Role of Histone-Modifying Enzymes and Their Complexes in

Current Topic pubs.acs.org/biochemistry

Role of Histone-Modifying Enzymes and Their Complexes in Regulation of Chromatin Biology Renee DesJarlais and Peter J. Tummino*

Downloaded via UNIV OF TOLEDO on June 17, 2018 at 18:48:36 (UTC). See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles.

Lead Discovery, Janssen Research & Development, Spring House, Pennsylvania 19477, United States ABSTRACT: In 1964, Alfrey and colleagues proposed that acetylation and methylation of histones may regulate RNA synthesis and described “the possibility that relatively minor modifications of histone structure, taking place on the intact protein molecule, offer a means of switching-on or off RNA synthesis at different loci along the chromosome” [Allfrey, V., Faulkner, R., and Mirsky, A. (1964) Proc. Natl. Acad. Sci. U.S.A. 51, 786]. Fifty years later, this prescient description provides a simple but conceptually accurate model for the biological role of histone post-translational modifications (PTMs). The basic unit of chromosomes is the nucleosome, with double-stranded DNA wrapped around a histone protein oligomer. The “tails” of histone proteins are post-translationally modified, which alters the physical properties of nucleosomes in a manner that impacts gene accessibility for transcription and replication. Enzymes that catalyze the addition and removal of histone PTMs, histone-modifying enzymes (HMEs), are present in large protein complexes, with DNA-binding proteins, ATP-dependent chromatin remodeling enzymes, and epigenetic reader proteins that bind to posttranslationally modified histone residues [Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K., and Schapira, M. (2012) Nat. Rev. Drug Discovery 11, 384−400]. The activity of HME complexes is coordinated with that of other chromatin-associated complexes that, together, regulate gene transcription, DNA repair, and DNA replication. In this context, the enzymes that catalyze addition and removal of histone PTMs are an essential component of the highly regulated mechanism for accessing compacted DNA. To fully understand the function of HMEs, the structure of nucleosomes, their natural substrate, will be described. Each major class of HMEs subsequently will be discussed with regard to its biochemistry, enzymatic mechanism, and biological function in the context of a prototypical HME complex.

■

CHROMATIN STRUCTURE AND FUNCTION The nuclear packing of the human genome must accomplish multiple functions. Two of the central functions are (1) to compact the 3 billion bp genome into the nucleus of the cell and (2) to regulate physical accessibility of genes for transcription, repair, and replication. Compaction is accomplished through the winding of double-stranded DNA (dsDNA) around a histone protein octamer, creating a nucleosome core particle. The core particles are separated by more nuclease sensitive regions of DNA (linker DNA).3−5 Nucleosomes themselves are arranged in a higher-order structure creating chromatin fibers, which are the structural components of chromosomes.6,7 These types of higher-order structures need to be altered in a regulated manner by DNA-binding proteins and/or complexes to allow access to DNA sequence for transcription, DNA repair, and DNA replication.8 The structure of the nucleosome was determined at atomic resolution by Luger et al. in 1997.5 Since then, more than 100 nucleosome structures have been determined providing a remarkably consistent picture. Figure 1 illustrates the human nucleosome structure as determined by Tachiwana et al.9 with the unordered histone tails computationally modeled in an arbitrary conformation. The protein core of the nucleosome is composed of a histone octamer that includes two copies each of protein from histone classes H2A, H2B, H3, and H4, collectively © 2016 American Chemical Society

known as the histone core proteins. The core histones fold as heterodimers, H2A/H2B and H3/H4, with two of each heterodimer in the octamer. A stretch of DNA 145−167 bp in length winds around the histone assembly. Protruding from the nucleosomes are the N-terminal tails of each core histone as well as the C-terminal tails of the two H2A proteins. These 10 histone tails are primary sites of post-translational modifications, known as histone marks, whose addition and removal is catalyzed by the enzymes discussed in this review. A number of well-characterized histone marks are shown as spheres and provide perspective on the length of each tail relative to the nucleosome itself (Figure 1). While unique conformations for the tails are not seen experimentally, the tails assume structure when bound to HMEs or epigenetic reader proteins. It is interesting to note that many of the “tail” modifications are adjacent to the surface of the core nucleosome particle. Four of the 10 tails are near the DNA entry/exit from the nucleosome, and others protrude from the flat surface of the histone octamer. The former could impact the winding of DNA around a single nucleosome, whereas the Special Issue: Epigenetics Received: November 8, 2015 Revised: December 23, 2015 Published: January 8, 2016 1584

DOI: 10.1021/acs.biochem.5b01210 Biochemistry 2016, 55, 1584−1599

Current Topic

Biochemistry

Figure 1. Human nucleosome structure (PDB entry 3AFA9) with histone tails modeled. The protein backbone is shown as a ribbon with sites of posttranslational modification displayed as spheres. Each histone backbone is colored by histone type: H2A, pink; H2B, magenta; H3, green; H4, blue. The PTMs are colored by the modification present: acetylation, orange; methylation, red; phosphorylation, cyan; ubiquitylation, yellow; ubiquitin backbone, yellow ribbons (ubiquitin structure, PDB entry 1AAR209). The DNA double helix is shown as gray tubes. This illustration was prepared with PyMol.210

the concurrent report from Schreiber and colleagues on the first histone deacetylase, Rpd3p from yeast.23 Histone acetyltransferases, with acetyl-CoA as the acetyl donor, catalyze acetylation of the ε-amine of histone lysines. Enzyme mechanistic data and molecular modeling are consistent with two proposed mechanisms for the acetyltransferase reaction catalyzed by HATs. In the direct attack acetyl transfer mechanism, acetyl-CoA and histone substrate bind to the enzyme in an ordered sequential manner to form a ternary complex, followed by an active site glutamate deprotonating the histone lysine, resulting in nucleophilic attack at the acetyl-CoA carbonyl carbon (Figure 2A). A tetrahederal intermediate forms, which then progresses to acetylated histone lysine and coenzyme A (CoA).24 Data for the direct attack acetyltransferase mechanism have been reported for full-length Gcn5,25−27 P/CAF,28 and p300/CBP.29,30 In the alternative two-step acetyl transfer mechanism, acetyl-CoA binds to the HAT and an active site Cys attacks acetyl-CoA, resulting in an acetylated enzyme intermediate. The CoA product dissociates, and histone substrate binds, followed by deprotonation of the histone lysine nucleophile by an active site Glu base, nucleophilic attack of the acetylated Cys, and dissociation of product.24 The second mechanism has been reported only for the truncated form of the HAT Esa1; whether any full-length HATcatalyzed reaction proceeds by this mechanism is unclear.31 Fatty acyl-CoAs, C14−C18, have been shown to be HAT biochemical and cellular inhibitors, consistent with protein docking studies that indicate fatty acyl-CoA binds to Gcn5 with binding interactions identical to those of acetyl-CoA.32 Similarly, the CoA of the HAT-catalyzed reaction exhibits product inhibition.33 These findings implicate CoA and fatty acyl-CoAs as potential metabolic regulators of histone acetylation.34,35 In humans, there are 18 histone acetyltransferases, composed of three types:2,36 (1) MYST, named for the founding members, human MOZ, yeast Ybf2, Sas2, and mammalian TIP60; (2) GNAT, (glycine-N-acyltransferase-like protein 1), with founding members Gcn5 and PCAF (p300/CBP-associated factor); and (3) EP300 (E1A-associated protein p300). Many of the HAT enzymes have been shown to function as large multiprotein complexes in which catalytic activity and

later could affect the ability of nucleosomes to pack against each other. Between the nucleosomes are regions of linker DNA that are associated with linker histone H1.10 The linker histones, not related to the core histones in either sequence or structure, have a central folded domain flanked by a short N-terminal tail and a long, highly basic C-terminal tail. Linker histones are also the target of many post-translational modifications that, similar to core histone modification, have the ability to modify chromatin structure and recruit non-histone proteins.11,12 Eukaryotic chromatin is in equilibrium between two distinct higher-order structures: heterochromatin is a more condensed structure, transcriptionally silent, and in regions surrounding centromeres and telomeres; euchromatin is a less condensed structure and transcriptionally competent.13 Histones in both heterochromatin and euchromatin are post-translationally modified, though the PTMs have a different biological role based on the function of the domains. Moreover, the boundaries between heterochromatin and euchromatin are largely regulated by histone PTMs.14,15 Acetylation of histone lysines weakens the capability of Nterminal histone tails to hydrogen bond with nucleosomal DNA, resulting in a more relaxed chromatin structure.2 A relaxed nucleosome conformation increases the accessibility of histone chaperones, chromatin remodeling complexes, and other complexes for transcription, DNA repair, and DNA replication. Because of the fundamental role of histone PTMs in transcriptional regulation, HMEs have been found to be important for many aspects of human biology and disease, including regulation of pluripotency, differentiation, and cell identity.16,17 Dysregulation of HME function by overexpression, gene amplification, and somatic and germline gene mutations plays a central role in multiple types of cancer,18 neurological diseases, immunological diseases,19,20 and infectious diseases.21

■

HISTONE ACETYLATION

Histone Acetyltransferases. The first reports of a histonemodifying enzyme were published fewer than 20 years ago by Allis and colleagues, with the findings that Tetrahymena HAT A and yeast Gcn5p are histone acetyltransferases (HATs),22 and 1585


Current Topic

Biochemistry

Figure 2. (A) Histone acetyltransferase mechanism adapted from ref 24. (B) Histone deacetylase (HDAC) class I, II, and IV mechanism adapted from ref 72. (C) HDAC class III mechanism adapted from ref 72.

specificity are dependent on components of the complex.37,38 The human histone acetyltransferase TIP60 (Tat interactive protein 60) exists in a complex of the same name composed of at least 16 proteins (see Figure 3).39,40 This complex contains multiple recognition mechanisms by which the TIP60 complex is recruited to specific sites on chromatin. The TIP60 enzyme and a

scaffolding protein in the complex (TRRAP, transformation/ transcription domain-associated protein) both bind to transcription factors, including MYC.41 BRD8 and ING3 are epigenetic readers that bind specific acetylated and methylated histone lysines, respectively. MRG15 possesses two domains with putative functions of binding a specific DNA sequence as a 1586


Current Topic

Biochemistry

Figure 3. Comparison of histone-modifying enzyme complexes. TIP60 complex proteins.40 TIP60 (Tat interactive protein 60) histone acetyltransferase, p400, BAF53A (Brg/Brm-associated factor 53A), RUVBL1 and RUVBL2 (RUVB-like protein 1 and 2, respectively211), BRD8 (bromodomain 8), ING3 (inhibitor of growth family, member 3), MRG15 (MORF-related gene 15), TRRAP (transformation/transcription domainassociated protein), DMAP1 (DNA methyltransferase 1-associated protein 1), GAS41 (glioma-amplified sequence 41), EPC1 (enhancer of polycomb homologue 1), hEAF6 (human Esa1-associated factor 6 homologue), MRGBP (MRG/MORF4L-binding protein), YL-1 (also known as VPS72, vacuolar protein sorting-associated protein 72 homologue), and actin. NuRD (nucleosome-remodeling and deacetylase) core complex proteins.60−63 HDAC1 or HDAC2 histone deacetylases, RbAp46/48 (retinoblastoma protein-associated protein 46/48), and CHD3 or CHD4 (chromodomainhelicase-DNA-binding protein 3 or 4, respectively) possess both histone methyllysine reader and helicase domains, MBD2 and MBD3 (methyl-CpGbinding domain proteins 2 and 3, respectively), and p66α and p66β zinc finger-containing proteins.212 Core PRC2 (polycomb repressive complex 2) proteins.80 EHZ1/2 (enhancer of zeste 1/2) histone lysine methyltransferase, RbAp46/48 (retinoblastoma protein-associated protein 46/48), EED (embryonic ectoderm development), SUZ12 (suppressor of zeste 12 homologue). Canonical PRC1 (polycomb repressive complex 1) proteins.155,156 RING1A/1B [(Really Interesting New Gene)1A/1B] ubiquitylase; CBX (chromobox homologue) proteins 1−5; SCML (sex comb on midleg like-2) proteins SCML1, SCML2, and SMLH1; HPH (human and polyhomeotic homologue) proteins 1−3; and PCGF (polycomb group ring finger) proteins 1−6.

from histone lysines and utilize either zinc or NAD+ as cofactors for catalysis.46 Generally, histone deacetylation promotes chromatin condensation and transcriptional repression. The human deacetylases are composed of four classes46−48 described in Table 1. There are multiple isoforms of some HDACs, such as HDAC9, due to alternative splicing.49 HDACs of classes I, II, and IV belong to the arginase/deacetylase superfamily of enzymes.46 The catalytic mechanism for these enzymes is similar to that of thermolysin,50 in which the catalytic Zn2+ and a His general base activate a bound water molecule for nucleophilic attack on the

transcription factor and binding of methylated histone lysines. This combined set of recognition proteins directs the histone acetyltransferase, DNA helicase, and chromatin remodeling activities of the TIP60 complex. The combined recognition and catalytic activities of the TIP60 complex play an essential role in the DNA damage response (DDR), a process that involves nonhomologous end joining, homologous recombination, and DNA repair.42 The mammalian histone variant H2A.X is phosphorylated at sites of doublestranded DNA breaks by several kinases (described below, Histone Phosphorylation). The TIP60 complex is recruited to the phosphorylated sites and binds H3K9me3. This binding stimulates TIP60-mediated H2A.X acetylation and ATPdependent exchange of acetylated H2A.X with an unmodified H2A.X protein. Inactivation of TIP60 HAT activity or depletion of TRRAP results in a loss of DNA repair function.43−45 This exemplifies the role of chromatin structure and its regulation in eukaryotic DNA repair machinery. Histone Deacetylases. In humans, there are 18 histone deacetylases (HDACs) that catalyze the removal of acetyl groups

Table 1. Classes of Histone Deacetylase (HDAC) Enzymes class I II III IV 1587

description includes HDAC1−3 and -8; homologous to yeast Rpd3 deacetylase, Zn2+-dependent enzymes includes include HDAC4−7, -9, and -10; homologous to yeast Hda1 deacetylase, Zn2+-dependent enzymes sirtuins, SIRT1−7; homologous to yeast Sir2 (silent information regulator 2), NAD+-dependent enzymes HDAC11; homologous to yeast Hda 1, Zn2+-dependent enzymes DOI: 10.1021/acs.biochem.5b01210 Biochemistry 2016, 55, 1584−1599

Current Topic

Biochemistry

Figure 4. (A) Histone methyltransferase mechanism adapted from ref 72. (B) Mono- and dimethylated products of arginine methylation. (C) Mechanism of FAD-dependent lysine demethylase adapted from ref 213. (D) Mechanism of Jumonji lysine demethylase adapted from ref 72.

catalyze an unusual chemical reaction that converts acetylated lysine and NAD+ to deacetylated lysine, nicotinamide, and 2′-Oacetyl-ADP ribose.57 Acetyllysine and NAD+ bind to the enzyme sequentially. The first chemical step in the proposed mechanism is nucleophilic addition of the acetyllysine acetamide at the C1 position of nicotinamide ribose to form an alkylamidate intermediate and free nicotinamide, followed by release of nicotinamide, deacetylated lysine, and 2′-O-acetyl-ADP ribose in an ordered manner (Figure 2C).58,59

carbonyl of the acetyl-L-lysine group, which is coordinated to the active site Zn2+ (Figure 2B).51 Interestingly, HDAC452 and HDAC753 possess a second bound structural zinc, which may be important for substrate recognition and protein−protein interactions in an HME complex. The class III sirtuins are called histone deacetylases; however, only SIRT1−SIRT3 possess robust HDAC catalytic activity, and among those three, only SIRT1 is present in the nucleus54,55 (reviewed in detail elsewhere56). Sirtuin histone deacetylases 1588


Current Topic

Biochemistry

histone demethylase), and PCL2 (polycomb-like 2, an epigenetic reader that recognizes H3K36me382). PRC2-mediated histone methylation proceeds in a coordinated manner with PRC1mediated (polycomb repressive complex 1) histone ubiquitylation as a transcriptional regulatory mechanism (described subsequently). EZH1 and EZH2 have different expression patterns, and EZH2 has a greater role in maintaining H3K27me3 on chromatin.79 Recombinant EZH2 does not possess biochemical HMT catalytic activity as a single protein, and the minimum PRC2 complex required to reconstitute H3K27 methyltransferase activity is EZH2-SUZ12-EED.83 EZH2 is responsible for H3K27 trimethylation in cells, and because the enzyme mechanism is distributive,76 its histone substrates include unmethylated, monomethylated, and dimethylated H3K27. Multiple groups have demonstrated that recombinant core PRC2 possesses relatively high catalytic activity with the unmethylated substrate, less activity with the monomethylated substrate, and almost no catalytic activity with H3K27me2.73,84,85 This result implies that H3K27me3 may be less prevalent than other H3K27 methylation states in cells, as has been observed in human CD4+ T-cells.86 The EED protein in PRC2 binds to the final product of the PRC2-catalyzed reaction, H3K27me3, and this interaction increases the methyltranferase activity of the complex.87,88 This positive feedback mechanism has been suggested to play a role in epigenetic transmission of the methyl mark from mother to daughter cells.87 The structure of a minimal PRC2 complex (EZH2, SUZ12, and EED) reveals details regarding substrate binding and allosteric regulation.89 The necessity of the three proteins to make a catalytically competent complex is demonstrated by their intimate interactions. PRC2 has four distinct H3 tail-binding sites, three of which are seen in the described structure, including the regulatory binding site for an H3K27me3 peptide.89 EZH2 has been implicated to have an oncogenic role in many cancer types,90 and in non-Hodgkins lymphoma (NHL), there are EZH2 heterozygous active site point mutations (Y641, A677, and A687).85,91,92 Interestingly, all of the these EZH2 active site mutations alter the substrate specificity of the enzyme to H3K27me2 > H3K27me1 > H3K27me0, which is opposite of that of the wild-type enzyme (first reported by Copeland et al., 7 6 , 8 5 , 9 1 and confirmed subsequently by multiple groups76,85,91). Hence, in a cancer cell with a heterozygous mutation, both wild-type and mutant EZH2 exixt and when combined can effectively utilize all three histone substrates (un-, mono-, and dimethylated H3K27). This ability should result in a greater proportion of H3K27me3 in mutant NHL cells relative to NHL cells with wild-type ENZ2, which it does.85 The dysregulation and oncogenic nature in EZH2 mutations in NHL reflect the biological importance of this histone mark. Mammalian PRMTs methylate the terminal guanidino side chain of Arg to one of three species: (1) monomethylarginine, (2) asymmetric dimethylarginine, and (3) symmetric dimethylarginine (Figure 4B).93,94 There are nine mammalian PRMTs, all of which catalyze the formation of monomethylarginine. Among these, type I PRMTs also catalyze the formation of asymmetric dimethylarginine (PRMT1−4, -6, and -8), and type II PRMTs also catalyze the formation of symmetric dimethylarginine (PRMT5).94,95 PRMT7 catalyzes only monomethylarginine formation, and PRMT9 is active but has not yet been characterized. Enzyme and structural studies indicate that PRMT-catalyzed reactions proceed via an ordered sequential bi-bi kinetic mechanism with Ado-Met, as the methyl donor,

HDAC activities are modulated by protein−protein interactions and post-translational modifications and may be regulated by expression, alternative splicing, and subcellular localization. HDAC1 and HDAC2 possess low catalytic activity when purified as single proteins and have been found to exist in three distinct multiprotein complexes: Sin3, NuRD (nucleosome-remodeling and deacetylase), and CoREST (REST protein corepressor) complexes. The core NuRD complex, shown in Figure 3, is approximately 2 MDa in size.60−63 Similar to TIP60, this complex has proteins for recognition of DNA sequence and histone PTMs, along with chromatin-remodeling enzymes. It has two additional types of proteins. The first is MBD2 or MBD3 (methyl-CpG-binding domain), which binds specifically to CpGrich regions of methylated DNA and binds to HDAC1/2, increasing its enzymatic activity.64−66 The second type consists of histone chaperone proteins, RbAp46 and/or RbAp48, which are responsible for the proper assembly of histone proteins into octamers.67 NuRD often exists as a much larger complex, with additional histone-modifying enzymes and recognition proteins, for more complex regulation of gene activation and silencing. Examples include the LSD1/NurD complex implicated in metastatic breast cancer,68 the NuRD−protein arginine methyltransferase PRMT5 interaction,66 and the NuRD−histone demethylase KDM5a interaction.69

■

HISTONE METHYLATION Histone Methyltransferases. Methylation of histone proteins is a common PTM that occurs on side chain lysines and arginines, basic groups that are hydrogen bond donors in key interactions with DNA, RNA, and other proteins. Histone lysine methyltransferases (termed protein lysine methyltransferases, PKMTs, because of their histone and non-histone substrates) and histone arginine methyltransferases (termed protein arginine methyltransferases, PRMTs)70 catalyze the transfer of a methyl group from S-adenosyl-L-methionine (Ado-Met) to N-terminal histone lysines (producing mono-, di-, and trimethylate) and arginines (producing mono- or dimethylate in a symmetric or asymmetric manner), respectively, with release of S-adenosyl-Lhomocysteine (Ado-Hyc) (see Figure 4A2). A range of 60−96 histone methyltransferases (HMTs) have been identified in the human genome through phylogenetic analysis, though not all putative HMTs have been shown to methylate histones.2,70 With the one exception of DOT1L, all PKMTs contain a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain71 that catalyzes methylation of the lysine ε-amino group with Ado-Met as a methyl donor by a sequential bi-bi kinetic mechanism with random substrate association and product release.72,73 There are examples of SET domain HKMTs that monomethylate only (SET7/974) and that mono-, di-, and trimethylate (G9a, EZH2) histone lysines. PKMT-catalyzed trimethylation has been found to proceed by both processive (G9A75) and distributive (EZH276) biochemical mechanisms. DOT1L mono-, di-, and trimethylates H3K79 with an Ado-Met methyl donor, but with an active site distinct in protein sequence and structure from that of a SET domain.77,78 The histone lysine methyltransferases EZH1 and EZH2 trimethylate H3K27, resulting in chromatin compaction and transcriptional repression.79 EZH1 and EZH2 are constituents of polycomb repressive complex 2 (PRC2), which plays an important role in pluripotency, differentiation, and cell identity. PRC2 core proteins are shown in Figure 3.80 Additional proteins associated with PRC2 include AEBP2 (zinc finger DNA-binding protein, which enhances H3K29me3 activity81), JARID2 (a 1589


Current Topic

Biochemistry Table 2. Biological Activities of Protein Arginine Methyltransferase PRMT4 PRMT4 attribute regulated by post-translational modification

regulates splicing role in maintenance of pluripotency regulates a chromatin-remodeling complex constituent of the nuclear receptor (NR) co-activator complex

co-activator of non-nuclear receptor systems

biological relevance

refs

phosphorylated at S217, which abolishes SAM binding and catalytic activity and promotes cytosolic localization of the histone methyltransferase automethylated at R551; does not alter enzymatic activity but appears to be important for CARM1-activated transcription and pre-mRNA splicing plays a role in coupling of transcription and splicing; methylation of splicing factors may be the mechanism for exon skipping and alternative splicing plays a role in expression of SOX2 and Nanog; HRMT and other protein methylation roles associated with biological activity methylates BAF144 in the SWI/SNF chromatin-remodeling complex, which alters transcription and may be tumorigenic in breast cancer NR co-activator complex constituents: PRMT4; GRIP1 (a p160 co-activator) and the histone acetyltransferase p300/ CBP; NR transcriptional activation is dependent on the synergistic activity of the co-activator complex

100, 188

androgen receptor (AR); potential role in AR-mediated prostate cancer estrogen receptor α (ERα); regulates E2F1 expression, potential role in ERa+ breast cancer glucocorticoid receptor (GR); potential role in control of the hypothalamus-pituitary-adrenal axis peroxisome proliferator-activated receptor γ (PPARγ); role in adipocyte differentiation NFkB; acts as a promoter-specific regulator of NF-κB recruitment to chromatin; transcriptional activation does not require enzymatic activity p53; PRMT4, GRIP1, CBP, and PRMT1 bind to p53 and function cooperatively for p53-dependent nucleosomal histone modifications and p53-dependent transcription IFN-γ; role in IFN-g-mediated MHC-II gene expression myocyte enhancer factor-2 (MEF2C); necessary co-activator for muscle differentiation β-catenin; interacts with β-catenin and co-activates β-catenin-mediated gene expression; potential role in dysregulated Wnt/β-catenin signaling in colorectal cancer

197 198, 199 200 201 202, 203

binding followed by binding of the arginine-containing protein.71 Similar to that of PKMTs, PRMT-catalyzed methyl transfer likely proceeds through an SN2 mechanism, and data indicate that the reaction is processive from arginine to dimethylarginine (Figure 4A).70,72,96 PRMT4, often termed CARM1 (co-activator-associated arginine methyltransferase), is one of the most carefully studied PRMTs and exemplifies many of the structural and functional characteristics of this enzyme subclass. PRMT4, which catalyzes the asymmetric dimethylation of H3R17 and H3R26, is a transcription co-activator of nuclear hormone receptors identified by Stallcup and colleagues.97 The protein contains a methyltransferase domain, which is highly conserved among PRMTs and two flanking regions essential for its role in transcriptional activation.98 The N-terminus contains a loosely structured pleckstrin homology domain, important for specific protein−protein interactions in a transcriptional complex.98 The catalytic domain undergoes large structural changes upon binding of the ADO-Hyc cofactor, and Ado-Met binding might result in a similar ordered conformation required for catalysis. The function of the C-terminal domain, not present in other PRMTs, is not known, though it is essential for H3 methylation activity.96 The N-terminus is required for H3R26, but not H3R17, methylation, and H3R17 methylation is potentiated by acetylation at H3K18, indicative of coordinated reading and writing of marks required for the histone code.96 PRMT4 exists as a homodimer, as observed for other PRMTs, and this may be important for the processive nature of the enzymatic activity.99,100 The monomethylated histone arginine may dissociate from one monomer and rebind to the second monomer for conversion to the asymmetric dimethylarginine prior to dissociation into solution. Also, PRMTs form active higher-order homo-oligomers, and the oligomerization state may regulate catalytic activity.101,102 PRMT4 and the histone acetyltransferase p300/CBP [(cAMP response element-binding protein)-binding protein] are recruited by p160 co-activators, such as GRIP1 (glucocorticoid

189, 190 191, 192 193−195

97, 105, 196

204 205, 206 207 208

receptor-interacting protein 1), to form a complex that binds to hormone-activated nuclear receptors in mammalian cells.103,104 PRMT1 also is a co-activator with the p160 complex where activities of the two PRMTs are synergistic for transcriptional activation.105 Table 2 summarizes both the regulation of PRMT4 through PTM of the enzyme itself and the breadth of reported biological roles of PRMT4. Most of these biological roles require the histone methyltransferase activity of PRMT4. Similar to other HME complexes, the PRMT4 complex plays a role in both transcriptional regulation and mRNA splicing, where an HME complex may provide the coordinated regulation required between these two biological processes. Moreover, PRMT4 is found to play an integral role in cell pluripotency and differentiation, as has been reported also for the PRC2 and NuRD complexes.106 A growing body of recent work is clarifying the role of chromatin-modifying complexes in cell identity.16,106 Histone Demethylases. For many years after the discovery and characterization of histone methylation, it was proposed that this PTM is highly stable107,108 and that only nonenzymatic mechanisms, such as histone protein exchange, are responsible for histone demethylation.109,110 Only recently was this disproven by Shi and colleagues with the first report of a histone demethylase, lysine-specific demethylase 1 (LSD1).111 There are two types of histone demethylases based on the chemistry of the enzyme-catalyzed reaction, the lysine-specific demethylases (LSD) and the Jumonji C (JMJC) demethylases (comprehensively reviewed by Shi112 and Helin113). LSD1 and LSD2 are able to demethylate di- and monomethylated H3K4. Both enzymes are flavin adenine dinucleotide (FAD)-dependent amine oxidases that catalyze a two-electron oxidation of methylated H3K4, generating FADH2 and H2O2,114 to form an imine that reduces upon addition of water to form demethylated lysine and formaldehyde (Figure 4C). JMJC domain-containing histone demethylases, first reported by Zhang et al.,115 utilize αketoglutarate and Fe2+ as cofactors to catalyze an oxidation/ reduction reaction with products of hydroxylated methyllysine and a proton (Figure 4D). The hydroxymethyllysine non1590


Current Topic

Biochemistry

isolated SANT2 domain of CoREST is capable of binding DNA.122 Taken together, these data have led to the proposal of a bivalent interaction between LSD1/CoREST,122 which has been corroborated by small-angle X-ray scattering studies.124 The LSD1/CoREST complex shows dramatic flexibility that is altered upon peptide binding as evidenced in extensive protein molecular dynamics simulations conducted by Baron et al.125 The molecular dynamics simulations coupled with the evidence of bivalent binding suggest that binding of a peptide could affect in an allosteric manner the interaction of the SANT2 domain with the nucleosome.124

catalytically reduces to yield demethylated lysine, succinate, and formaldehyde (Figure 4D). Distinct from lysine-specific demethylases, JMJC enzymes are able to demethylate mono-, di-, and trimethylated histones.116−119 LSD1 exists in a complex with CoREST [a corepressor protein to the REST/NRSF transcription factor (RE1 silencing transcription factor/neural restrictive silencing factor)120]. LSD1 alone is capable of demethylating isolated histone proteins but demethylates nucleosomal histones only in complex with CoREST.121 The structure of LSD1 and a C-terminal fragment of CoREST has been determined, revealing an extended protein complex with the LSD1 catalytic domain and the SWIRM (SWI 3p, Rsc8p, and Moira) domain at one end, a long helical bundle with two helices contributed by LSD1 and another from CoREST, and the SANT2 domain (SWI-SNF, ADA, N-CoR, and TFIIIB) of CoREST at the opposite end (see Figure 5).122 The C-terminal fragment of CoREST present in this complex is sufficient to allow processing of nucleosome substrates.123 The

■

HISTONE DEIMINATION Protein arginine deiminases (PADIs) catalyze the deimination of the positively charged guanidino side chain of histone arginines to form a citrulline residue with release of NH4+.126 There are five highly conserved mammalian PADI enzymes, PADI1−PADI4 and PADI6,127 all of which require Ca2+ for enzymatic activity. While deimination of protein arginines has been known for many years,128 only recently has deimination been reported to be a histone PTM catalyzed by PADI4.126,129 PADI4, the only nuclear PADI, deiminates arginines on histones H2A, H3, and H4,130,131 which is transcriptionally repressive.130,132 PADI4 deimination of a specific H1 histone arginine plays a role in the regulation of pluripotency.133 There are no reports of an enzyme that catalyzes conversion of a histone citrulline residue back to arginine. While in vitro and in vivo data clearly demonstrate PADI4 deiminase activity with histone arginine substrates, several in vitro studies did not detect demethylimination of either mono- or dimethylarginine in synthetic substrates, histone tail peptide substrates, or histone substrates.130,134,135 This observation may be understood from examination of the cocrystal structures of a catalytically dead, C645A mutant PADI4 with argininecontaining substrates. The terminal nitrogens of the histone arginine side chain make three hydrogen bonds to aspartate residues 350 and 473, and the fourth hydrogen interacts with a water molecule that makes additional interactions with the PADI4 enzyme. A single methyl group could fit in the active site, displacing the water and maintaining all other hydrogen bonds. While this would be sterically allowed, the methyl group would be unable to replace hydrogen bonds that the water makes with PAD4I. The loss of two hydrogen bonds to water would decrease the binding affinity of a methylarginine versus that of an unmodified arginine substrate. With a dimethylarginine substrate, one or two additional hydrogen bonds would be lost and a steric clash with one of the aspartates would need to be relieved. The resulting energetic cost is likely to prevent binding of a substrate with dimethylamine, consistent with in vitro data.130

■

HISTONE PHOSPHORYLATION

Histone phosphorylation plays an important role in the DNA damage response (DDR), transcriptional regulation, and chromatin compaction. Serine, threonine, and tyrosine histone residues are phosphorylated and dephosphorylated by multiple kinases and phosphatases.136 The mammalian kinases ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3related) are sensors of double-stranded and single-stranded DNA breaks, respectively, and initiate the DDR by phosphorylating more than 700 proteins.137 One of the more than 700 substrates is Ser139 of the H2A.X variant histone, and this posttranslational modification is an essential event in DDR.138,139 Similarly, WSTF (Williams-Beuren syndrome transcription

Figure 5. LSD1/CoREST complex bound to an H3 N-terminal peptide (PDB entry 2V1D214). The LSD1 catalytic domain is colored green and the SWIRM domain yellow. The LSD1 helical linker is colored cyan. The CoREST SANT2 domain is colored magenta. The CoREST helix is colored gray. A peptide inhibitor, which mimics substrate binding, is shown as balls and sticks, colored by atom with purple carbons. This illustration was prepared with PyMol.210 1591


Current Topic

Biochemistry

Ring1A/B in vivo has not been identified, though E2 enzymes for Ring1B that are active in vitro have been reported, including UbcH5c.157 Chromobox homologue (CBX) proteins target canonical PRC1 to specific regions of the genome where it works in a concerted manner with PRC2 to ubiquitylate H2A-K119 to repress gene transcription at H3K27me3 marks.158 PRC1mediated H3K119 ubiquitylation is essential for transcriptional repression of homeobox (HOX) genes, which encode transcription factors important in vertebrate development.159 Noncanonical PRC1 complexes have been identified, which do not contain CBX protein and target different sites on the genome with different biological functions. In mouse embryonic stem cells (ESCs), the histone demethylase KDM2b (Fbxl10)160 binds to Ring1B and directs PRC1-catalyzed H2A-K119 ubiquitylation to methylated DNA regions in the genome, essential for proper embryonic stem cell (ESC) differentiation. Rybp (RING1 and YY1-binding protein) also forms a noncanonical PRC1 and directs ubiquitylation essential for Xinactive specific transcript RNA-mediated silencing in ESCs.161 L3MBLT2, an epigenetic methyllysine reader protein, forms a noncanonical PRC1 complex and directs ubiquitylation activity for transcriptional repression, and whose presence is essential for pluripotency and differentiation.162,163 Hence, HMEs and epigenetic readers direct the ubiquitylation activity of noncanonical PRC1 to specific gene loci for gene silencing. In addition to PRC1, H2A-K119 ubiquitylation is regulated through deubiquitylating enzymes (DUBs). The complex polycomb repressive deubiquitinase (PR-DUB), composed of human ASXL1 and the DUB BRCA1-associated protein 1 (BAP1), was shown to deubiquitylate H2A.164 PR-DUB is not associated with PRC1. It is noteworthy that germline and somatic inactivating mutations of BAP1 are associated with multiple cancer types, including malignant pleural mesothelioma, uveal melanoma, cutaneous melanoma, and renal cell carcinoma.165−168 MYSM1 (Myb-Like, SWIRM, and MPN domains 1) deubiquitylates H2A-K119, in a coordinated manner with histone acetylation,169 and activates transcription important in early B-cell development,170 regulation of genetic stability in hematopoetic stem cells,171 and maturation of natural killer cells.172

factor), in complex with the chromatin remodeling protein SNF2H, phosphorylates H2A.X Tyr142 in response to dsDNA breaks as a component of DDR.140 Multiple enzymes have been reported to catalyze dephosphorylation of H2A.X, including PP2A,141,142 PP4,143 PP6,144and Wip1,145 and thus play a direct role in turning off DDR. Additionally, all histones (H1, H2A, H2B, H3, and H4) have been reported to be phosphorylated at serine, threonine, and tyrosine residues as a regulatory step in mitosis, meiosis, or transcription (reviewed in detail136). An important example of this is the role of Aurora B in mitosis. During M-phase, Aurora B, a component of the chromosomal passenger complex, phosphorylates H3S10. This phosphorylation inhibits the binding of heterochromatin protein HP1α to the H3 N-terminus at mitotic chromosomes, essential for chromatin condensation during mitosis.146,147 HP1α possesses an epigenetic reader domain that binds specifically to H3K9me2/3. Methylation of this residue is abrogated by phosphorylation at the contiguous H3S10, catalyzed by Aurora B. There is additional complexity in this histone modification−recognition mechanism. Haspin phosphorylates H3T3, which recruits the Aurora B kinasecontaining chromosome passenger complex to centromeric chromatin.148 In yeast, H3S10 phosphorylation recruits the histone deacetylase Hst2p, which deacetylates H4K16, and results in N-terminal H4 association with neighboring nucleosomes during chromatin condensation.149 In the structure reported by Luger and colleagues, H4K16 binds through a salt bridge interaction to an acidic patch on a neighboring nucleosome.5 Acetylation of H4K16 would disrupt this higherorder chromatin structure and result in less compact chromatin. Consistent with this hypothesis, it has been shown that acetylation at H4K16 interferes with the formation of 30 nm chromatin fibrils.150,151 This exemplifies the functional interaction among four histone marks (H3T3ph, H3K9me, H3S10ph, and H4K16ac) as a cellular regulatory mechanism of chromatin compaction during mitosis. The regulatory mechanism requires the “reading of histone marks” to recruit specific protein complexes and a decrease in the basicity of the N-terminus of histone tails.

■

■

HISTONE UBIQUITYLATION The central function of non-histone protein polyubiquitylation, which is the linkage of multiple 76-amino acid ubiquitin groups through the ε-amino group of lysine, is to mark proteins for degradation by the 26S proteasome. There is no evidence to date that histone proteins are ubiquitylated for this purpose. Rather, C- and N-terminal lysine monoubiquitylation serves as a histone mark, and thus, ubiquitlyation and deubiquitylation play a role in transcriptional regulation.152 Monoubiquitylation of H2A (on lysines 13, 15, and 119) and H2B (on lysines 34, 120, and 125) is the most prominent and has been shown to play important biological roles (nucleosomal ubiquitylation shown in Figure 1).153 Polycomb repressive complex type 1 (PRC1) is a multiprotein complex that ubiquitylates histone H2A K119.154 While there are variant forms of PRC1 composed of different proteins, the canonical complex is shown in Figure 3.155,156 A distinguishing feature of PRC1 among HME complexes is the high number of homologues of each protein complex member (Ring, 2; CBX, 5; SCML, 3; HPH, 3; PCGF, 6). This diversity of components allows hundreds of variations in canonical PRC1, which may be important in gene-loci specificity required for transcriptional regulation. The cognate E2 ubiquitin-conjugating enzyme for

FUTURE DIRECTIONS In addition to the widely recognized histone marks discussed above, recent work is revealing many less studied posttranslational modifications, including crotonylation, hydroxylation, succinylation, 2-hydroxyisobutyrylation, and ADP ribosylation of histones. The extent of these modifications is illustrated in a recent summary,173 and a list of known histone PTMs is compiled in Table 3. While the biological relevance of many newly discovered marks is yet to be determined, examples of their importance are emerging. The HAT p300 can use either acetylCoA or crotonyl-CoA as an alkyl group donor to acetylate or crotonylate histones.174 The histone residue is the same for either reaction, and the product is dependent on the levels of acetyl-CoA and crotonyl-CoA within the assay or cell. Both acetyl and crotonyl are activating marks, with crotonyl being more activating.174 2-Hydroxyisobutyrylation is another recently identified histone mark found on many lysines in all histones.175 The mark can occur at the same sites as acetyl and crotonyl as well as unique sites where other marks have not been reported. Levels of 2-hydroxyisobutyryl are dynamically regulated during spermatogenesis, showing patterns different from those of 1592


Biochemistry

■

Table 3. Post-translational Modifications modification

amino acid

methylation acetylation phosphorylation ubiquitylation citrullination propionylation butyrylation cronylation 2-hydroxyisobutyrylation malonylation succinylation formylation hydroxylation O-GlcNacylation ADP ribosylation

lysine, arginine lysine, serine, threonine serine, threonine, histidine lysine arginine lysine lysine lysine lysine lysine lysine lysine tyrosine serine, threonine lysine, glutamic acid

Current Topic

AUTHOR INFORMATION

Corresponding Author

*Phone: 215-628-5530. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS We thank Dash Dhanak and Kay Ahn for valuable comments on the manuscript.

■

ABBREVIATIONS Ado-Hyc, adenosylhomocysteine; Ado-Met, adenosylmethionine; CoA, coenzyme A; DDR, DNA damage response; EZH1, enhancer of zeste 1; EZH2, enhancer of zeste 2; HAT, histone acetyltransferase; HME, histone-modifying enzyme; HMT, histone methyltransferase; lncRNA, long intervening noncoding RNA; NHL, non-Hodgkins lymphoma; PADI, protein arginine deiminase; PDB, Protein Data Bank; PKMT, protein lysine methyltransferase; PRC1, polycomb repressive complex type 1; PRC2, polycomb repressive complex type 2; PRMT, protein arginine methyltransferase; PTM, post-translational modification; SET, suppressor of variegation, enhancer of zeste, and trithorax.

acetylation or crotonylation. The distinct pattern of the 2hydroxyisobutyryl mark suggests a unique biological role.175 Additional types of regulation of histone-modifying enzymes and, thus, the histone code have been reported recently. Large intervening noncoding RNAs (lncRNAs) have been shown to recruit and activate HME catalytic activity in protein complexes.176 Examples include lncRNA HOTAIR binding to PRC2 with modulation of H3K27 methylation177 and Oct4p4 lncRNA binding to the histone methyltransferase SUV39H1 with an increased level of H3K9 trimethylation and repressed Oct4 transcription factor-mediated transcription.178 Also, there is substantial evidence that cellular metabolites and cofactors can modulate the activity of HMEs. Fatty acyl-CoAs inhibit histone acetyltransferases biochemically and histone acetylation in cells,32 and post-translational modification of HME proteins can regulate their biological activity. CaM kinase II specifically phosphorylates HDAC4, targeting it for nuclear export and a decreased level of histone acetylation at HDAC4 target gene loci.179 This provides an example of a signaling kinase pathway impacting transcriptional regulation through a histone-modifying enzyme. An important area of current research in chromatin biology not described in this review is the development of potent, selective HME inhibitors. The histone deacetylase inhibitors vorinostat and romidepsin are approved by the FDA for the treatment of cutaneous t-cell lymphoma, and additional inhibitors are in clinical trials.180 Inhibitors of the histone methyltransferases DOT1L181 and EZH2182,183 and histone demethylase LSD1184,185 are in oncology clinical trials. In preclinical drug discovery and basic research, recent years have been highly productive in the discovery of potent, selective inhibitors against all classes of HMEs.2,186,187 In addition to the promise that some of these inhibitors may be developed into effective disease treatments, they also are highly valuable research tools. Many studies have examined HME protein function by knockdown and knockout of the proteins, but this perturbation is quite different from selective pharmacological inhibition of HME catalytic activity in cells. Knockdown/knockout of a protein eliminates enzymatic activities, but also scaffolding and/or epigenetic reader functions of the HME. Selective pharmacological inhibitors are expected to decrease catalytic activity only and, therefore, provide a powerful tool for understanding the biological role of histone marks and the enzymes that modulate them.

■

REFERENCES

(1) Allfrey, V., Faulkner, R., and Mirsky, A. (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. U. S. A. 51, 786. (2) Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K., and Schapira, M. (2012) Epigenetic protein families: a new frontier for drug discovery. Nat. Rev. Drug Discovery 11, 384−400. (3) Kornberg, R. D. (1974) Chromatin Structure: A Repeating Unit of Histones and DNA. Science 184, 868−871. (4) Shaw, B. R., Herman, T. M., Kovacic, R. T., Beaudreau, G. S., and Van Holde, K. E. (1976) Analysis of subunit organization in chicken erythrocyte chromatin. Proc. Natl. Acad. Sci. U. S. A. 73, 505−509. (5) Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251−260. (6) Robinson, P. J., Fairall, L., Huynh, V. A., and Rhodes, D. (2006) EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure. Proc. Natl. Acad. Sci. U. S. A. 103, 6506−6511. (7) Tremethick, D. J. (2007) Higher-order structures of chromatin: the elusive 30 nm fiber. Cell 128, 651−654. (8) Bell, O., Tiwari, V. K., Thomä, N. H., and Schübeler, D. (2011) Determinants and dynamics of genome accessibility. Nat. Rev. Genet. 12, 554−564. (9) Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., and Kurumizaka, H. (2010) Structural basis of instability of the nucleosome containing a testisspecific histone variant, human H3T. Proc. Natl. Acad. Sci. U. S. A. 107, 10454−10459. (10) Allan, J., Hartman, P., Crane-Robinson, C., and Aviles, F. (1980) Nature 288, 675. (11) Kuzmichev, A., Jenuwein, T., Tempst, P., and Reinberg, D. (2004) Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3. Mol. Cell 14, 183−193. (12) Wiśniewski, J. R., Zougman, A., Krüger, S., and Mann, M. (2006) Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue. Mol. Cell. Proteomics 6, 72− 87. (13) Grewal, S. I., and Moazed, D. (2003) Heterochromatin and epigenetic control of gene expression. Science 301, 798−802.

1593


Current Topic

Biochemistry (14) Noma, K.-i., Allis, C. D., and Grewal, S. I. (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150−1155. (15) Hathaway, N. A., Bell, O., Hodges, C., Miller, E. L., Neel, D. S., and Crabtree, G. R. (2012) Dynamics and memory of heterochromatin in living cells. Cell 149, 1447−1460. (16) Kim, K., Doi, A., Wen, B., Ng, K., Zhao, R., Cahan, P., Kim, J., Aryee, M., Ji, H., Ehrlich, L., et al. (2010) Epigenetic memory in induced pluripotent stem cells. Nature 467, 285−290. (17) Á lvarez-Errico, D., Vento-Tormo, R., Sieweke, M., and Ballestar, E. (2014) Epigenetic control of myeloid cell differentiation, identity and function. Nat. Rev. Immunol. 15, 7−17. (18) Rodríguez-Paredes, M., and Esteller, M. (2011) Cancer epigenetics reaches mainstream oncology. Nat. Med., 330−339. (19) Renaudineau, Y. (2010) The revolution of epigenetics in the field of autoimmunity. Clin. Rev. Allergy Immunol. 39, 1−2. (20) Youngblood, B., Hale, J. S., and Ahmed, R. (2013) T-cell memory differentiation: insights from transcriptional signatures and epigenetics. Immunology 139, 277−284. (21) Stein, R. A. (2011) Epigeneticsthe link between infectious diseases and cancer. JAMA 305, 1484−1485. (22) Brownell, J. E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D. G., Roth, S. Y., and Allis, C. D. (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843−851. (23) Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408−411. (24) Berndsen, C. E., and Denu, J. M. (2008) Catalysis and substrate selection by histone/protein lysine acetyltransferases. Curr. Opin. Struct. Biol. 18, 682−689. (25) Tanner, K. G., Trievel, R. C., Kuo, M.-H., Howard, R. M., Berger, S. L., Allis, C. D., Marmorstein, R., and Denu, J. M. (1999) Catalytic mechanism and function of invariant glutamic acid 173 from the histone acetyltransferase GCN5 transcriptional coactivator. J. Biol. Chem. 274, 18157−18160. (26) Tanner, K. G., Langer, M. R., Kim, Y., and Denu, J. M. (2000) Kinetic mechanism of the histone acetyltransferase GCN5 from yeast. J. Biol. Chem. 275, 22048−22055. (27) Jiang, J., Lu, J., Lu, D., Liang, Z., Li, L., Ouyang, S., Kong, X., Jiang, H., Shen, B., and Luo, C. (2012) Investigation of the acetylation mechanism by GCN5 histone acetyltransferase. PLoS One 7, e36660. (28) Tanner, K. G., Langer, M. R., and Denu, J. M. (2000) Kinetic mechanism of human histone acetyltransferase P/CAF. Biochemistry 39, 11961−11969. (29) Lau, O. D., Courtney, A. D., Vassilev, A., Marzilli, L. A., Cotter, R. J., Nakatani, Y., and Cole, P. A. (2000) p300/CBP-associated Factor Histone Acetyltransferase Processing of a Peptide Substrate KINETIC ANALYSIS OF THE CATALYTIC MECHANISM. J. Biol. Chem. 275, 21953−21959. (30) Zhang, X., Ouyang, S., Kong, X., Liang, Z., Lu, J., Zhu, K., Zhao, D., Zheng, M., Jiang, H., Liu, X., Marmorstein, R., and Luo, C. (2014) Catalytic mechanism of histone acetyltransferase p300: from the proton transfer to acetylation reaction. J. Phys. Chem. B 118, 2009−2019. (31) Yan, Y., Harper, S., Speicher, D. W., and Marmorstein, R. (2002) The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. Nat. Struct. Biol. 9, 862−869. (32) Montgomery, D. C., Sorum, A. W., Guasch, L., Nicklaus, M. C., and Meier, J. L. (2015) Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors. Chem. Biol. 22, 1030− 1039. (33) Wiktorowicz, J. E., Campos, K. L., and Bonner, J. (1981) Substrate and product inhibition initial rate kinetics of histone acetyltransferase. Biochemistry 20, 1464−1467. (34) Meier, J. L. (2013) Metabolic mechanisms of epigenetic regulation. ACS Chem. Biol. 8, 2607−2621. (35) Fan, J., Krautkramer, K. A., Feldman, J. L., and Denu, J. M. (2015) Metabolic regulation of histone post-translational modifications. ACS Chem. Biol. 10, 95−108.

(36) Hodawadekar, S., and Marmorstein, R. (2007) Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design. Oncogene 26, 5528−5540. (37) Lee, K. K., and Workman, J. L. (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat. Rev. Mol. Cell Biol. 8, 284−295. (38) Ogryzko, V. (2001) Mammalian histone acetyltransferases and their complexes. Cell. Mol. Life Sci. 58, 683−692. (39) Doyon, Y., Selleck, W., Lane, W. S., Tan, S., and Côté, J. (2004) Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Molecular and cellular biology 24, 1884−1896. (40) Yamada, H. Y. (2012) Human Tip60 (NuA4) complex and cancer, INTECH, Rijeka, Croatia. (41) Frank, S. R., Parisi, T., Taubert, S., Fernandez, P., Fuchs, M., Chan, H. M., Livingston, D. M., and Amati, B. (2003) MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep. 4, 575− 580. (42) Ikura, T., Ogryzko, V. V., Grigoriev, M., Groisman, R., Wang, J., Horikoshi, M., Scully, R., Qin, J., and Nakatani, Y. (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102, 463−473. (43) Kusch, T., Florens, L., MacDonald, W. H., Swanson, S. K., Glaser, R. L., Yates, J. R., Abmayr, S. M., Washburn, M. P., and Workman, J. L. (2004) Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306, 2084−2087. (44) Murr, R., Loizou, J. I., Yang, Y.-G., Cuenin, C., Li, H., Wang, Z.-Q., and Herceg, Z. (2006) Histone acetylation by Trrap−Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks. Nat. Cell Biol. 8, 91−99. (45) Sun, Y., Jiang, X., and Price, B. D. (2010) Tip60: connecting chromatin to DNA damage signaling. Cell Cycle 9, 930−936. (46) Seto, E., and Yoshida, M. (2014) Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor Perspect. Biol. 6, a018713. (47) Gregoretti, I., Lee, Y.-M., and Goodson, H. V. (2004) Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J. Mol. Biol. 338, 17−31. (48) Xu, W., Parmigiani, R., and Marks, P. (2007) Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene 26, 5541−5552. (49) Zhou, X., Marks, P. A., Rifkind, R. A., and Richon, V. M. (2001) Cloning and characterization of a histone deacetylase, HDAC9. Proc. Natl. Acad. Sci. U. S. A. 98, 10572−10577. (50) Matthews, B. W. (1988) Structural basis of the action of thermolysin and related zinc peptidases. Acc. Chem. Res. 21, 333−340. (51) Lombardi, P. M., Cole, K. E., Dowling, D. P., and Christianson, D. W. (2011) Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes. Curr. Opin. Struct. Biol. 21, 735−743. (52) Bottomley, M. J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkühler, C., Gallinari, P., and Carfi, A. (2008) Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain. J. Biol. Chem. 283, 26694− 26704. (53) Schuetz, A., Min, J., Allali-Hassani, A., Schapira, M., Shuen, M., Loppnau, P., Mazitschek, R., Kwiatkowski, N. P., Lewis, T. A., Maglathin, R. L., McLean, T. H., Bochkarev, A., Plotnikov, A. N., Vedadi, M., and Arrowsmith, C. H. (2008) Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. J. Biol. Chem. 283, 11355−11363. (54) Michishita, E., Park, J. Y., Burneskis, J. M., Barrett, J. C., and Horikawa, I. (2005) Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Molecular biology of the cell 16, 4623−4635. (55) Vaquero, A., Scher, M. B., Lee, D. H., Sutton, A., Cheng, H.-L., Alt, F. W., Serrano, L., Sternglanz, R., and Reinberg, D. (2006) SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis. Genes Dev. 20, 1256−1261. 1594


Current Topic

Biochemistry (56) Haigis, M. C., and Guarente, L. P. (2006) Mammalian sirtuins emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913−2921. (57) Feldman, J. L., Dittenhafer-Reed, K. E., and Denu, J. M. (2012) Sirtuin catalysis and regulation. J. Biol. Chem. 287, 42419−42427. (58) Avalos, J. L., Boeke, J. D., and Wolberger, C. (2004) Structural basis for the mechanism and regulation of Sir2 enzymes. Mol. Cell 13, 639−648. (59) Borra, M. T., Langer, M. R., Slama, J. T., and Denu, J. M. (2004) Substrate specificity and kinetic mechanism of the Sir2 family of NAD +-dependent histone/protein deacetylases. Biochemistry 43, 9877− 9887. (60) Ayer, D. E. (1999) Histone deacetylases: transcriptional repression with SINers and NuRDs. Trends Cell Biol. 9, 193−198. (61) Ahringer, J. (2000) NuRD and SIN3: histone deacetylase complexes in development. Trends Genet. 16, 351−356. (62) Hayakawa, T., and Nakayama, J.-i. (2011) Physiological roles of class I HDAC complex and histone demethylase. J. Biomed. Biotechnol. 2011, 1. (63) Denslow, S., and Wade, P. (2007) The human Mi-2/NuRD complex and gene regulation. Oncogene 26, 5433−5438. (64) Ng, H.-H., Zhang, Y., Hendrich, B., Johnson, C. A., Turner, B. M., Erdjument-Bromage, H., Tempst, P., Reinberg, D., and Bird, A. (1999) MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat. Genet. 23, 58−61. (65) Zhang, Y., Ng, H.-H., Erdjument-Bromage, H., Tempst, P., Bird, A., and Reinberg, D. (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13, 1924−1935. (66) Le Guezennec, X., Vermeulen, M., Brinkman, A. B., Hoeijmakers, W. A., Cohen, A., Lasonder, E., and Stunnenberg, H. G. (2006) MBD2/ NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties. Molecular and cellular biology 26, 843−851. (67) Das, C., Tyler, J. K., and Churchill, M. E. (2010) The histone shuffle: histone chaperones in an energetic dance. Trends Biochem. Sci. 35, 476−489. (68) Wang, Y., Zhang, H., Chen, Y., Sun, Y., Yang, F., Yu, W., Liang, J., Sun, L., Yang, X., Shi, L., Li, R., Li, Y., Zhang, Y., Li, Q., Yi, X., and Shang, Y. (2009) LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell 138, 660−672. (69) Nishibuchi, G., Shibata, Y., Hayakawa, T., Hayakawa, N., Ohtani, Y., Sinmyozu, K., Tagami, H., and Nakayama, J.-i. (2014) Physical and functional interactions between the histone h3k4 demethylase kdm5a and the nucleosome remodeling and deacetylase (nurd) complex. J. Biol. Chem. 289, 28956−28970. (70) Copeland, R. A., Solomon, M. E., and Richon, V. M. (2009) Protein methyltransferases as a target class for drug discovery. Nat. Rev. Drug Discovery 8, 724−732. (71) Tschiersch, B., Hofmann, A., Krauss, V., Dorn, R., Korge, G., and Reuter, G. (1994) The protein encoded by the Drosophila positioneffect variegation suppressor gene Su (var) 3−9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO Journal 13, 3822. (72) Smith, B. C., and Denu, J. M. (2009) Chemical mechanisms of histone lysine and arginine modifications. Biochim. Biophys. Acta, Gene Regul. Mech. 1789, 45−57. (73) Kipp, D. R., Quinn, C. M., and Fortin, P. D. (2013) Enzymedependent lysine deprotonation in EZH2 catalysis. Biochemistry 52, 6866−6878. (74) Xiao, B., Jing, C., Wilson, J. R., Walker, P. A., Vasisht, N., Kelly, G., Howell, S., Taylor, I. A., Blackburn, G. M., and Gamblin, S. J. (2003) Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421, 652−656. (75) Patnaik, D., Chin, H. G., Esteve, P.-O., Benner, J., Jacobsen, S. E., and Pradhan, S. (2004) Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J. Biol. Chem. 279, 53248−53258.

(76) Swalm, B. M., Knutson, S. K., Warholic, N. M., Jin, L., Kuntz, K. W., Keilhack, H., Smith, J. J., Pollock, R. M., Moyer, M. P., Scott, M. P., Copeland, R. A., and Wigle, T. J. (2014) Reaction Coupling between Wild-Type and Disease-Associated Mutant EZH2. ACS Chem. Biol. 9, 2459−2464. (77) Min, J., Feng, Q., Li, Z., Zhang, Y., and Xu, R.-M. (2003) Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 112, 711−723. (78) Frederiks, F., Tzouros, M., Oudgenoeg, G., van Welsem, T., Fornerod, M., Krijgsveld, J., and van Leeuwen, F. (2008) Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states. Nat. Struct. Mol. Biol. 15, 550−557. (79) Margueron, R., Li, G., Sarma, K., Blais, A., Zavadil, J., Woodcock, C. L., Dynlacht, B. D., and Reinberg, D. (2008) Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503− 518. (80) Margueron, R., and Reinberg, D. (2011) The Polycomb complex PRC2 and its mark in life. Nature 469, 343−349. (81) Kim, H., Kang, K., and Kim, J. (2009) AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2. Nucleic Acids Res. 37, 2940−2950. (82) Cai, L., Rothbart, S. B., Lu, R., Xu, B., Chen, W.-Y., Tripathy, A., Rockowitz, S., Zheng, D., Patel, D. J., Allis, C. D., Strahl, B. D., Song, J., and Wang, G. G. (2013) An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Mol. Cell 49, 571−582. (83) Cao, R., and Zhang, Y. (2004) SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EEDEZH2 complex. Mol. Cell 15, 57−67. (84) Sneeringer, C. J., Scott, M. P., Kuntz, K. W., Knutson, S. K., Pollock, R. M., Richon, V. M., and Copeland, R. A. (2010) Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas. Proc. Natl. Acad. Sci. U. S. A. 107, 20980−20985. (85) McCabe, M. T., Graves, A. P., Ganji, G., Diaz, E., Halsey, W. S., Jiang, Y., Smitheman, K. N., Ott, H. M., Pappalardi, M. B., Allen, K. E., et al. (2012) Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27). Proc. Natl. Acad. Sci. U. S. A. 109, 2989−2994. (86) Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129, 823− 837. (87) Margueron, R., Justin, N., Ohno, K., Sharpe, M. L., Son, J., Drury Iii, W. J., Voigt, P., Martin, S. R., Taylor, W. R., De Marco, V., Pirrotta, V., Reinberg, D., and Gamblin, S. J. (2009) Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762− 767. (88) Van Aller, G. S., Pappalardi, M. B., Ott, H. M., Diaz, E., Brandt, M., Schwartz, B. J., Miller, W. H., Dhanak, D., McCabe, M. T., Verma, S. K., Creasy, C. L., Tummino, P. J., and Kruger, R. G. (2014) Long residence time inhibition of EZH2 in activated polycomb repressive complex 2. ACS Chem. Biol. 9, 622−629. (89) Jiao, L., and Liu, X. (2015) Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2. Science 350, aac4383. (90) Simon, J. A., and Lange, C. A. (2008) Roles of the EZH2 histone methyltransferase in cancer epigenetics. Mutat. Res., Fundam. Mol. Mech. Mutagen. 647, 21−29. (91) Morin, R. D., Johnson, N. A., Severson, T. M., Mungall, A. J., An, J., Goya, R., Paul, J. E., Boyle, M., Woolcock, B. W., Kuchenbauer, F., et al. (2010) Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181−185. (92) Majer, C. R., Jin, L., Scott, M. P., Knutson, S. K., Kuntz, K. W., Keilhack, H., Smith, J. J., Moyer, M. P., Richon, V. M., Copeland, R. A., and Wigle, T. J. (2012) A687V EZH2 is a gain-of-function mutation found in lymphoma patients. FEBS Lett. 586, 3448−3451. 1595


Current Topic

Biochemistry (93) Bedford, M. T., and Clarke, S. G. (2009) Protein arginine methylation in mammals: who, what, and why. Mol. Cell 33, 1−13. (94) Di Lorenzo, A., and Bedford, M. T. (2011) Histone arginine methylation. FEBS Lett. 585, 2024−2031. (95) Hadjikyriacou, A., Yang, Y., Bedford, M., and Clarke, S. (2015) Characterization of the Activity and Biological Function of Human Protein Arginine Methyltransferase 9 (PRMT9). FASEB J. 29, LB211. (96) Yue, W. W., Hassler, M., Roe, S. M., Thompson-Vale, V., and Pearl, L. H. (2007) Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase. EMBO J. 26, 4402− 4412. (97) Chen, D., Ma, H., Hong, H., Koh, S. S., Huang, S.-M., Schurter, B. T., Aswad, D. W., and Stallcup, M. R. (1999) Regulation of transcription by a protein methyltransferase. Science 284, 2174−2177. (98) Troffer-Charlier, N., Cura, V., Hassenboehler, P., Moras, D., and Cavarelli, J. (2007) Functional insights from structures of coactivatorassociated arginine methyltransferase 1 domains. EMBO J. 26, 4391− 4401. (99) Zhang, X., Zhou, L., and Cheng, X. (2000) Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J. 19, 3509−3519. (100) Higashimoto, K., Kuhn, P., Desai, D., Cheng, X., and Xu, W. (2007) Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1. Proc. Natl. Acad. Sci. U. S. A. 104, 12318− 12323. (101) Lim, Y., Kwon, Y.-H., Won, N. H., Min, B.-H., Park, I.-S., Paik, W. K., and Kim, S. (2005) Multimerization of expressed protein-arginine methyltransferases during the growth and differentiation of rat liver. Biochim. Biophys. Acta, Gen. Subj. 1723, 240−247. (102) Herrmann, F., Pably, P., Eckerich, C., Bedford, M. T., and Fackelmayer, F. O. (2009) Human protein arginine methyltransferases in vivo−distinct properties of eight canonical members of the PRMT family. J. Cell Sci. 122, 667−677. (103) Teyssier, C., Chen, D., and Stallcup, M. R. (2002) Requirement for multiple domains of the protein arginine methyltransferase CARM1 in its transcriptional coactivator function. J. Biol. Chem. 277, 46066− 46072. (104) Lee, Y.-H., Coonrod, S. A., Kraus, W. L., Jelinek, M. A., and Stallcup, M. R. (2005) Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. Proc. Natl. Acad. Sci. U. S. A. 102, 3611−3616. (105) Koh, S. S., Chen, D., Lee, Y.-H., and Stallcup, M. R. (2001) Synergistic enhancement of nuclear receptor function by p160 coactivators and two coactivators with protein methyltransferase activities. J. Biol. Chem. 276, 1089−1098. (106) Chen, T., and Dent, S. Y. (2013) Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat. Rev. Genet. 15, 93−106. (107) Shepherd, G., Hardin, J., and Noland, B. (1971) Methylation of lysine residues of histone fractions in synchronized mommalian cells. Arch. Biochem. Biophys. 143, 1−5. (108) Byvoet, P., Shepherd, G., Hardin, J., and Noland, B. (1972) The distribution and turnover of labeled methyl groups in histone fractions of cultured mammalian cells. Arch. Biochem. Biophys. 148, 558−567. (109) Jenuwein, T. (2001) Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol. 11, 266−273. (110) Ahmad, K., and Henikoff, S. (2002) The histone variant H3. 3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9, 1191−1200. (111) Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J. R., Cole, P. A., Casero, R. A., and Shi, Y. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941−953. (112) Mosammaparast, N., and Shi, Y. (2010) Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu. Rev. Biochem. 79, 155−179. (113) Kooistra, S. M., and Helin, K. (2012) Molecular mechanisms and potential functions of histone demethylases. Nat. Rev. Mol. Cell Biol. 13, 297−311.

(114) Forneris, F., Binda, C., Vanoni, M. A., Mattevi, A., and Battaglioli, E. (2005) Histone demethylation catalysed by LSD1 is a flavindependent oxidative process. FEBS Lett. 579, 2203−2207. (115) Tsukada, Y.-i., Fang, J., Erdjument-Bromage, H., Warren, M. E., Borchers, C. H., Tempst, P., and Zhang, Y. (2005) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811−816. (116) Klose, R. J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J., and Zhang, Y. (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442, 312−316. (117) Cloos, P. A., Christensen, J., Agger, K., Maiolica, A., Rappsilber, J., Antal, T., Hansen, K. H., and Helin, K. (2006) The putative oncogene GASC1 demethylates tri-and dimethylated lysine 9 on histone H3. Nature 442, 307−311. (118) Fodor, B. D., Kubicek, S., Yonezawa, M., O’Sullivan, R. J., Sengupta, R., Perez-Burgos, L., Opravil, S., Mechtler, K., Schotta, G., and Jenuwein, T. (2006) Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20, 1557− 1562. (119) Whetstine, J. R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M., and Shi, Y. (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467−481. (120) Andrés, M. E., Burger, C., Peral-Rubio, M. J., Battaglioli, E., Anderson, M. E., Grimes, J., Dallman, J., Ballas, N., and Mandel, G. (1999) CoREST: a functional corepressor required for regulation of neural-specific gene expression. Proc. Natl. Acad. Sci. U. S. A. 96, 9873− 9878. (121) Lee, M. G., Wynder, C., Cooch, N., and Shiekhattar, R. (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437, 432−435. (122) Yang, M., Gocke, C. B., Luo, X., Borek, D., Tomchick, D. R., Machius, M., Otwinowski, Z., and Yu, H. (2006) Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol. Cell 23, 377−387. (123) Shi, Y.-J., Matson, C., Lan, F., Iwase, S., Baba, T., and Shi, Y. (2005) Regulation of LSD1 Histone Demethylase Activity by Its Associated Factors. Mol. Cell 19, 857−864. (124) Pilotto, S., Speranzini, V., Tortorici, M., Durand, D., Fish, A., Valente, S., Forneris, F., Mai, A., Sixma, T. K., Vachette, P., and Mattevi, A. (2015) Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation. Proc. Natl. Acad. Sci. U. S. A. 112, 2752−2757. (125) Baron, R., and Vellore, N. A. (2012) LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition. Proc. Natl. Acad. Sci. U. S. A. 109, 12509−12514. (126) Nakashima, K., Hagiwara, T., and Yamada, M. (2002) Nuclear localization of peptidylarginine deiminase V and histone deimination in granulocytes. J. Biol. Chem. 277, 49562−49568. (127) Vossenaar, E. R. (2004) Citrullination, the spark that ignites the fire in rheumatoid arthritis? (128) Fearon, W. R. (1939) The carbamido diacetyl reaction: a test for citrulline. Biochem. J. 33, 902. (129) Hagiwara, T., Nakashima, K., Hirano, H., Senshu, T., and Yamada, M. (2002) Deimination of arginine residues in nucleophosmin/B23 and histones in HL-60 granulocytes. Biochem. Biophys. Res. Commun. 290, 979−983. (130) Cuthbert, G. L., Daujat, S., Snowden, A. W., ErdjumentBromage, H., Hagiwara, T., Yamada, M., Schneider, R., Gregory, P. D., Tempst, P., Bannister, A. J., and Kouzarides, T. (2004) Histone deimination antagonizes arginine methylation. Cell 118, 545−553. (131) Hagiwara, T., Hidaka, Y., and Yamada, M. (2005) Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes. Biochemistry 44, 5827−5834. (132) Wang, Y., Wysocka, J., Sayegh, J., Lee, Y.-H., Perlin, J. R., Leonelli, L., Sonbuchner, L. S., McDonald, C. H., Cook, R. G., and Dou, Y. (2004) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306, 279−283. 1596


Current Topic

Biochemistry (133) Christophorou, M. A., Castelo-Branco, G., Halley-Stott, R. P., Oliveira, C. S., Loos, R., Radzisheuskaya, A., Mowen, K. A., Bertone, P., Silva, J. C., Zernicka-Goetz, M., Nielsen, M. L., Gurdon, J. B., and Kouzarides, T. (2014) Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature 507, 104−108. (134) Kearney, P. L., Bhatia, M., Jones, N. G., Yuan, L., Glascock, M. C., Catchings, K. L., Yamada, M., and Thompson, P. R. (2005) Kinetic Characterization of Protein Arginine Deiminase 4: A Transcriptional Corepressor Implicated in the Onset and Progression of Rheumatoid Arthritis†. Biochemistry 44, 10570−10582. (135) Raijmakers, R., Zendman, A. J. W., Egberts, W. V., Vossenaar, E. R., Raats, J., Soede-Huijbregts, C., Rutjes, F. P. J. T., van Veelen, P. A., Drijfhout, J. W., and Pruijn, G. J. M. (2007) Methylation of Arginine Residues Interferes with Citrullination by Peptidylarginine Deiminases in vitro. J. Mol. Biol. 367, 1118−1129. (136) Rossetto, D., Avvakumov, N., and Côté, J. (2012) Histone phosphorylation: a chromatin modification involved in diverse nuclear events. Epigenetics 7, 1098−1108. (137) Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R., Hurov, K. E., Luo, J., Bakalarski, C. E., Zhao, Z., Solimini, N., Lerenthal, Y., Shiloh, Y., Gygi, G. P., and Elledge, S. J. (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160−1166. (138) Burma, S., Chen, B. P., Murphy, M., Kurimasa, A., and Chen, D. J. (2001) ATM phosphorylates histone H2AX in response to DNA double-strand breaks. J. Biol. Chem. 276, 42462−42467. (139) Ward, I. M., and Chen, J. (2001) Histone H2AX is phosphorylated in an ATR-dependent manner in response to replicational stress. J. Biol. Chem. 276, 47759−47762. (140) Xiao, A., Li, H., Shechter, D., Ahn, S. H., Fabrizio, L. A., Erdjument-Bromage, H., Ishibe-Murakami, S., Wang, B., Tempst, P., Hofmann, K., Patel, D. J., Elledge, S. J., and Allis, C. D. (2009) WSTF regulates the H2A. X DNA damage response via a novel tyrosine kinase activity. Nature 457, 57−62. (141) Chowdhury, D., Keogh, M.-C., Ishii, H., Peterson, C. L., Buratowski, S., and Lieberman, J. (2005) γ-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair. Mol. Cell 20, 801−809. (142) Chen, L., Lai, Y., Zhu, X., Ma, L., Bai, Q., Vazquez, I., Xiao, Y., Liu, C., Li, D., Gao, C., et al. (2015) The role of specific PP2A complexes in the dephosphorylation of γ-H2AX. J. Cell Sci. 128, 421. (143) Chowdhury, D., Xu, X., Zhong, X., Ahmed, F., Zhong, J., Liao, J., Dykxhoorn, D. M., Weinstock, D. M., Pfeifer, G. P., and Lieberman, J. (2008) A PP4-phosphatase complex dephosphorylates γ-H2AX generated during DNA replication. Mol. Cell 31, 33−46. (144) Douglas, P., Zhong, J., Ye, R., Moorhead, G. B., Xu, X., and LeesMiller, S. P. (2010) Protein phosphatase 6 interacts with the DNAdependent protein kinase catalytic subunit and dephosphorylates γH2AX. Molecular and cellular biology 30, 1368−1381. (145) Macůrek, L., Lindqvist, A., Voets, O., Kool, J., Vos, H., and Medema, R. (2010) Wip1 phosphatase is associated with chromatin and dephosphorylates γH2AX to promote checkpoint inhibition. Oncogene 29, 2281−2291. (146) Hirota, T., Lipp, J. J., Toh, B.-H., and Peters, J.-M. (2005) Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438, 1176−1180. (147) Fischle, W., Tseng, B. S., Dormann, H. L., Ueberheide, B. M., Garcia, B. A., Shabanowitz, J., Hunt, D. F., Funabiki, H., and Allis, C. D. (2005) Regulation of HP1−chromatin binding by histone H3 methylation and phosphorylation. Nature 438, 1116−1122. (148) Wang, F., Dai, J., Daum, J. R., Niedzialkowska, E., Banerjee, B., Stukenberg, P. T., Gorbsky, G. J., and Higgins, J. M. (2010) Histone H3 Thr-3 phosphorylation by Haspin positions Aurora B at centromeres in mitosis. Science 330, 231−235. (149) Wilkins, B. J., Rall, N. A., Ostwal, Y., Kruitwagen, T., HiragamiHamada, K., Winkler, M., Barral, Y., Fischle, W., and Neumann, H. (2014) A cascade of histone modifications induces chromatin condensation in mitosis. Science 343, 77−80.

(150) Shogren-Knaak, M., Ishii, H., Sun, J.-M., Pazin, M. J., Davie, J. R., and Peterson, C. L. (2006) Histone H4-K16 Acetylation Controls Chromatin Structure and Protein Interactions. Science 311, 844−847. (151) Robinson, P. J. J., An, W., Routh, A., Martino, F., Chapman, L., Roeder, R. G., and Rhodes, D. (2008) 30 nm Chromatin Fibre Decompaction Requires both H4-K16 Acetylation and Linker Histone Eviction. J. Mol. Biol. 381, 816−825. (152) Osley, M. A. (2006) Regulation of histone H2A and H2B ubiquitylation. Briefings Funct. Genomics Proteomics 5, 179−189. (153) Weake, V. M. (2014) Histone Ubiquitylation Control of Gene Expression. In Fundamentals of Chromatin, pp 257−307, Springer, Berlin. (154) Wang, H., Wang, L., Erdjument-Bromage, H., Vidal, M., Tempst, P., Jones, R. S., and Zhang, Y. (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873−878. (155) Gao, Z., Zhang, J., Bonasio, R., Strino, F., Sawai, A., Parisi, F., Kluger, Y., and Reinberg, D. (2012) PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344−356. (156) Gil, J., and O’Loghlen, A. (2014) PRC1 complex diversity: where is it taking us? Trends Cell Biol. 24, 632−641. (157) Buchwald, G., van der Stoop, P., Weichenrieder, O., Perrakis, A., van Lohuizen, M., and Sixma, T. K. (2006) Structure and E3-ligase activity of the Ring−Ring complex of Polycomb proteins Bmi1 and Ring1b. EMBO J. 25, 2465−2474. (158) Aloia, L., Di Stefano, B., and Di Croce, L. (2013) Polycomb complexes in stem cells and embryonic development. Development 140, 2525−2534. (159) Cao, R., Tsukada, Y.-i., and Zhang, Y. (2005) Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol. Cell 20, 845−854. (160) Wu, X., Johansen, J. V., and Helin, K. (2013) Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 49, 1134−1146. (161) Tavares, L., Dimitrova, E., Oxley, D., Webster, J., Poot, R., Demmers, J., Bezstarosti, K., Taylor, S., Ura, H., Koide, H., Wutz, A., Vidal, M., Elderkin, S., and Brockdorff, N. (2012) RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell 148, 664−678. (162) Trojer, P., Cao, A. R., Gao, Z., Li, Y., Zhang, J., Xu, X., Li, G., Losson, R., Erdjument-Bromage, H., Tempst, P., Farnham, P. J., and Reinberg, D. (2011) L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol. Cell 42, 438−450. (163) Qin, J., Whyte, W. A., Anderssen, E., Apostolou, E., Chen, H.-H., Akbarian, S., Bronson, R. T., Hochedlinger, K., Ramaswamy, S., Young, R. A., and Hock, H. (2012) The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Cell Stem Cell 11, 319− 332. (164) Scheuermann, J. C., de Ayala Alonso, A. G., Oktaba, K., LyHartig, N., McGinty, R. K., Fraterman, S., Wilm, M., Muir, T. W., and Müller, J. (2010) Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465, 243−247. (165) Harbour, J. W., Onken, M. D., Roberson, E. D., Duan, S., Cao, L., Worley, L. A., Council, M. L., Matatall, K. A., Helms, C., and Bowcock, A. M. (2010) Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330, 1410−1413. (166) Bott, M., Brevet, M., Taylor, B. S., Shimizu, S., Ito, T., Wang, L., Creaney, J., Lake, R. A., Zakowski, M. F., Reva, B., et al. (2011) The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21. 1 losses in malignant pleural mesothelioma. Nat. Genet. 43, 668−672. (167) Peña-Llopis, S., Vega-Rubín-de-Celis, S., Liao, A., Leng, N., Pavía-Jiménez, A., Wang, S., Yamasaki, T., Zhrebker, L., Sivanand, S., Spence, P., et al. (2012) BAP1 loss defines a new class of renal cell carcinoma. Nat. Genet. 44, 751−759. (168) Carbone, M., Yang, H., Pass, H. I., Krausz, T., Testa, J. R., and Gaudino, G. (2013) BAP1 and cancer. Nat. Rev. Cancer 13, 153−159. 1597


Current Topic

Biochemistry (169) Zhu, P., Zhou, W., Wang, J., Puc, J., Ohgi, K. A., ErdjumentBromage, H., Tempst, P., Glass, C. K., and Rosenfeld, M. G. (2007) A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Mol. Cell 27, 609−621. (170) Jiang, X.-X., Nguyen, Q., Chou, Y., Wang, T., Nandakumar, V., Yates, P., Jones, L., Wang, L., Won, H., Lee, H.-R., Jung, J. U., Müschen, M., Huang, X. F., and Chen, S.-Y. (2011) Control of B cell development by the histone H2A deubiquitinase MYSM1. Immunity 35, 883−896. (171) Nijnik, A., Clare, S., Hale, C., Raisen, C., McIntyre, R. E., Yusa, K., Everitt, A. R., Mottram, L., Podrini, C., Lucas, M., et al. (2012) The critical role of histone H2A-deubiquitinase Mysm1 in hematopoiesis and lymphocyte differentiation. Blood 119, 1370−1379. (172) Nandakumar, V., Chou, Y., Zang, L., Huang, X. F., and Chen, S.Y. (2013) Epigenetic control of natural killer cell maturation by histone H2A deubiquitinase, MYSM1. Proc. Natl. Acad. Sci. U. S. A. 110, E3927− E3936. (173) Huang, H., Sabari, B. R., Garcia, B. A., Allis, C. D., and Zhao, Y. (2014) SnapShot: histone modifications. Cell 159, 458−458 e451. (174) Sabari, B. R., Tang, Z., Huang, H., Yong-Gonzalez, V., Molina, H., Kong, H. E., Dai, L., Shimada, M., Cross, J. R., Zhao, Y., Roeder, R. G., and Allis, C. D. (2015) Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation. Mol. Cell 58, 203−215. (175) Dai, L., Peng, C., Montellier, E., Lu, Z., Chen, Y., Ishii, H., Debernardi, A., Buchou, T., Rousseaux, S., Jin, F., et al. (2014) Lysine 2hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol. 10, 365−370. (176) Lee, J. T. (2012) Epigenetic regulation by long noncoding RNAs. Science 338, 1435−1439. (177) Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M.-C., Hung, T., Argani, P., Rinn, J. L., et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071−1076. (178) Scarola, M., Comisso, E., Pascolo, R., Chiaradia, R., Maria Marion, R., Schneider, C., Blasco, M. A., Schoeftner, S., and Benetti, R. (2015) Epigenetic silencing of Oct4 by a complex containing SUV39H1 and Oct4 pseudogene lncRNA. Nat. Commun. 6, 7631. (179) Backs, J., Song, K., Bezprozvannaya, S., Chang, S., and Olson, E. N. (2006) CaM kinase II selectively signals to histone deacetylase 4 during cardiomyocyte hypertrophy. J. Clin. Invest. 116, 1853. (180) West, A. C., and Johnstone, R. W. (2014) New and emerging HDAC inhibitors for cancer treatment. J. Clin. Invest. 124, 30−39. (181) Stein, E. M., Garcia-Manero, G., Rizzieri, D. A., Savona, M., Tibes, R., Altman, J. K., Jongen-Lavrencic, M., Döhner, H., Armstrong, S., and Pollock, R. M. (2014) The DOT1L inhibitor EPZ-5676: safety and activity in relapsed/refractory patients with MLL-rearranged leukemia. Blood 124, 387−387. (182) Knutson, S. K., Kawano, S., Minoshima, Y., Warholic, N. M., Huang, K.-C., Xiao, Y., Kadowaki, T., Uesugi, M., Kuznetsov, G., Kumar, N., et al. (2014) Selective inhibition of EZH2 by EPZ-6438 leads to potent antitumor activity in EZH2-mutant non-Hodgkin lymphoma. Mol. Cancer Ther. 13, 842−854. (183) Keilhack, H., and Smith, J. J. (2015) Small molecule inhibitors of EZH2: the emerging translational landscape. Epigenomics 7, 337−341. (184) Mohammad, H. P., Smitheman, K. N., Kamat, C. D., Soong, D., Federowicz, K. E., Van Aller, G. S., Schneck, J. L., Carson, J. D., Liu, Y., Butticello, M., et al. (2015) A DNA Hypomethylation Signature Predicts Antitumor Activity of LSD1 Inhibitors in SCLC. Cancer Cell 28, 57−69. (185) Maes, T., Carceller, E., Salas, J., Ortega, A., and Buesa, C. (2015) Advances in the development of histone lysine demethylase inhibitors. Curr. Opin. Pharmacol. 23, 52−60. (186) Helin, K., and Dhanak, D. (2013) Chromatin proteins and modifications as drug targets. Nature 502, 480−488. (187) Campbell, R. M., and Tummino, P. J. (2014) Cancer epigenetics drug discovery and development: the challenge of hitting the mark. J. Clin. Invest. 124, 64−69. (188) Feng, Q., He, B., Jung, S.-Y., Song, Y., Qin, J., Tsai, S. Y., Tsai, M.J., and O’Malley, B. W. (2009) Biochemical control of CARM1 enzymatic activity by phosphorylation. J. Biol. Chem. 284, 36167−36174.

(189) Kuhn, P., Chumanov, R., Wang, Y., Ge, Y., Burgess, R. R., and Xu, W. (2011) Automethylation of CARM1 allows coupling of transcription and mRNA splicing. Nucleic Acids Res. 39, 2717. (190) Wang, L., Charoensuksai, P., Watson, N. J., Wang, X., Zhao, Z., Coriano, C. G., Kerr, L. R., and Xu, W. (2013) CARM1 automethylation is controlled at the level of alternative splicing. Nucleic Acids Res. 41, 6870−6880. (191) Ohkura, N., Takahashi, M., Yaguchi, H., Nagamura, Y., and Tsukada, T. (2005) Coactivator-associated arginine methyltransferase 1, CARM1, affects pre-mRNA splicing in an isoform-specific manner. J. Biol. Chem. 280, 28927−28935. (192) Cheng, D., Côté, J., Shaaban, S., and Bedford, M. T. (2007) The arginine methyltransferase CARM1 regulates the coupling of transcription and mRNA processing. Mol. Cell 25, 71−83. (193) Torres-Padilla, M.-E., Parfitt, D.-E., Kouzarides, T., and Zernicka-Goetz, M. (2007) Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature 445, 214−218. (194) Wu, Q., Bruce, A. W., Jedrusik, A., Ellis, P. D., Andrews, R. M., Langford, C. F., Glover, D. M., and Zernicka-Goetz, M. (2009) CARM1 is required in embryonic stem cells to maintain pluripotency and resist differentiation. Stem Cells 27, 2637−2645. (195) Zhao, H.-y., Zhang, Y.-j., Dai, H., Zhang, Y., and Shen, Y.-f. (2011) CARM1 mediates modulation of Sox2. PLoS One 6, e27026. (196) Lee, Y.-H., Koh, S. S., Zhang, X., Cheng, X., and Stallcup, M. R. (2002) Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Molecular and cellular biology 22, 3621−3632. (197) Majumder, S., Liu, Y., Ford, O. H., Mohler, J. L., and Whang, Y. E. (2006) Involvement of arginine methyltransferase CARM1 in androgen receptor function and prostate cancer cell viability. Prostate 66, 1292−1301. (198) Chen, D., Huang, S.-M., and Stallcup, M. R. (2000) Synergistic, p160 coactivator-dependent enhancement of estrogen receptor function by CARM1 and p300. J. Biol. Chem. 275, 40810−40816. (199) Frietze, S., Lupien, M., Silver, P. A., and Brown, M. (2008) CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1. Cancer Res. 68, 301−306. (200) Ma, H., Baumann, C. T., Li, H., Strahl, B. D., Rice, R., Jelinek, M. A., Aswad, D. W., Allis, C. D., Hager, G. L., and Stallcup, M. R. (2001) Hormone-dependent, CARM1-directed, arginine-specific methylation of histone H3 on a steroid-regulated promoter. Curr. Biol. 11, 1981− 1985. (201) Yadav, N., Cheng, D., Richard, S., Morel, M., Iyer, V. R., Aldaz, C. M., and Bedford, M. T. (2008) CARM1 promotes adipocyte differentiation by coactivating PPARγ. EMBO Rep. 9, 193−198. (202) Covic, M., Hassa, P. O., Saccani, S., Buerki, C., Meier, N. I., Lombardi, C., Imhof, R., Bedford, M. T., Natoli, G., and Hottiger, M. O. (2005) Arginine methyltransferase CARM1 is a promoter-specific regulator of NF-κB-dependent gene expression. EMBO J. 24, 85−96. (203) Jayne, S., Rothgiesser, K. M., and Hottiger, M. O. (2009) CARM1 but not its enzymatic activity is required for transcriptional coactivation of NF-κB-dependent gene expression. J. Mol. Biol. 394, 485−495. (204) An, W., Kim, J., and Roeder, R. G. (2004) Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 117, 735−748. (205) Zika, E., and Ting, J. P. (2005) Epigenetic control of MHC-II: interplay between CIITA and histone-modifying enzymes. Curr. Opin. Immunol. 17, 58−64. (206) Rybtsova, N., Leimgruber, E., Seguin-Estevez, Q., DunandSauthier, I., Krawczyk, M., and Reith, W. (2007) Transcription-coupled deposition of histone modifications during MHC class II gene activation. Nucleic Acids Res. 35, 3431−3441. (207) Chen, S. L., Loffler, K. A., Chen, D., Stallcup, M. R., and Muscat, G. E. (2002) The Coactivator-associated Arginine Methyltransferase Is Necessary for Muscle Differentiation CARM1 COACTIVATES MYOCYTE ENHANCER FACTOR-2. J. Biol. Chem. 277, 4324−4333. (208) Ou, C.-Y., LaBonte, M. J., Manegold, P. C., So, A. Y.-L., Ianculescu, I., Gerke, D. S., Yamamoto, K. R., Ladner, R. D., Kahn, M., 1598


Current Topic

Biochemistry Kim, J. H., and Stallcup, M. R. (2011) A coactivator role of CARM1 in the dysregulation of β-catenin activity in colorectal cancer cell growth and gene expression. Mol. Cancer Res. 9, 660−670. (209) Cook, W., Jeffrey, L., Carson, M., Chen, Z., and Pickart, C. (1992) Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2). J. Biol. Chem. 267, 16467− 16471. (210) The PyMOL Molecular Graphics System, version 1.7.4, Schrödinger, LLC, Portland, OR. (211) Qiu, X.-B., Lin, Y.-L., Thome, K. C., Pian, P., Schlegel, B. P., Weremowicz, S., Parvin, J. D., and Dutta, A. (1998) An eukaryotic RuvBlike protein (RUVBL1) essential for growth. J. Biol. Chem. 273, 27786− 27793. (212) Feng, Q., Cao, R., Xia, L., Erdjument-Bromage, H., Tempst, P., and Zhang, Y. (2002) Identification and functional characterization of the p66/p68 components of the MeCP1 complex. Molecular and cellular biology 22, 536−546. (213) Culhane, J. C., and Cole, P. A. (2007) LSD1 and the chemistry of histone demethylation. Curr. Opin. Chem. Biol. 11, 561−568. (214) Forneris, F., Binda, C., Adamo, A., Battaglioli, E., and Mattevi, A. (2007) Structural basis of LSD1-CoREST selectivity in histone H3 recognition. J. Biol. Chem. 282, 20070−20074.

1599


Role of Histone-Modifying Enzymes and Their Complexes in

Recommend Documents