevalent modification occurring on histone proteins. However, although numerous lysine methyltransferase and demethylase enzymes have been extensively characterized with respect to their ability to control methylation at specific histone residues, their known targets have been rapidly expanding to include the methylation of non-histone proteins as well. These findings extend the role of lysine methylation well-beyond the established histone code and its role in epigenetic regulation. To date, this lysine methylation has been found to directly regulate protein sub-cellular localization, protein-protein interactions, and has also been found to interplay with other post-translational modifications. As a result, lysine methylation is now known to coordinate protein function and be a key driving of a growing list of cellular signaling events, including apoptosis, DNA damage repair, protein translation, cell growth, and signal transduction among others. This chapter will provide insight into the role of protein lysine methylation and its role in regulating protein function and its impact on human development and disease.

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References

  • Accari SL, Fisher PR (2015) Emerging roles of JmjC domain-containing proteins. Int Rev Cell Mol Biol 319:165–220

    Article  CAS  PubMed  Google Scholar 

  • Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786–794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ambler R, Rees M (1959) Epsilon-N-methyl-lysine in bacterial flagellar protein. Nature 184:56–57

    Article  CAS  PubMed  Google Scholar 

  • Anderson D, Koch CA, Grey L et al (1990) Binding of SH2 domains of phospholipase C gamma 1, GAP, and Src to activated growth factor receptors. Science 250:979–982

    Article  CAS  PubMed  Google Scholar 

  • Arrowsmith CH, Bountra C, Fish PV et al (2012) Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 11:384–400

    Article  CAS  PubMed  Google Scholar 

  • Baek SH, Kim K (2016) Regulation of HIF-1α stability by lysine methylation. BMB Rep 49:245–246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barbier M, Owings JP, Martínez-Ramos I et al (2013) Lysine trimethylation of EF-Tu mimics platelet-activating factor to initiate Pseudomonas aeruginosa pneumonia. MBio 4:e00207–e00213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biet F, de Melo Marques MA, Grayon M et al (2007) Mycobacterium smegmatis produces an HBHA homologue which is not involved in epithelial adherence. Microbes Infect 9:175–182

    Article  CAS  PubMed  Google Scholar 

  • Biggar KK, Li SS (2015) Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 16:5–17

    Article  CAS  PubMed  Google Scholar 

  • Brahms H, Meheus L, de Brabandere V et al (2001) Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B’ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7:1531–1542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao XJ, Garcia BA (2016) Global proteomics analysis of protein lysine methylation. Curr Protoc Protein Sci 86:24.8.1–24.8.19

    Article  Google Scholar 

  • Cao XJ, Arnaudo AM, Garcia BA (2013) Large-scale global identification of protein lysine methylation in vivo. Epigenetics 8:477–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carlson SM, Gozani O (2016) Nonhistone lysine methylation in the regulation of cancer pathways. Cold Spring Harb Perspect Med 6:11

    Article  CAS  Google Scholar 

  • Carlson SM, Moore KE, Green EM et al (2014) Proteome-wide enrichment of proteins modified by lysine methylation. Nat Protoc 9:37–50

    Article  CAS  PubMed  Google Scholar 

  • Casciello F, Windloch K, Gannon F et al (2015) Functional role of G9a histone methyltransferase in cancer. Front Immunol 6:487

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chao CC, Wu SL, Ching WM (2004) Using LC-MS with de novo software to fully characterize the multiple methylations of lysine residues in a recombinant fragment of an outer membrane protein from a virulent strain of Rickettsia prowazekii. Biochim Biophys Acta 1702:145–152

    Article  CAS  PubMed  Google Scholar 

  • Chao CC, Zhang Z, Wang H et al (2008) Serological reactivity and biochemical characterization of methylated and unmethylated forms of a recombinant protein fragment derived from outer membrane protein B of Rickettsia typhi. Clin Vaccine Immunol 15:684–690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Zhu WG (2016) Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage. Acta Biochim Biophys Sin 48:603–616

    Article  CAS  PubMed  Google Scholar 

  • Chen H, Xue Y, Huang N et al (2006a) MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res 34:W249–W253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Z, Zang J, Whetstine J et al (2006b) Structural insights into histone demethylation by JMJD2 family members. Cell 125:691–702

    Article  CAS  PubMed  Google Scholar 

  • Chen L, Vasilatos SN, Qin Y et al (2017) Functional characterization of lysine-specific demethylase 2 (LSD2/KDM1B) in breast cancer progression. Oncotarget 8:81737–81753

    PubMed  PubMed Central  Google Scholar 

  • Cho HS, Hayami S, Toyokawa G et al (2012) RB1 methylation by SMYD2 enhances cell cycle progression through an increase of RB1 phosphorylation. Neoplasia 14:476–486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chuikov S, Kurash JK, Wilson JR et al (2004) Regulation of p53 activity through lysine methylation. Nature 432:353–360

    Article  CAS  PubMed  Google Scholar 

  • Ciccia A, Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40:179–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke SG (2013) Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem Sci 38:243–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cloutier P, Lavallée-Adam M, Faubert D et al (2014) Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin. J Proteome 100:115–124

    Article  CAS  Google Scholar 

  • D’Oto A, Tian QW, Davidoff AM et al (2016) Histone demethylases and their roles in cancer epigenetics. J Med Oncol Ther 1:34

    PubMed  PubMed Central  Google Scholar 

  • Debler EW, Jain K, Warmack RA et al (2016) A glutamate/aspartate switch controls product specificity in a protein arginine methyltransferase. Proc Natl Acad Sci USA 113:2068–2073

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delogu G, Chiacchio T, Vanini V et al (2011) Methylated HBHA produced in M. smegmatis discriminates between active and non-active TB disease among the QFT-IT-responders. Eur Respir J 38:1901

    Google Scholar 

  • Dhami GK, Liu H, Galka M et al (2013) Dynamic methylation of Numb by Set8 regulates its binding to p53 and apoptosis. Mol Cell 50:565–576

    Article  CAS  PubMed  Google Scholar 

  • Duan G, Walther D (2015) The roles of post-translational modifications in the context of protein interaction networks. PLoS Comput Biol 11:1–23

    Article  CAS  Google Scholar 

  • Dulev S, Tkach J, Lin S et al (2014) SET8 methyltransferase activity during the DNA double-strand break response is required for recruitment of 53BP1. EMBO Rep 15(11):1163–1174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8:286–298

    Article  CAS  PubMed  Google Scholar 

  • Falnes PØ, Jakobsson ME, Davydova E et al (2016) Protein lysine methylation by seven-β-strand methyltransferases. Biochem J 473:1995–2009

    Article  CAS  PubMed  Google Scholar 

  • Fang R, Chen F, Dong Z et al (2013) LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell 49:558–570

    Article  CAS  PubMed  Google Scholar 

  • Freitag M (2017) Histone methylation by SET domain proteins in fungi. Annu Rev Microbiol 71:413–439

    Article  CAS  PubMed  Google Scholar 

  • Gayatri S, Bedford MT (2014) Readers of histone methylarginine marks. Biochim Biophys Acta 1839:702–710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greer EL, Shi Y (2012) Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13:343–357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo A, Gu H, Zhou J et al (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol Cell Proteomics 13:372–387

    Article  CAS  PubMed  Google Scholar 

  • Hamamoto R, Silva FP, Tsuge M et al (2006) Enhanced SMYD3 expression is essential for the growth of breast cancer cells. Cancer Sci 97:113–118

    Article  CAS  PubMed  Google Scholar 

  • Hamamoto R, Saloura V, Nakamura Y (2015) Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat Rev Cancer 15:110–124

    Article  CAS  PubMed  Google Scholar 

  • Helin K, Dhanak D (2013) Chromatin proteins and modifications as drug targets. Nature 502:480–488

    Article  CAS  PubMed  Google Scholar 

  • Horton JR, Upadhyay AK, Qi HH et al (2010) Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol 17:38–43

    Article  CAS  PubMed  Google Scholar 

  • Hou H, Yu H (2010) Structural insights into histone lysine demethylation. Curr Opin Struct Biol 20:739–748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu LL, Li Z, Wang K et al (2011) Prediction and analysis of protein methylarginine and methyllysine based on Multisequence features. Biopolymers 95:763–771

    CAS  PubMed  Google Scholar 

  • Huang J, Perez-Burgos L, Placek BJ et al (2006) Repression of p53 activity by Smyd2-mediated methylation. Nature 444:629–632

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Sengupta R, Espejo AB et al (2007) p53 is regulated by the lysine demethylase LSD1. Nature 449:105–108

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Dorsey J, Chuikov S et al (2010) G9a and Glp methylate lysine 373 in the tumor suppressor p53. J Biol Chem 285:9636–9641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hyun K, Jeon J, Park K et al (2017) Writing, erasing and reading histone lysine methylations. Exp Mol Med 49:e324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jakobsson ME, Moen A, Bousset L et al (2013) Identification and characterization of a novel human methyltransferase modulating Hsp70 function through lysine methylation. J Biol Chem 288:27752–27763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jørgensen S, Elvers I, Trelle MB et al (2007) The histone methyltransferase SET8 is required for S-phase progression. J Cell Biol 179:1337–1345

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kernstock S, Davydova E, Jakobsson M et al (2012) Lysine methylation of VCP by a member of a novel human protein methyltransferase family. Nat Commun 3:1038

    Article  PubMed  CAS  Google Scholar 

  • Kim S, Paik WK (1965) Studies on the origin of epsilon-N-methyl-L-lysine in protein. J Biol Chem 240:4629–4634

    CAS  PubMed  Google Scholar 

  • Kim Y, Nam HJ, Lee J et al (2016a) Methylation-dependent regulation of HIF-1α stability restricts retinal and tumour angiogenesis. Nat Commun 7:10347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim JH, Yoo BC, Yang WS et al (2016b) The role of protein arginine methyltransferases in inflammatory responses. Mediat Inflamm 2016:4028353

    Google Scholar 

  • Klose RJ, Kallin EM, Zhang Y (2006) JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 7:715–727

    Article  CAS  PubMed  Google Scholar 

  • Kooistra SM, Helin K (2012) Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol 13:297–311

    Article  CAS  PubMed  Google Scholar 

  • Kunizaki M, Hamamoto R, Silva FP et al (2007) The lysine 831 of vascular endothelial growth factor receptor 1 is a novel target of methylation by SMYD3. Cancer Res 67:10759–10765

    Article  CAS  PubMed  Google Scholar 

  • Lachner M, O’Carroll D, Rea S et al (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116–120

    Article  CAS  PubMed  Google Scholar 

  • Lanouette S, Mongeon V, Figeys D et al (2014) The functional diversity of protein lysine methylation. Mol Syst Biol 10:724

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee JY, Park JH, Choi HJ et al (2017) LSD1 demethylates HIF1α to inhibit hydroxylation and ubiquitin-mediated degradation in tumor angiogenesis. Oncogene 36:5512–5521

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Galka M, Mori E et al (2013) A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response. Mol Cell 50:723–735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Chen Z, Xu C et al (2015) Repression of hypoxia-inducible factor α signaling by Set7-mediated methylation. Nucleic Acids Res 43:5081–5098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Wang Y, Chen C et al (2017) LSD1 binds to HPV16 E7 and promotes the epithelial-mesenchymal transition in cervical cancer by demethylating histones at the Vimentin promoter. Oncotarget 8:11329–11342

    PubMed  Google Scholar 

  • Lu X, Simon MD, Chodaparambil JV et al (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol 15:1122–1124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marabelli C, Marrocco B, Mattevi A (2016) The growing structural and functional complexity of the LSD1/KDM1A histone demethylase. Curr Opin Struct Biol 41:135–144

    Article  CAS  PubMed  Google Scholar 

  • Mazur PK, Reynoird N, Khatri P et al (2014) SMYD3 links lysine methylation of MAP 3K2 to Ras-driven cancer. Nature 510:283–287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Murray K (1964) The occurrence of epsilon-N-methyl lysine in histones. Biochemistry 3:10–15

    Article  CAS  PubMed  Google Scholar 

  • Nagasawa S, Sedukhina AS, Nakagawa Y et al (2015) LSD1 overexpression is associated with poor prognosis in basal-like breast cancer, and sensitivity to PARP inhibition. PLoS One 10:e0118002

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ng SS, Kavanagh KL, McDonough M et al (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 448:87–91

    Article  CAS  PubMed  Google Scholar 

  • Ng SS, Yue WW, Oppermann U et al (2009) Dynamic protein methylation in chromatin biology. Cell Mol Life Sci 66:407–422

    Article  CAS  PubMed  Google Scholar 

  • Nishioka K, Rice JC, Sarma K et al (2002) PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell 9:1201–1213

    Article  CAS  PubMed  Google Scholar 

  • Petrossian TC, Clarke SG (2009a) Bioinformatic identification of novel methyltransferases. Epigenomics 1:163–175

    Article  CAS  PubMed  Google Scholar 

  • Petrossian TC, Clarke SG (2009b) Multiple motif scanning to identify methyltransferases from the yeast proteome. Mol Cell Proteomics 8:1516–1526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poulard C, Rambaud J, Hussein N et al (2014) JMJD6 regulates ERα methylation on arginine. PLoS One 9:e87982

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Qiu WR, Xiao X, Lin WZ et al (2014) iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach. Biomed Res Int 2014:947416

    PubMed  PubMed Central  Google Scholar 

  • Scoumanne A, Chen X (2008) Protein methylation: a new regulator of the p53 tumor suppressor. Histol Histopathol 23:1143–1149

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shao J, Xu D, Tsai SN et al (2009) Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One 4:e4920

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shi Y, Lan F, Matson C et al (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953

    Article  CAS  PubMed  Google Scholar 

  • Shi X, Kachirskaia I, Yamaguchi H et al (2007) Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 27:636–646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi SP, Qiu JD, Sun XY et al (2012) PMeS: prediction of methylation sites based on enhanced feature encoding scheme. PLoS One 7:e38772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi Y, Guo Y, Hu Y et al (2015) Position-specific prediction of methylation sites from sequence conservation based on information theory. Sci Rep 5:12403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shien DM, Lee TY, Chang WC et al (2009) Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem 30:1532–1543

    Article  CAS  PubMed  Google Scholar 

  • Singer MS, Kahana A, Wolf AJ et al (1998) Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150:613–632

    CAS  PubMed  PubMed Central  Google Scholar 

  • Smith BC, Denu JM (2009) Chemical mechanisms of histone lysine and arginine modifications. Biochim Biophys Acta 1789:45–57

    Article  CAS  PubMed  Google Scholar 

  • Spillantini MG, Schmidt ML, Lee VM et al (1997) Alpha-synuclein in Lewy bodies. Nature 388:839–840

    Article  CAS  PubMed  Google Scholar 

  • Stocker B, McDonough MA (1961) Gene determining presence or absence of [varepsilon]-N-methyl-lysine in Salmonella flagellar protein. Nature 189:556–558

    Article  Google Scholar 

  • Walport LJ, Hopkinson RJ, Chowdhury R et al (2016) Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun 7:11974

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • West LE, Gozani O (2011) Regulation of p53 function by lysine methylation. Epigenomics 3:363–369

    Article  CAS  Google Scholar 

  • West LE, Roy S, Lachmi-Weiner K et al (2010) The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression. J Biol Chem 285:37725–37732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Z, Connolly J, Biggar KK (2017) Beyond histones: the expanding roles of lysine methylation. FEBS J 284:2732–2744

    Article  CAS  PubMed  Google Scholar 

  • Xie Q, Hao Y, Tao L et al (2012) Lysine methylation of FOXO3 regulates oxidative stress-induced neuronal cell death. EMBO Rep 13:371–377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Hu L, Wang P et al (2010) Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 20:886

    Article  CAS  PubMed  Google Scholar 

  • Yang SJ, Park YS, Cho JH et al (2017) Regulation of hypoxia responses by flavin adenine dinucleotide-dependent modulation of HIF-1α protein stability. EMBO J 36:1011–1028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X, Zhou L, Cheng X (2000) Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J 19:3509–3519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu W (2012) Methylation of FoxO3 regulates neuronal cell death. Acta Pharmacol Sin 33:577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by an NSERC discovery grant to K.K. Biggar.

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Adhikary, H., Bakos, O., Biggar, K.K. (2019). The Role of Protein Lysine Methylation in the Regulation of Protein Function: Looking Beyond the Histone Code. 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_18

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