Abstract
Accumulating evidence suggests that epigenetic factors exemplified by histone posttranslational modification (PTM) cooperate with DNA sequence to control a diverse range of biological processes, including cell differentiation and reprogramming, organism development, and tissue homeostasis. Protein deimination of nucleosomal histones is a relatively less-characterized form of histone PTM. However, it appears to play a unique and incompletely understood role in epigenetics. At a molecular level, histone deimination directly antagonizes arginine methylation on histone tails, thereby interfering with the transcriptional consequences of such an effect. In addition, deimination can also affect the activity of important histone-modifying enzymes, such as the acetyl transferase p300, consequently amplifying the transcriptional outputs. In physiological or pathological conditions, histone deimination mediates chromatin decondensation and elicits cell-specific innate immune response in neutrophils; increased histone deimination has been observed in the normal-appearing white matter of multiple sclerosis (MS) patients. In this chapter, we first review the concepts in epigenetics and then discuss the roles that protein deimination play in human health and disease.
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References
Agarwal N, Hardt T, Brero A, Nowak D, Rothbauer U, Becker A, Leonhardt H, Cardoso MC (2007) MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation. Nucleic Acids Res 35:5402–5408
An W, Kim J, Roeder RG (2004) Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 117:735–748
Banerjee T, Chakravarti D (2011) A peek into the complex realm of histone phosphorylation. Mol Cell Biol 31:4858–4873
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837
Bauer UM, Daujat S, Nielsen SJ, Nightingale K, Kouzarides T (2002) Methylation at arginine 17 of histone H3 is linked to gene activation. EMBO Rep 3:39–44
Beniac DR, Wood DD, Palaniyar N, Ottensmeyer FP, Moscarello MA, Harauz G (2000) Cryoelectron microscopy of protein-lipid complexes of human myelin basic protein charge isomers differing in degree of citrullination. J Struct Biol 129:80–95
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315–326
Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669–681
Brinkmann V, Reichard U, Goosmann C, Fauler B, Uhlemann Y, Weiss DS, Weinrauch Y, Zychlinsky A (2004) Neutrophil extracellular traps kill bacteria. Science 303:1532–1535
Cao L, Goodin R, Wood D, Moscarello MA, Whitaker JN (1999) Rapid release and unusual stability of immunodominant peptide 45–89 from citrullinated myelin basic protein. Biochemistry 38:6157–6163
Chang X, Han J (2006) Expression of peptidylarginine deiminase type 4 (PAD4) in various tumors. Mol Carcinog 45:183–196
Chang B, Chen Y, Zhao Y, Bruick RK (2007) JMJD6 is a histone arginine demethylase. Science 318:444–447
Chen D, Huang SM, Stallcup MR (2000) Synergistic, p160 coactivator-dependent enhancement of estrogen receptor function by CARM1 and p300. J Biol Chem 275:40810–40816
Cheng X, Blumenthal RM (2008) Mammalian DNA methyltransferases: a structural perspective. Structure 16:341–350
Cherrington BD, Morency E, Struble AM, Coonrod SA, Wakshlag JJ (2010) Potential role for peptidylarginine deiminase 2 (PAD2) in citrullination of canine mammary epithelial cell histones. PLoS One 5:e11768
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4:80–93
Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T, Yamada M, Schneider R, Gregory PD, Tempst P, Bannister AJ et al (2004) Histone deimination antagonizes arginine methylation. Cell 118:545–553
de Seze J, Dubucquoi S, Lefranc D, Virecoulon F, Nuez I, Dutoit V, Vermersch P, Prin L (2001) IgG reactivity against citrullinated myelin basic protein in multiple sclerosis. J Neuroimmunol 117:149–155
Denis H, Deplus R, Putmans P, Yamada M, Metivier R, Fuks F (2009) Functional connection between deimination and deacetylation of histones. Mol Cell Biol 29:4982–4993
Deraos G, Chatzantoni K, Matsoukas MT, Tselios T, Deraos S, Katsara M, Papathanasopoulos P, Vynios D, Apostolopoulos V, Mouzaki A et al (2008) Citrullination of linear and cyclic altered peptide ligands from myelin basic protein (MBP(87–99)) epitope elicits a Th1 polarized response by T cells isolated from multiple sclerosis patients: implications in triggering disease. J Med Chem 51:7834–7842
Di Lorenzo A, Bedford MT (2011) Histone arginine methylation. FEBS Lett 585:2024–2031
Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3:224–229
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385
Feil R, Fraga MF (2011) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13:97–109
Greer EL, Shi Y (2012) Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13:343–357
Guccione E, Bassi C, Casadio F, Martinato F, Cesaroni M, Schuchlautz H, Luscher B, Amati B (2007) Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 449:933–937
Guo Q, Fast W (2011) Citrullination of inhibitor of growth 4 (ING4) by peptidylarginine deminase 4 (PAD4) disrupts the interaction between ING4 and p53. J Biol Chem 286:17069–17078
Hagiwara T, Hidaka Y, Yamada M (2005) Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. Biochemistry 44:5827–5834
Hassan YI, Zempleni J (2006) Epigenetic regulation of chromatin structure and gene function by biotin. J Nutr 136:1763–1765
Heyn H, Esteller M (2012) DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 13:679–682
Hyllus D, Stein C, Schnabel K, Schiltz E, Imhof A, Dou Y, Hsieh J, Bauer UM (2007) PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev 21:3369–3380
Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J et al (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6:e22
Kan R, Yurttas P, Kim B, Jin M, Wo L, Lee B, Gosden R, Coonrod SA (2011) Regulation of mouse oocyte microtubule and organelle dynamics by PADI6 and the cytoplasmic lattices. Dev Biol 350:311–322
Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, Bahler J, Green RD, Kouzarides T (2007) Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449:928–932
Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Green RD, Kouzarides T (2009) Distinct transcriptional outputs associated with mono- and dimethylated histone H3 arginine 2. Nat Struct Mol Biol 16:449–451
Kleinschmidt MA, de Graaf P, van Teeffelen HA, Timmers HT (2012) Cell cycle regulation by the PRMT6 arginine methyltransferase through repression of cyclin-dependent kinase inhibitors. PLoS One 7:e41446
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Lee YH, Koh SS, Zhang X, Cheng X, Stallcup MR (2002) Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Mol Cell Biol 22:3621–3632
Lee YH, Coonrod SA, Kraus WL, Jelinek MA, Stallcup MR (2005) Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. Proc Natl Acad Sci U S A 102:3611–3616
Lee YH, Ma H, Tan TZ, Ng SS, Soong R, Mori S, Fu XY, Zernicka-Goetz M, Wu Q (2012) Protein arginine methyltransferase 6 regulates embryonic stem cell identity. Stem Cells Dev 28:2613–22
Li P, Yao H, Zhang Z, Li M, Luo Y, Thompson PR, Gilmour DS, Wang Y (2008) Regulation of p53 target gene expression by peptidylarginine deiminase 4. Mol Cell Biol 28:4745–4758
Li P, Li M, Lindberg MR, Kennett MJ, Xiong N, Wang Y (2010a) PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps. J Exp Med 207:1853–1862
Li P, Wang D, Yao H, Doret P, Hao G, Shen Q, Qiu H, Zhang X, Wang Y, Chen G (2010b) Coordination of PAD4 and HDAC2 in the regulation of p53-target gene expression. Oncogene 29:3153–3162
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260
Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447
Ma H, Baumann CT, Li H, Strahl BD, Rice R, Jelinek MA, Aswad DW, Allis CD, Hager GL, Stallcup MR (2001) Hormone-dependent, CARM1-directed, arginine-specific methylation of histone H3 on a steroid-regulated promoter. Curr Biol 11:1981–1985
Masson-Bessiere C, Sebbag M, Girbal-Neuhauser E, Nogueira L, Vincent C, Senshu T, Serre G (2001) The major synovial targets of the rheumatoid arthritis-specific antifilaggrin autoantibodies are deiminated forms of the alpha- and beta-chains of fibrin. J Immunol 166:4177–4184
Mastronardi FG, Wood DD, Mei J, Raijmakers R, Tseveleki V, Dosch HM, Probert L, Casaccia-Bonnefil P, Moscarello MA (2006) Increased citrullination of histone H3 in multiple sclerosis brain and animal models of demyelination: a role for tumor necrosis factor-induced peptidylarginine deiminase 4 translocation. J Neurosci 26:11387–11396
Mastronardi FG, Noor A, Wood DD, Paton T, Moscarello MA (2007) Peptidyl argininedeiminase 2 CpG island in multiple sclerosis white matter is hypomethylated. J Neurosci Res 85:2006–2016
Maunakea AK, Chepelev I, Zhao K (2010) Epigenome mapping in normal and disease States. Circ Res 107:327–339
Messner S, Hottiger MO (2011) Histone ADP-ribosylation in DNA repair, replication and transcription. Trends Cell Biol 21:534–542
Migliori V, Muller J, Phalke S, Low D, Bezzi M, Mok WC, Sahu SK, Gunaratne J, Capasso P, Bassi C et al (2012) Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol 19:136–144
Moscarello MA, Wood DD, Ackerley C, Boulias C (1994) Myelin in multiple sclerosis is developmentally immature. J Clin Invest 94:146–154
Moscarello MA, Mastronardi FG, Wood DD (2007) The role of citrullinated proteins suggests a novel mechanism in the pathogenesis of multiple sclerosis. Neurochem Res 32:251–256
Musse AA, Li Z, Ackerley CA, Bienzle D, Lei H, Poma R, Harauz G, Moscarello MA, Mastronardi FG (2008) Peptidylarginine deiminase 2 (PAD2) overexpression in transgenic mice leads to myelin loss in the central nervous system. Dis Model Mech 1:229–240
Neault M, Mallette FA, Vogel G, Michaud-Levesque J, Richard S (2012) Ablation of PRMT6 reveals a role as a negative transcriptional regulator of the p53 tumor suppressor. Nucleic Acids Res 40:9513–9521
Nicholas AP, Sambandam T, Echols JD, Barnum SR (2005) Expression of citrullinated proteins in murine experimental autoimmune encephalomyelitis. J Comp Neurol 486:254–266
Raijmakers R, Zendman AJ, Egberts WV, Vossenaar ER, Raats J, Soede-Huijbregts C, Rutjes FP, van Veelen PA, Drijfhout JW, Pruijn GJ (2007) Methylation of arginine residues interferes with citrullination by peptidylarginine deiminases in vitro. J Mol Biol 367:1118–1129
Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F et al (2011) PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 43:275–284
Rando OJ (2012) Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 22:148–155
Shanshiashvili LV, Kalandadze IV, Ramsden JJ, Mikeladze DG (2012) Adhesive properties and inflammatory potential of citrullinated myelin basic protein Peptide 45–89. Neurochem Res 37:1959–1966
Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Pena P, Lan F, Kaadige MR et al (2006) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442:96–99
Slack JL, Causey CP, Thompson PR (2011) Protein arginine deiminase 4: a target for an epigenetic cancer therapy. Cell Mol Life Sci 68:709–720
Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45
Suzuki A, Yamada R, Chang X, Tokuhiro S, Sawada T, Suzuki M, Nagasaki M, Nakayama-Hamada M, Kawaida R, Ono M et al (2003) Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet 34:395–402
Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N et al (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028
Tanikawa C, Ueda K, Nakagawa H, Yoshida N, Nakamura Y, Matsuda K (2009) Regulation of protein Citrullination through p53/PADI4 network in DNA damage response. Cancer Res 69:8761–8769
Tanikawa C, Espinosa M, Suzuki A, Masuda K, Yamamoto K, Tsuchiya E, Ueda K, Daigo Y, Nakamura Y, Matsuda K (2012) Regulation of histone modification and chromatin structure by the p53-PADI4 pathway. Nat Commun 3:676
Thompson PR, Fast W (2006) Histone citrullination by protein arginine deiminase: is arginine methylation a green light or a roadblock? ACS Chem Biol 1:433–441
Unoki M, Brunet J, Mousli M (2009) Drug discovery targeting epigenetic codes: the great potential of UHRF1, which links DNA methylation and histone modifications, as a drug target in cancers and toxoplasmosis. Biochem Pharmacol 78:1279–1288
Vossenaar ER, Zendman AJ, van Venrooij WJ, Pruijn GJ (2003) PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. Bioessays 25:1106–1118
Waddington CH (1942) The epigenotype. Int J Epidemiol 41:10–13
Wang Y, Wysocka J, Sayegh J, Lee YH, Perlin JR, Leonelli L, Sonbuchner LS, McDonald CH, Cook RG, Dou Y et al (2004) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306:279–283
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ et al (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40:897–903
Wang Y, Li M, Stadler S, Correll S, Li P, Wang D, Hayama R, Leonelli L, Han H, Grigoryev SA et al (2009) Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation. J Cell Biol 184:205–213
Williams K, Christensen J, Helin K (2012) DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep 13:28–35
Wu J, Xu W (2012) Histone H3R17me2a mark recruits human RNA polymerase-associated factor 1 complex to activate transcription. Proc Natl Acad Sci U S A 109:5675–5680
Wu H, Zhang Y (2011) Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev 25:2436–2452
Wu H, Coskun V, Tao J, Xie W, Ge W, Yoshikawa K, Li E, Zhang Y, Sun YE (2010) Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329:444–448
Yamada R, Suzuki A, Chang X, Yamamoto K (2005) Citrullinated proteins in rheumatoid arthritis. Front Biosci 10:54–64
Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT (2010) TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell 40:1016–1023
York B, O'Malley BW (2010) Steroid receptor coactivator (SRC) family: masters of systems biology. J Biol Chem 285:38743–38750
Yun M, Wu J, Workman JL, Li B (2011) Readers of histone modifications. Cell Res 21:564–578
Yurttas P, Vitale AM, Fitzhenry RJ, Cohen-Gould L, Wu W, Gossen JA, Coonrod SA (2008) Role for PADI6 and the cytoplasmic lattices in ribosomal storage in oocytes and translational control in the early mouse embryo. Development 135:2627–2636
Zhang X, Gamble MJ, Stadler S, Cherrington BD, Causey CP, Thompson PR, Roberson MS, Kraus WL, Coonrod SA (2011) Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells. PLoS Genet 7:e1002112
Zhang X, Bolt M, Guertin MJ, Chen W, Zhang S, Cherrington BD, Slade DJ, Dreyton CJ, Subramanian V, Bicker KL et al (2012) Peptidylarginine deiminase 2-catalyzed histone H3 arginine 26 citrullination facilitates estrogen receptor alpha target gene activation. Proc Natl Acad Sci U S A 109:13331–13336
Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ, Cerruti L, Curtis DJ, Patel DJ, Allis CD et al (2009) PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 16:304–311
Zhou SR, Whitaker JN, Wood DD, Moscarello MA (1993) Immunological analysis of the amino terminal and the C8 isomer of human myelin basic protein. J Neuroimmunol 46:91–96
Zhou SR, Moscarello MA, Whitaker JN (1995) The effects of citrullination or variable amino-terminus acylation on the encephalitogenicity of human myelin basic protein in the PL/J mouse. J Neuroimmunol 62:147–152
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Liang, J., Casaccia, P. (2014). The Role of Protein Deimination in Epigenetics. In: Nicholas, A., Bhattacharya, S. (eds) Protein Deimination in Human Health and Disease. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8317-5_18
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