Abstract

Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation, play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed ‘histone code’ in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level. Many PTMs occur on non-histone proteins as well as histones, regulating protein–protein interactions, stability, localization, and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation, and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular processes.

Introduction

Eukaryotic DNA is packaged by histone proteins into the higher-order structure of chromatin. The basic unit of chromatin is the nucleosome, which contains ∼146 bp of DNA wound around an octamer of four core histones: H2A, H2B, H3, and H4A. A key molecular mechanism for regulating accessibility of the underlying DNA—the genetic information—is achieved via covalent posttranslational modifications (PTMs) of histone proteins, especially on their N-terminal unstructured tails. Examples of such modifications are acetylation, methylation, phosphorylation, and ubiquitylation. Histone acetylation is, in general, associated with gene activation. In contrast, methylation on a specific lysine (K) residue is correlated with either an active or a silent state of gene expression, depending on the residues being methylated. Moreover, each methylated lysine residue can exist in a mono-, di-, or tri-methylated state, further extending the indexing potential of this modification. In general, methylation on histone H3 lysine 4 (H3K4), H3K36, and H3K79 is linked to active gene expression, whereas di- and tri-methylation on H3K9, H3K27, and H4K20 are associated with gene silencing. Histone lysine methylation has also been shown to modulate other chromatin-related processes such as replication, recombination, and DNA repair.

Dynamic PTMs serve as a means to regulate protein–protein interactions, protein stability, protein localization, and/or enzymatic activities. Many PTMs, such as phosphorylation, ubiquitylation, and acetylation, occur on numerous proteins involved in diverse cellular processes. Although ∼80 enzymes have been shown to dynamically regulate histone lysine methylation, only a few non-histone proteins have been reported as substrates of these enzymes. In the past few years, more attention has been drawn to methylation of non-histone proteins. In this review, we briefly review all the enzymes known to regulate histone lysine methylation and summarize the current knowledge of lysine methylation of non-histone proteins and its role in regulating proteins involved in diverse cellular processes.

Modifying Enzymes for Lysine Methylation

The enzymes involved in lysine methylation were first found to target histone and thus were initially named histone methyltransferases and histone demethylases, following the naming model for histone acetyltransferase and histone deacetylase. With accumulating evidence that these modifications are not histone specific, a new nomenclature has been advocated for more generic names for these enzymes [1]. The enzymes that add or remove the methylation mark on lysine residues are now named lysine methyltransferases (KMTs) and lysine demethylases (KDMs), respectively, for their broad or potentially broad spectra of protein substrates. We follow the new nomenclature throughout this review.

Lysine methyltransferases

KMTs catalyze mono-, di-, or tri-methylation by transfering one, two, or three methyl groups, respectively, from S-adenosyl-L-methionine to the ε-amino group of a lysine residue. Except for KMT4/DOT1L, all known KMTs contain a conserved SET (Su(var)3-9, Enhancer of Zeste, Trithorax) domain harboring the enzymatic activity [2]. Besides the SET domain, most KMTs also contain some other defined protein domain or homologous sequence that is used to classify KMTs into distinct subfamilies [1,3]. The enzymatic activities and substrate specificities of the eight KMT subfamilies are summarized here (Table 1).

Table 1

Human KMTs and their histone and non-histone substrates

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aReference for non-histone substrates only.

KMT1 family

Most KMT1 group proteins are members of the SUV39 family that specifically methylate H3K9. This family includes KMT1A/SUV39H1, KMT1B/SUV39H2, KMT1C/G9a, KMT1D/EHMT1/GLP, KMT1E/SETDB1, and KMT1F/SETDB2. The methylation activity of KMT1A–KMT1D requires both the SET domain and two adjacent regions called pre-SET and post-SET, whereas KMT1E and 1F have a large insertion within their SET domains, which are fully functional [2].

KMT1A and 1B are the first SET domain-containing KMTs identified [32]. They are the dominant enzymes generating H3K9 trimethylation (H3K9me3) at pericentric heterochromatin, a highly compacted, transcriptionally silent chromatin domain [33]. A structural characteristic of KMT1A and 1B is a SET domain-adjacent chromodomain that recognizes methylated histone lysines [34,35], whereas KMT1C and 1E contain an ankyrin repeat domain (ANK) that is also capable of binding to methylated histones [36]. KMT1C and 1D specifically mono- and di-methylate H3K9 at euchromatin, and therefore are also known as euchromatic histone methyltransferases [33,37]. These two proteins form homomeric or heteromeric dimers in vivo via their SET domains, and the stability of the KMT1C protein depends on KMT1D. KMT1E and 1F trimethylate histone H3K9 and facilitate transcriptional repression [38,39]. They both contain a methyl-CpG-binding domain with affinity to methylated DNA, and KMT1E contains an extra Tudor domain, which also functions as a reader for methyl-lysines [40,41].

KMT2 family

The KMT2 family includes Drosophila Trithorax homologs MLL family proteins (MLL1–MLL5, named KMT2A–KMT2E, respectively), two proteins with great similarity to yeast Set1 proteins SET1A/KMT2F and SET1B/KMT2G and ASH1/KMT2H protein. All KMT2 family proteins are H3K4 methyltransferases, and they share a distinct SET domain with an essential post-SET region at the C-terminus. KMT2A/MLL1 is a major regulator of hematopoiesis and embryonic development through regulation of HOX gene expression, and the MLL gene is frequently rearranged in human acute leukemias [42]. The H3K4 trimethylation activity of KDM2A requires components of its core complex, including WDR5, RbBP5, and Ash2L, despite the isolated KMT2A SET domain having weak H3K4 mono-methylation activity [43]. KMT2D/MLL4 is closely related to KMT2A in protein complex composition and target gene regulation [44,45]. KMT2B and 2C associate with H3K27 demethylase KDM6A/UTX, which also occupies the promoters of HOX gene clusters and regulates their transcriptional output [46].

KMT3 family

The KMT3 family includes yeast Set2 homolog SETD2/KMT3A, nuclear receptor binding SET domain protein 1, NSD1/KMT3B, and SET and MYND domain-containing proteins SMYD2/KMT3C, SMYD1/KMT3D, and SMYD3/KMT3E. This group of proteins methylates mainly histone H3K36, but their KMT activities are not restricted to H3K36. KMT3A is a Huntingtin-interacting protein, and it is responsible for global transcription-dependent H3K36 trimethylation, a specific epigenetic mark for transcriptional activation enriched at the gene body [47,48]. KMT3B is involved in regulation of gene activation through its dimethylation activity at H3K36 [49], but it was also shown to methylate H4K20 [50]. A recurrent translocation of KMT3B fused to nucleoporin-98 has been reported in childhood acute myeloid leukemia, indicating the oncogenic property of KMT3B [49,51]. KMT3B/NSD1 has two homologs, NSD2/MMSET/WHSC1 and NSD3/WHSC1L1, which are also associated with multiple cancers. Although NSD2 and NSD3 have not been classified in the KMT3 family, both were shown to possess strong H3K36 di-/tri-methylation activity in addition to their activities toward other histone lysine residues [52–54]. KMT3C has methylation activity toward both H3K4 and H3K36 [55,56], whereas KMT3D and KMT3E were shown to methylate H3K4 [57,58].

KMT4

KMT4/DOT1L is a H3K79-specific methyltransferase and represents the only class of KMT without a SET domain [59]. KMT4-mediated H3K79 di- and tri-methylation are evolutionarily conserved from yeast to human and ubiquitously correlated with active transcription [60]. It is the sole enzyme responsible for H3K79 methylation, as knockout of Dot1 in yeast, flies, and mice results in complete loss of H3K79 methylation [61–63]. In mammals, KMT4 is an essential gene for embryogenesis, hematopoiesis, and cardiac function. Its H3K79 methylation activity is essential for MLL-AF4 and MLL-AF9 fusion-induced leukemias, suggesting that KMT4 could serve as a potential therapeutic target for MLL-rearranged leukemias [64–66]. Indeed, a recent study has demonstrated that a potent KMT4 inhibitor selectively kills cells bearing the MLL gene translocation in vitro, and leads to extension of survival in a mouse MLL xenograft model [67].

KMT5 family

The KMT5 family consists of enzymes that methylate H4K20. KMT5A/SET8 specifically mono-methylates H4K20, which has been shown to associate with both gene repression and activation, depending on its chromatin context [68–71]. KMT5A and H4K20me1 are also essential for multiple other chromatin-associated processes, such as cell cycle progression, DNA replication, and DNA damage response [72–77]. KMT5B/SUV420H1 and its homolog KMT5C/SUV420H2 catalyze di- and tri-methylation of H4K20, which, along with H3K9me2/3, is essential for maintenance of repressive heterochromatin at pericentric and telomeric regions [78,79]. Dimethylation of H4K20 is recognized by the Tudor domain of 53BP1 in mammals and by its homolog Crb2 in Schizosaccharomyces pombe, and targets these proteins to DNA damage sites [80,81].

KMT6 family

Two H3K27-specific KMTs, KMT6A/EZH2, and KMT6B/EZH1 belong to the KMT6 family. The methylation activity of KMT6A and KMT6B requires other core components of their associated protein complex, polycomb repressive complex 2 (PRC2) [82,83]. As the catalytic subunit of PRC2, KMT6A participates in maintaining the transcriptional repressive state of chromatin and is upregulated in a broad range of human cancers [84,85]. Rapidly dividing cells such as embryonic stem cells and cancer stem cells exhibit high levels of KMT6A expression and H3K27me3 [86]. Interestingly, PTMs such as phosphorylation of enhancer of Zeste homolog 2 (EZH2) proteins appear to be essential mechanisms in regulating EZH2 enzymatic activity and transcriptional repression function [87–89]. KMT6B is present in a non-canonical PRC2 complex as an H3K27 methyltransferase, and is functionally redundant with EZH2 [90,91].

KMT7 family

This family contains only one protein, SET7/9, which mono-methylates histone at H3K4 [92]. KMT7 was found to methylate, besides histone, a number of non-histone proteins, including p53, DNA methyltransferase 1 (DNMT1), estrogen receptor alpha (ERα), nuclear factor kappaB (NFκB), and components of the TATA binding protein (TBP) complex, TBP-associated factors TAF10 and TAF7 [93]. The consensus recognition sequence in substrates for SET7-mediated lysine methylation, K/R–S/T–K (target lysine is bold), is also recognized by the H3K4 demethylase KDM1A/LSD1, which is capable of removing the methyl mark on most of these substrates [17,94]. Therefore KMT7/KDM1A has emerged as a classic model for dynamic lysine methylation of both histone and non-histone proteins.

KMT8 family

Currently this family comprises only one member, PRDM2/RIZ1. KMT8 was identified as retinoblastoma (RB) protein-interacting zinc-finger protein (RIZ1), and it belongs to the PRDM family of proteins which are characterized by the presence of a N-terminal positive regulatory (PR) domain (PRDI-BF1 and RIZ) [95]. The PR domain is a homolog of the SET domain and shares 20%–30% identity with the SET module. Some PR domains show intrinsic methyltransferase activity, whereas the methylation activity of most other PRDM proteins has not been identified [96]. KMT8 possesses H3K9 methylation activity and functions as corepressor for gene regulation [97]. Many other PRDM proteins, although lacking methylation activity, also play a role in regulating chromatin dynamics during stem cell self-renewal, differentiation, and development [96].

Lysine demethylases

Histone lysine methylation was regarded as enzymatically irreversible for decades until the recent discovery of the first histone KDM, LSD1/KDM1A [98]. Soon after, Jumonji (JmjC) domain was identified as another module that possesses enzymatic activity in removing methyl groups from lysine residues [99]. As a large number of proteins in the human genome contain the JmjC domain, numerous JmjC domain-containing KDMs were discovered in the past few years, which in turn provide novel insights into the mechanisms of histone modification and epigenetic regulation [100–102]. Like the KMTs, KDMs are classified according to the new nomenclature into several distinct groups based on their substrate specificities and protein domain organization (Table 2).

Table 2

Human KDMs and their substrates

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aReference for non-histone substrates only.

KDM1 family

KDM1A/LSD1 is a flavin adenine dinucleotide-dependent monoamine oxidase that can remove mono- and di-methyl, but not tri-methyl, groups from methylated lysines such as H3K4 [98]. Other core components of its protein complex, such as CoREST and BHC80, are essential for its demethylating activity on nucleosomes [105,106]. KDM1 has been shown to alter its substrates' specificity toward H3K9 methylation when associated with nuclear receptors, thereby acting as a transcriptional coactivator [107–109]. Furthermore, KMT1 has a broad spectrum of non-histone substrates, such as p53 and DNMT1 [110]. As a homolog of KDM1A, KDM1B/LSD2 was recently identified and characterized as another H3K4 demethylase [111–113]. In contrast to KDM1A, which functions at promoters, KDM1B removes intragenic H3K4 methylation for gene activation [114]. Like KDM1A, KDM1B was reported to be able to remove mono- and di-methylation at histone H3K9 [115].

KDM2 family

KDM2A/JHDM1A is the first JmjC domain-containing histone demethylase identified [99]. KDM2A and KDM2B demethylate mono- and di-methylation from H3K36, while KDM2B is also implicated in demethylation of H3K4 [116]. This family of proteins has been shown to function as transcriptional corepressors for regulation of several tumor-associated genes, including c-Jun and p15Ink4b [116–119]. The F-Box present in KDM2 family members suggests that KDM2 proteins might also be involved in additional mechanisms of chromatin regulation, such as ubiquitylation [120].

KDM3 family

Soon after the discovery of the JmjC domain as a signature demethylation motif, the KDM3 family of proteins was identified as the second family of JmjC histone demethylases (JHDM2). KDM3A/JHDM2A and KDM3B/JHDM2B have specific action toward mono- and di-methylation of H3K9, and they therefore function as transcriptional coactivators for gene expression. KDM3A and 3B have been shown to be involved in multiple biological processes such as androgen receptor (AR) signaling and spermatogenesis [121–124]. Another JHDM2 family member, JHDM2C/TRIP8, has not yet been shown to have enzymatic activity.

KDM4 family

The KDM4 family encompasses four homologous demethylases, KDM4A–4D (JMJD2A–2D, respectively). KDM4 proteins are the first demethylases that show demethylation activity on trimethylation. All KDM4 family members are able to remove di- and tri-methylation from H3K9 and/or H3K36 [125–127]. Besides the JmjC domain, they share a highly conserved JmjN domain, and three of them (all except KDM4D) contain tandem PHD fingers and Tudor domains that read distinct histone methylation [128,129]. KDM4 family proteins function in hormone response. KDM4A and KDM4D were shown to be AR coactivators [130], and KDM4B demethylates H3K9me3 for transcription activation by ER [131,132]. Recent in vitro studies demonstrated that this family of proteins can also act on non-histone proteins [133,134].

KDM5 family

KDM5 family members KDM5A–5D/JARID1A–1D specifically remove di- and tri-methylation from H3K4 [135–141]. They are multi domain-containing proteins characterized by a combination of JmjC and JmjN catalytic domains with an ARID DNA-binding domain, a C5HC2 zinc finger, and two to three PHD fingers. Distinct PHD fingers of KDM5A and KDM5C were shown to bind methylated H3K4 or H3K9, respectively [137,142]. This family of proteins shows oncogenic activity, as KDM5A is overexpressed in gastric cancer and KDM5B is highly induced in breast cancer. Inhibition of these proteins can suppress cell growth and/or tumorigenesis, indicating that these enzymes may have potential as therapeutic targets [143].

KDM6 family

This family comprises two H3K27-specific histone demethylases, KDM6A/UTX and KDM6B/JMJD3, which are capable of removing di- and tri-methylation from H3K27 [46,144–148]. As H3K27 methylation is a repressive epigenetic mark elevated in multiple cancers, both KDM6A and KDM6B function as tumor suppressors, implicated in gene transcriptional activation, epigenetic reprogramming, and RB-dependent cell fate control [147,149,150]. KDM6A associates with the KMT2/MLL H3K4 methylation protein complexes in regulating HOX gene expression, and therefore is essential for proper development [46].

KDM7 family

The KDM7/PHF2 family consists of three members: KDM7A/JHDM1D, KDM7B/PHF8, and KDM7C/PHF2, which are involved in regulation of the expression of ribosomal RNA and genes involved in X-linked mental retardation. This family of proteins possesses strong demethylation activity toward H3K9 and H3K27 mono- and di-methylation [151–157]. Furthermore, PHF8 is able to remove mono-methylation from H4K20 [154,155,158]. All three KDM7 family proteins contain a PHD finger that binds to histone H3K4me3, and this recognition is essential for their substrate specificity, genomic occupancy, and regulation of target gene expression [151,152,159–161].

So far, KDMs have been identified for nearly all known histone methyl-lysines, with the exception of residue H3K79. However, evidence suggests that H3K79 methylation is also reversible [60]. It is possible that methylated H3K79 may be targeted by other yet undefined JmjC types of KDMs, or by novel KDMs different from KDM1 and the JmjC demethylases.

Lysine Methylation of Non-histone Proteins

Although lysine methylation of histones has been studied extensively as an essential mechanism for epigenetic regulation of chromatin, our understanding of this modification on non-histone proteins has just begun. Methylation of p53 protein by KMT7/SET7 is the first reported KMT-mediated methylation event on a non-histone protein [18]. Since that discovery, several KMTs, as well as KDM1A, have been identified as p53 regulators that methylate or demethylate p53 protein, making p53 the most extensively studied non-histone protein undergoing lysine methylation [4,13,16,18,162]. Here we use p53 as a model to discuss the functions of lysine methylation of non-histone proteins. We also summarize the current knowledge of this modification on other proteins in diverse cellular processes (Table 1).

Lysine methylation of p53

The p53 gene is the most frequently mutated tumor suppressor gene in human cancers [163]. One critical mechanism by which p53 protein is regulated upon genotoxic stresses is through PTMs, including ubiquitylation, phosphorylation, acetylation, methylation, sumoylation, and neddylation [164]. Under unstressed growth conditions, p53 is tightly controlled at low level through ubiquitylation-dependent degradation, modulated mainly by MDM2 E3 ubiquitin ligase. Upon genotoxic stresses such as DNA damage, p53 proteins are quickly accumulated and activated in the setting of multiple PTMs such as phosphorylation and acetylation for full activation. Accumulating evidence suggests that lysine methylation of p53, especially on its C-terminus, also plays a key role in regulating protein stability, protein–protein interactions, and transactivation activity of p53 (Fig. 1; Table 1) [4,13,16,18,162].

Figure 1

Schematic representation of PTMs of p53 Protein domains are shown as rectangular boxes. TAD, transactivation domain; TET, tetramerisation domain; REG, regulatory domain. Modifications are shown as filled circles: P, phosphorylation; Ac, acetylation; Ub, ubiquitylation; Me, methylation; Ne, neddylation; Su, sumoylation.

Figure 1

Schematic representation of PTMs of p53 Protein domains are shown as rectangular boxes. TAD, transactivation domain; TET, tetramerisation domain; REG, regulatory domain. Modifications are shown as filled circles: P, phosphorylation; Ac, acetylation; Ub, ubiquitylation; Me, methylation; Ne, neddylation; Su, sumoylation.

Crosstalk between methylation and other PTMs of p53

Crosstalk (or cross-regulation) between histone PTMs provides a wealth of potential for epigenetic regulation of chromatin dynamics [165,166]. Accumulating evidence suggests that crosstalk between lysine methylation and other modifications is also a frequent mechanism of regulating non-histone proteins, such as p53. Reinberg and colleagues reported the first lysine methylation event on p53 in 2004 [18]. They found that KMT7 specifically methylates p53 at K372 within the C-terminus regulatory region. This methylation increases upon DNA damage, stabilizes p53 proteins, and promotes p53 transactivation activity on its target genes [18]. Subsequent studies suggest that the role of p53 K372 methylation is, at least in part, to stimulate p53 protein acetylation, as knockdown of KMT7 impairs K373/382 acetylation of p53 [167]. In an independent study, Kurash and colleagues also showed that this methylation (K369 in mouse) is essential for p53 acetylation, and it may serve as an anchor site for a lysine acetyltransferase, Tip60, providing a molecular mechanism for the crosstalk between different PTMs (see discussion below) [168].

Acetylation at K382 serves as an activation mark for p53's transcriptional regulation activity. This acetylation is directly inhibited by methylation on the same residue by KMT5A/SET8, an enzyme previously reported to mono-methylate H4K20 [16]. K382 methylation robustly suppresses p53-mediated transcription activation of highly responsive target genes, and depletion of KMT5A augments the proapoptotic and checkpoint activation functions of p53 upon DNA damage [16]. It would be interesting to know whether p53K382 methylation works in concert with other inhibitory marks to directly counteract other p53 activation marks, such as K373 acetylation and K372 methylation.

The crosstalk between different PTMs in the vicinity of the p53 C-terminus seems a frequent mechanism for modulating p53 activities. In addition to acetylation, KMT7-mediated p53K372 methylation also interplays with methylation at nearby K residues. p53 can be methylated by another methyltransferase, KMT3C/SMYD2, at K370, two amino acids apart from the KMT7 methylation site [13]. Knockdown of KMT3C enhances p53-dependent apoptosis upon DNA damage, indicating that this methylation is a repressive mark. Methylation at K372 and K370 is directly inhibitory of each other. Inhibition of p53K370 methylation by KMT7-mediated K372 methylation is thought to directly block the interaction between p53 and KMT3C [169]. In contrast, however, p53 peptide with K370 methylation is still accessible to KMT7 [13].

That KMT7-mediated p53 K372 methylation stabilizes p53 protein suggests that this methylation event may also modulate p53 ubiquitylation, which also occurs at the C-terminus of p53. Although direct evidence is still lacking, a recent study showed that besides ubiquitylation of p53, MDM2 recruits two H3K9 KMTs, KMT1A and KMT1D, to modulate p53 activity [162]. KMT1D and its closely related homolog KMT1C are able to methylate p53 specifically at K373 and repress p53 transactivation activity [4,162]. Knockdown of each p53-associated KMT1 protein increases p53 activity during the stress response, whereas their overexpression inhibits p53 activity. Although modification of p53 by these KMT1 proteins is enhanced by MDM2, changes in total p53 protein levels were not observed in these cells, indicating a more complicated regulation [162].

Regulation of protein–protein interactions by p53 methylation

One main function of histone lysine methylation is modulating interactions of chromatin with proteins containing ‘reader’ domains that specifically recognize this modification [170]. Methylation of non-histone proteins is likely to function through a similar mechanism. As we already discussed, Tip60 associates with and acetylates p53 upon DNA damage. This interaction seems to be dependent on K372 methylation, as Tip60 is able to pull down more p53 proteins premethylated by KMT7, and addition of methylated p53 peptide specifically competes off interactions between p53 and Tip60 [168]. Therefore, KMT7-mediated methylation of p53K372 may serve as an anchor for Tip60. Interestingly, Tip60 contains a chromodomain, a reader domain of methyl-histones. Although there is no direct evidence, it is likely that the Tip60 chromodomain specifically recognizes methylation of p53K372 to facilitate Tip60–p53 protein–protein interactions.

Two conserved domains, the MBT domain of L3MBTL1 and Tudor domain of 53BP1, both of which function as readers for histone methylation, have been shown to also read p53 methylation. Gozani and colleagues reported that KMT5A-mediated p53K382 methylation promotes the interaction between p53 and L3MBTL1, a general transcriptional corepressor. Compelling evidence from biochemical analyses and crystallographic studies showed that the MBT domain of L3MBTL1 specifically recognizes p53K382me1, with a KD value comparable with that of L3MBTL1 MBT-H3K20me1 [171]. This interaction is essential for the chromatin occupancy of L3MBTL1 at p53 target promoters, as either knockdown of L3MBTL1 or mutation of the MBT domains that abolishes L3MBTL1–p53 interaction results in a p53-dependent increase in p21 and PUMA transcript levels in the absence of DNA damage [171].

In a study of the regulation of p53 by the lysine demethylase KDM1A/LSD1, Berger and colleagues identified 53BP1 as a reader for p53K370 dimethylation (p53K370me2) [103]. In addition to mono-methylation (by KMT3C), p53 K370 can also be dimethylated in vivo. Although the primary KMT putting on this methylation mark has not been identified, KDM1A was shown to specifically remove p53K370me2 in cells [103]. Surprisingly, K370me2 has a different role in regulating p53 function than K370me1: K370me1 represses p53 function, whereas K370me2 promotes p53 activity [103]. The tandem Tudor domain of 53BP1 was identified by a protein domain array as a reader for p53K370me2. The interaction between p53 and 53BP1 is K370me2 dependent, as mutation of p53K370 to either alanine or arginine totally abolishes their interaction in cells, whereas knockdown of KDM1A leads to increases of p53K382me2 levels and p53–53BP1 interaction [103].

In more comprehensive studies, it was showed that, in vitro, the tandem Tudor domain of 53BP1 binds to several dimethylated lysine residues at the p53 C-terminus, with a preference for p53K382me2 [172,173]. The KD value of 53BP1 Tudor–p53K382me2 is about 0.9 µM, whereas that of 53BP1 Tudor–p53K372me2 is 20 µM, indicating that the binding of 53BP1 Tudor to p53K382me2 is much stronger [173]. Further, generation of K382me2 in the p53K370R mutant retains the ability of p53 protein to interact with 53BP1 in vivo, suggesting that p53 K382 dimethylation is more likely the primary target of 53BP1 Tudor domains [172]. Since other regions of p53 and 53BP1 also interact, further study is needed to define the specificity and functions of p53 C-terminal lysine methylation for 53BP1 association and other activities.

A recent study showed that KMT7 inhibits the association of p53 with SIRT1, a histone deacetylase that regulates p53 acetylation [19]. Interestingly, KMT7 can also directly methylate SIRT1 at several K residues. It is currently not known whether the inhibition of p53–SIRT1 interaction by KMT7 is dependent on p53 methylation or SIRT methylation. Nevertheless, this study suggests that KMT7 might modulate p53 function indirectly as well as through a direct p53 methylation-dependent mechanism.

Methylation and function of p53 in vivo

Although studies using cultured cells have demonstrated that KMT7-mediated methylation of p53 at K372 is important for stabilization and transcriptional activation of p53 [18,19,167,168], two recent studies challenged the notion that KMT7-mediated p53 methylation plays a significant role in p53 function in vivo [174,175]. Testa and colleagues made an independent KMT7 knockout mouse strain, and defined its function in vivo. They found that deletion of KMT7 had no effect on p53-dependent cell-cycle arrest or apoptosis in response to DNA damage induced by radiation, genotoxic agents or oncogene c-myc. Both acetylation of p53 and transactivation of its target genes were preserved in the absence of KMT7, suggesting that in vivo KMT7 is not required for the p53-dependent gene expression program [175]. In an independent study, Rossi and colleagues drew a similar conclusion that KMT7 is dispensable for p53-dependent senescence, transcription, cell-cycle arrest, and apoptosis in vivo [174]. The conclusions are in sharp contrast to findings from a previous in vivo study by Gaudet and colleagues demonstrating that KMT7-mediated p53 methylation is required for p53 acetylation and is important for p53 activation [168]. Although this discrepancy may arise from different genetic backgrounds of the mice used in these studies, independent studies from both the Rossi group and the Testa suggested that the antiserum raised against human p53K372me which was used by the Gaudet and colleagues [174] cannot detect the methylation of murine p53K369 in vitro [174], or cannot distinguish the unmethylated and methylated forms of murine p53 in vivo [175]. Of note, a previous study showed that in MEFs the substitution of the six C-terminal lysines of p53 (including K369) with arginine had no effect on the stabilization and activation of p53 [176,177], suggesting that the C-terminal lysine residues play functional redundant roles in fine-tuning p53 functions in stress responses.

Methylation of other non-histone proteins

Methylation of a few non-histone proteins other than p53 has also been reported. Most of these proteins are either transcriptional factors (such as ERα, NFκB, E2F1, RB, and STAT3) or histone- or DNA-modifying enzymes (such as DNMT1 and KMT1C) (Table 1) [93]. Interestingly, most of these proteins are methylated by KMT7. KMT7 is the only H3K4 mono-methyltransferase so far identified [178]. It exhibits strong activity on free histones, but very weak activity on nucleosomal histones, indicating that its main function may be regulating proteins other than histones.

One mechanism by which KMT7 modulates proteins is regulation, either enhancement or inhibition, of protein–protein interactions, similar to histone methylation. For example, KMT7 methylates TBP-associated factor TAF10 and increases the affinity of TAF10 for RNA polymerase II, thereby helping in formation of pre-initiation complex [20,94]. Another example is that KMT7-mediated methylation of RB protein (at K873) promotes its association with HP1 protein for target gene repression and differentiation [21]. Interestingly, KMT7 can also methylate RB protein at a distinct K residue (K810), which impedes binding of CDK and thereby prevents subsequent phosphorylation of the associated serine residue [179].

Another function of KMT7-mediated methylation is to influence protein stability. Methylation of p53 and ERα by KMT7 stabilizes these proteins, and is necessary for their efficient recruitment to target genes and for their transactivation activities [18,22]. Methylation of MYPT1, a RB protein regulator, by SET7 also stabilizes MYPT1 proteins, and subsequently decreases the steady-state level of phosphorylated RB proteins [104]. In contrast, KMT7-mediated methylation of DNMT1, E2F1, STAT3, and the RelA subunit of NFκB negatively regulates their stability and transactivation activity [17,23–26,180].

It is worth noting that KMT7-mediated methylation in many proteins (such as p53, DNMT1, E2F1, STAT3, and MYPT1) undergoes demethylation by KDM1A, indicating a dynamic regulation of this modification on non-histone proteins [26]. A conserved motif for KMT7 methylation was determined by a stepwise iterative approach using peptide arrays, and >90 protein peptides were identified as KMT7 novel substrates, suggesting that lysine methylation is a common modification for non-histone proteins [27].

Although most known methylation events on non-histone proteins are mediated by KMT7, a few other KMTs have also been shown to methylate non-histone proteins. For instance, KMT3C is reported to methylate p53 as well as RB, making it an attractive drug target [13,14]. Both KMT3B and SETD6, a novel KMT that has not yet been assigned a name in the new nomenclature, methylate the RelA subunit of NFκB [12,181]. Interestingly, SETD6-mediated methylation is recognized by the KMT1D ANK domain to anchor KMT1D to RelA target genes to repress gene expression under basal conditions [181]. KMT1C is another KMT that methylates non-histone proteins. It methylates transcriptional factor C/EBPβ and chromatin-remodeling factor Reptin to negatively regulate their downstream target genes [5,6]. KMT1C also automethylates itself on a conserved methylation motif, similar to that of histone H3K9. This methylation is necessary and sufficient to mediate in vivo interaction with the epigenetic regulator HP1 to maintain a repressive chromatin [182]. Lysine methylation of non-histone proteins is conserved from yeast to human. Methylation of proteins from budding yeasts (such as Ipl Aurora kinase and ribosomal proteins) and plants (Rubisco subunits) has also been reported [11,183–185]. It is conceivable that many proteins can be modified by lysine methylation, in addition to other types of PTMs.

Perspective

In the past decade, a large number of KMTs and KDMs have been identified, significantly extending our knowledge of the dynamics of histone methylation and epigenetic regulation. However, the study of this modification of non-histone proteins is still in its infancy. Most studies of lysine methylation have focused on only a few target proteins via a candidate approach. High-throughput methods are needed to identify proteome-wide lysine methylation. One approach in identifying additional non-histone substrates of KMTs is to employ a peptide array to determine the substrate specificity of a given methyltransferase, and then to use the derived specificity profile of the enzyme to predict potential substrates [186,187]. Jeltsch and colleagues have taken steps using this approach to identify additional non-histone substrates of KMT7 and KMT1C [7,27]. As several KMTs show promiscuous activities, however, especially in in vitro systems, it is essential to determine whether the methylation events thus identified do occur in vivo.

Direct identification of protein methylation in vivo can be achieved through mass spectrometric analysis. A recently developed method called stable-isotope labeling by amino acids in cell culture enables proteomic analysis of proteins from whole-cell extracts or enriched fractions [188]. This method provides increased confidence in identification of PTMs and their relative quantification. Because most protein PTMs occur at low abundance, however, some degree of enrichment is necessary prior to mass spectrometric analysis, and the most widely used and efficient method is affinity purification [189–191]. Therefore, a key step in generating a proteome-wide protein lysine methylation profile is to develop state-specific, but not sequence-dependent, antibodies recognizing distinct levels of methylation on lysine residues. With advances in new technologies, we foresee that, in the next few years, a proteome-wide profile of lysine methylation and its biological functions will soon be elucidated. Understanding of the essential role of this tiny modification will further extend our knowledge of ‘histone code’ to ‘PTM code’ in regulating proteins involved in diverse processes.

Addendum: During the course of this review, a new gene nomenclature, KDM8, has been assigned to JMJD5 protein, which demethylates H3K36me2 [192,193].

Funding

This work was supported by the grants from the Welch Foundation (G1718), CPRIT (RP110471), and the Center for Cancer Epigenetics at University of Texas MD Anderson Cancer Center. X.S. is a recipient of a Sydney Kimmel Scholar award.

Acknowledgements

We thank Kathryn Hale for critical reading of this paper. We apologize to researchers whose papers are not cited here because of space constraints.

References

1
Allis
CD
Berger
SL
Cote
J
Dent
S
Jenuwien
T
Kouzarides
T
Pillus
L
, et al.  . 
New nomenclature for chromatin-modifying enzymes
Cell
 , 
2007
, vol. 
131
 (pg. 
633
-
636
)
2
Qian
C
Zhou
MM
SET domain protein lysine methyltransferases: structure, specificity and catalysis
Cell Mol Life Sci
 , 
2006
, vol. 
63
 (pg. 
2755
-
2763
)
3
Aravind
L
Abhiman
S
Iyer
LM
Natural history of the eukaryotic chromatin protein methylation system
Prog Mol Biol Transl Sci
 , 
2011
, vol. 
101
 (pg. 
105
-
176
)
4
Huang
J
Dorsey
J
Chuikov
S
Perez-Burgos
L
Zhang
X
Jenuwein
T
Reinberg
D
, et al.  . 
G9a and Glp methylate lysine 373 in the tumor suppressor p53
J Biol Chem
 , 
2010
, vol. 
285
 (pg. 
9636
-
9641
)
5
Pless
O
Kowenz-Leutz
E
Knoblich
M
Lausen
J
Beyermann
M
Walsh
MJ
Leutz
A
G9a-mediated lysine methylation alters the function of CCAAT/enhancer-binding protein-beta
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
26357
-
26363
)
6
Lee
JS
Kim
Y
Kim
IS
Kim
B
Choi
HJ
Lee
JM
Shin
HJ
, et al.  . 
Negative regulation of hypoxic responses via induced Reptin methylation
Mol Cell
 , 
2010
, vol. 
39
 (pg. 
71
-
85
)
7
Rathert
P
Dhayalan
A
Murakami
M
Zhang
X
Tamas
R
Jurkowska
R
Komatsu
Y
, et al.  . 
Protein lysine methyltransferase G9a acts on non-histone targets
Nat Chem Biol
 , 
2008
, vol. 
4
 (pg. 
344
-
346
)
8
Chin
HG
Esteve
PO
Pradhan
M
Benner
J
Patnaik
D
Carey
MF
Pradhan
S
Automethylation of G9a and its implication in wider substrate specificity and HP1 binding
Nucleic Acids Res
 , 
2007
, vol. 
35
 (pg. 
7313
-
7323
)
9
Huq
MD
Ha
SG
Wei
LN
Modulation of retinoic acid receptor alpha activity by lysine methylation in the DNA binding domain
J Proteome Res
 , 
2008
, vol. 
7
 (pg. 
4538
-
4545
)
10
Van Duyne
R
Easley
R
Wu
W
Berro
R
Pedati
C
Klase
Z
Kehn-Hall
K
, et al.  . 
Lysine methylation of HIV-1 Tat regulates transcriptional activity of the viral LTR
Retrovirology
 , 
2008
, vol. 
5
 pg. 
40
 
11
Zhang
K
Lin
W
Latham
JA
Riefler
GM
Schumacher
JM
Chan
C
Tatchell
K
, et al.  . 
The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation
Cell
 , 
2005
, vol. 
122
 (pg. 
723
-
734
)
12
Lu
T
Jackson
MW
Wang
B
Yang
M
Chance
MR
Miyagi
M
Gudkov
AV
, et al.  . 
Regulation of NF-kappaB by NSD1/FBXL11-dependent reversible lysine methylation of p65
Proc Natl Acad Sci USA
 , 
2010
, vol. 
107
 (pg. 
46
-
51
)
13
Huang
J
Perez-Burgos
L
Placek
BJ
Sengupta
R
Richter
M
Dorsey
JA
Kubicek
S
, et al.  . 
Repression of p53 activity by Smyd2-mediated methylation
Nature
 , 
2006
, vol. 
444
 (pg. 
629
-
632
)
14
Saddic
LA
West
LE
Aslanian
A
Yates
JR
III
Rubin
SM
Gozani
O
Sage
J
Methylation of the retinoblastoma tumor suppressor by SMYD2
J Biol Chem
 , 
2010
, vol. 
285
 (pg. 
37733
-
37740
)
15
Kunizaki
M
Hamamoto
R
Silva
FP
Yamaguchi
K
Nagayasu
T
Shibuya
M
Nakamura
Y
, et al.  . 
The lysine 831 of vascular endothelial growth factor receptor 1 is a novel target of methylation by SMYD3
Cancer Res
 , 
2007
, vol. 
67
 (pg. 
10759
-
10765
)
16
Shi
X
Kachirskaia
I
Yamaguchi
H
West
LE
Wen
H
Wang
EW
Dutta
S
, et al.  . 
Modulation of p53 function by SET8-mediated methylation at lysine 382
Mol Cell
 , 
2007
, vol. 
27
 (pg. 
636
-
646
)
17
Wang
J
Hevi
S
Kurash
JK
Lei
H
Gay
F
Bajko
J
Su
H
, et al.  . 
The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation
Nat Genet
 , 
2009
, vol. 
41
 (pg. 
125
-
129
)
18
Chuikov
S
Kurash
JK
Wilson
JR
Xiao
B
Justin
N
Ivanov
GS
McKinney
K
, et al.  . 
Regulation of p53 activity through lysine methylation
Nature
 , 
2004
, vol. 
432
 (pg. 
353
-
360
)
19
Liu
X
Wang
D
Zhao
Y
Tu
B
Zheng
Z
Wang
L
Wang
H
, et al.  . 
Methyltransferase Set7/9 regulates p53 activity by interacting with Sirtuin 1 (SIRT1)
Proc Natl Acad Sci USA
 , 
2011
, vol. 
108
 (pg. 
1925
-
1930
)
20
Kouskouti
A
Scheer
E
Staub
A
Tora
L
Talianidis
I
Gene-specific modulation of TAF10 function by SET9-mediated methylation
Mol Cell
 , 
2004
, vol. 
14
 (pg. 
175
-
182
)
21
Munro
S
Khaire
N
Inche
A
Carr
S
La Thangue
NB
Lysine methylation regulates the pRb tumour suppressor protein
Oncogene
 , 
2010
, vol. 
29
 (pg. 
2357
-
2367
)
22
Subramanian
K
Jia
D
Kapoor-Vazirani
P
Powell
DR
Collins
RE
Sharma
D
Peng
J
, et al.  . 
Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase
Mol Cell
 , 
2008
, vol. 
30
 (pg. 
336
-
347
)
23
Esteve
PO
Chin
HG
Benner
J
Feehery
GR
Samaranayake
M
Horwitz
GA
Jacobsen
SE
, et al.  . 
Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells
Proc Natl Acad Sci USA
 , 
2009
, vol. 
106
 (pg. 
5076
-
5081
)
24
Yang
J
Huang
J
Dasgupta
M
Sears
N
Miyagi
M
Wang
B
Chance
MR
, et al.  . 
Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes
Proc Natl Acad Sci USA
 , 
2010
, vol. 
107
 (pg. 
21499
-
21504
)
25
Yang
XD
Huang
B
Li
M
Lamb
A
Kelleher
NL
Chen
LF
Negative regulation of NF-kappaB action by Set9-mediated lysine methylation of the RelA subunit
EMBO J
 , 
2009
, vol. 
28
 (pg. 
1055
-
1066
)
26
Kontaki
H
Talianidis
I
Lysine methylation regulates E2F1-induced cell death
Mol Cell
 , 
2010
, vol. 
39
 (pg. 
152
-
160
)
27
Dhayalan
A
Kudithipudi
S
Rathert
P
Jeltsch
A
Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase
Chem Biol
 , 
2011
, vol. 
18
 (pg. 
111
-
120
)
28
Li
Y
Reddy
MA
Miao
F
Shanmugam
N
Yee
JK
Hawkins
D
Ren
B
, et al.  . 
Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
26771
-
26781
)
29
Pagans
S
Kauder
SE
Kaehlcke
K
Sakane
N
Schroeder
S
Dormeyer
W
Trievel
RC
, et al.  . 
The cellular lysine methyltransferase Set7/9-KMT7 binds HIV-1 TAR RNA, monomethylates the viral transactivator Tat, and enhances HIV transcription
Cell Host Microbe
 , 
2010
, vol. 
7
 (pg. 
234
-
244
)
30
Ko
S
Ahn
J
Song
CS
Kim
S
Knapczyk-Stwora
K
Chatterjee
B
Lysine methylation and functional modulation of androgen receptor by Set9 methyltransferase
Mol Endocrinol
 , 
2011
, vol. 
25
 (pg. 
433
-
444
)
31
Masatsugu
T
Yamamoto
K
Multiple lysine methylation of PCAF by Set9 methyltransferase
Biochem Biophys Res Commun
 , 
2009
, vol. 
381
 (pg. 
22
-
26
)
32
Rea
S
Eisenhaber
F
O'Carroll
D
Strahl
BD
Sun
ZW
Schmid
M
Opravil
S
, et al.  . 
Regulation of chromatin structure by site-specific histone H3 methyltransferases
Nature
 , 
2000
, vol. 
406
 (pg. 
593
-
599
)
33
Rice
JC
Briggs
SD
Ueberheide
B
Barber
CM
Shabanowitz
J
Hunt
DF
Shinkai
Y
, et al.  . 
Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains
Mol Cell
 , 
2003
, vol. 
12
 (pg. 
1591
-
1598
)
34
Nielsen
PR
Nietlispach
D
Mott
HR
Callaghan
J
Bannister
A
Kouzarides
T
Murzin
AG
, et al.  . 
Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9
Nature
 , 
2002
, vol. 
416
 (pg. 
103
-
107
)
35
Fischle
W
Wang
Y
Jacobs
SA
Kim
Y
Allis
CD
Khorasanizadeh
S
Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by polycomb and HP1 chromodomains
Genes Dev
 , 
2003
, vol. 
17
 (pg. 
1870
-
1881
)
36
Collins
RE
Northrop
JP
Horton
JR
Lee
DY
Zhang
X
Stallcup
MR
Cheng
X
The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules
Nat Struct Mol Biol
 , 
2008
, vol. 
15
 (pg. 
245
-
250
)
37
Tachibana
M
Ueda
J
Fukuda
M
Takeda
N
Ohta
T
Iwanari
H
Sakihama
T
, et al.  . 
Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9
Genes Dev
 , 
2005
, vol. 
19
 (pg. 
815
-
826
)
38
Falandry
C
Fourel
G
Galy
V
Ristriani
T
Horard
B
Bensimon
E
Salles
G
, et al.  . 
CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation
J Biol Chem
 , 
2010
, vol. 
285
 (pg. 
20234
-
20241
)
39
Wang
H
An
W
Cao
R
Xia
L
Erdjument-Bromage
H
Chatton
B
Tempst
P
, et al.  . 
mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression
Mol Cell
 , 
2003
, vol. 
12
 (pg. 
475
-
487
)
40
Clouaire
T
de Las Heras
JI
Merusi
C
Stancheva
I
Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA
Nucleic Acids Res
 , 
2010
, vol. 
38
 (pg. 
4620
-
4634
)
41
Huyen
Y
Zgheib
O
Ditullio
RA
Jr
Gorgoulis
VG
Zacharatos
P
Petty
TJ
Sheston
EA
, et al.  . 
Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks
Nature
 , 
2004
, vol. 
432
 (pg. 
406
-
411
)
42
Krivtsov
AV
Armstrong
SA
MLL translocations, histone modifications and leukaemia stem-cell development
Nat Rev Cancer
 , 
2007
, vol. 
7
 (pg. 
823
-
833
)
43
Dou
Y
Milne
TA
Ruthenburg
AJ
Lee
S
Lee
JW
Verdine
GL
Allis
CD
, et al.  . 
Regulation of MLL1 H3K4 methyltransferase activity by its core components
Nat Struct Mol Biol
 , 
2006
, vol. 
13
 (pg. 
713
-
719
)
44
Yokoyama
A
Wang
Z
Wysocka
J
Sanyal
M
Aufiero
DJ
Kitabayashi
I
Herr
W
, et al.  . 
Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression
Mol Cell Biol
 , 
2004
, vol. 
24
 (pg. 
5639
-
5649
)
45
Hughes
CM
Rozenblatt-Rosen
O
Milne
TA
Copeland
TD
Levine
SS
Lee
JC
Hayes
DN
, et al.  . 
Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus
Mol Cell
 , 
2004
, vol. 
13
 (pg. 
587
-
597
)
46
Lee
MG
Villa
R
Trojer
P
Norman
J
Yan
KP
Reinberg
D
Croce
LD
, et al.  . 
Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination
Science
 , 
2007
, vol. 
318
 (pg. 
447
-
450
)
47
Keogh
MC
Kurdistani
SK
Morris
SA
Ahn
SH
Podolny
V
Collins
SR
Schuldiner
M
, et al.  . 
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex
Cell
 , 
2005
, vol. 
123
 (pg. 
593
-
605
)
48
Carrozza
MJ
Li
B
Florens
L
Suganuma
T
Swanson
SK
Lee
KK
Shia
WJ
, et al.  . 
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
Cell
 , 
2005
, vol. 
123
 (pg. 
581
-
592
)
49
Wang
GG
Cai
L
Pasillas
MP
Kamps
MP
NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis
Nat Cell Biol
 , 
2007
, vol. 
9
 (pg. 
804
-
812
)
50
Rayasam
GV
Wendling
O
Angrand
PO
Mark
M
Niederreither
K
Song
L
Lerouge
T
, et al.  . 
NSD1 is essential for early post-implantation development and has a catalytically active SET domain
EMBO J
 , 
2003
, vol. 
22
 (pg. 
3153
-
3163
)
51
Schneider
R
Bannister
AJ
Kouzarides
T
Unsafe SETs: histone lysine methyltransferases and cancer
Trends Biochem Sci
 , 
2002
, vol. 
27
 (pg. 
396
-
402
)
52
Nimura
K
Ura
K
Shiratori
H
Ikawa
M
Okabe
M
Schwartz
RJ
Kaneda
Y
A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome
Nature
 , 
2009
, vol. 
460
 (pg. 
287
-
291
)
53
Pei
H
Zhang
L
Luo
K
Qin
Y
Chesi
M
Fei
F
Bergsagel
PL
, et al.  . 
MMSET regulates histone H4K20 methylation and 53BP1 accumulation at DNA damage sites
Nature
 , 
2011
, vol. 
470
 (pg. 
124
-
128
)
54
Zhou
Z
Thomsen
R
Kahns
S
Nielsen
AL
The NSD3L histone methyltransferase regulates cell cycle and cell invasion in breast cancer cells
Biochem Biophys Res Commun
 , 
2010
, vol. 
398
 (pg. 
565
-
570
)
55
Abu-Farha
M
Lambert
JP
Al-Madhoun
AS
Elisma
F
Skerjanc
IS
Figeys
D
The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase
Mol Cell Proteomics
 , 
2008
, vol. 
7
 (pg. 
560
-
572
)
56
Brown
MA
Sims
RJ
3rd
Gottlieb
PD
Tucker
PW
Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex
Mol Cancer
 , 
2006
, vol. 
5
 pg. 
26
 
57
Hamamoto
R
Furukawa
Y
Morita
M
Iimura
Y
Silva
FP
Li
M
Yagyu
R
, et al.  . 
SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells
Nat Cell Biol
 , 
2004
, vol. 
6
 (pg. 
731
-
740
)
58
Gottlieb
PD
Pierce
SA
Sims
RJ
Yamagishi
H
Weihe
EK
Harriss
JV
Maika
SD
, et al.  . 
Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis
Nat Genet
 , 
2002
, vol. 
31
 (pg. 
25
-
32
)
59
Feng
Q
Wang
H
Ng
HH
Erdjument-Bromage
H
Tempst
P
Struhl
K
Zhang
Y
Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain
Curr Biol
 , 
2002
, vol. 
12
 (pg. 
1052
-
1058
)
60
Nguyen
AT
Zhang
Y
The diverse functions of Dot1 and H3K79 methylation
Genes Dev
 , 
2011
, vol. 
25
 (pg. 
1345
-
1358
)
61
van Leeuwen
F
Gafken
PR
Gottschling
DE
Dot1p modulates silencing in yeast by methylation of the nucleosome core
Cell
 , 
2002
, vol. 
109
 (pg. 
745
-
756
)
62
Shanower
GA
Muller
M
Blanton
JL
Honti
V
Gyurkovics
H
Schedl
P
Characterization of the grappa gene, the Drosophila histone H3 lysine 79 methyltransferase
Genetics
 , 
2005
, vol. 
169
 (pg. 
173
-
184
)
63
Jones
B
Su
H
Bhat
A
Lei
H
Bajko
J
Hevi
S
Baltus
GA
, et al.  . 
The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure
PLoS Genet
 , 
2008
, vol. 
4
 pg. 
e1000190
 
64
Okada
Y
Feng
Q
Lin
Y
Jiang
Q
Li
Y
Coffield
VM
Su
L
, et al.  . 
hDOT1L links histone methylation to leukemogenesis
Cell
 , 
2005
, vol. 
121
 (pg. 
167
-
178
)
65
Krivtsov
AV
Feng
Z
Lemieux
ME
Faber
J
Vempati
S
Sinha
AU
Xia
X
, et al.  . 
H3K79 methylation profiles define murine and human MLL-AF4 leukemias
Cancer Cell
 , 
2008
, vol. 
14
 (pg. 
355
-
368
)
66
Bernt
KM
Zhu
N
Sinha
AU
Vempati
S
Faber
J
Krivtsov
AV
Feng
Z
, et al.  . 
MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L
Cancer Cell
 , 
2011
, vol. 
20
 (pg. 
66
-
78
)
67
Daigle
SR
Olhava
EJ
Therkelsen
CA
Majer
CR
Sneeringer
CJ
Song
J
Johnston
LD
, et al.  . 
Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor
Cancer Cell
 , 
2011
, vol. 
20
 (pg. 
53
-
65
)
68
Karachentsev
D
Sarma
K
Reinberg
D
Steward
R
PR-Set7-dependent methylation of histone H4 Lys 20 functions in repression of gene expression and is essential for mitosis
Genes Dev
 , 
2005
, vol. 
19
 (pg. 
431
-
435
)
69
Nishioka
K
Rice
JC
Sarma
K
Erdjument-Bromage
H
Werner
J
Wang
Y
Chuikov
S
, et al.  . 
PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin
Mol Cell
 , 
2002
, vol. 
9
 (pg. 
1201
-
1213
)
70
Li
Z
Nie
F
Wang
S
Li
L
Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation
Proc Natl Acad Sci USA
 , 
2011
, vol. 
108
 (pg. 
3116
-
3123
)
71
Congdon
LM
Houston
SI
Veerappan
CS
Spektor
TM
Rice
JC
PR-Set7-mediated monomethylation of histone H4 lysine 20 at specific genomic regions induces transcriptional repression
J Cell Biochem
 , 
2010
, vol. 
110
 (pg. 
609
-
619
)
72
Jorgensen
S
Eskildsen
M
Fugger
K
Hansen
L
Larsen
MS
Kousholt
AN
Syljuåsen
RG
, et al.  . 
SET8 is degraded via PCNA-coupled CRL4(CDT2) ubiquitylation in S phase and after UV irradiation
J Cell Biol
 , 
2011
, vol. 
192
 (pg. 
43
-
54
)
73
Centore
RC
Havens
CG
Manning
AL
Li
JM
Flynn
RL
Tse
A
Jin
J
, et al.  . 
CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase
Mol Cell
 , 
2010
, vol. 
40
 (pg. 
22
-
33
)
74
Abbas
T
Shibata
E
Park
J
Jha
S
Karnani
N
Dutta
A
CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation
Mol Cell
 , 
2010
, vol. 
40
 (pg. 
9
-
21
)
75
Huen
MS
Sy
SM
van Deursen
JM
Chen
J
Direct interaction between SET8 and proliferating cell nuclear antigen couples H4-K20 methylation with DNA replication
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
11073
-
11077
)
76
Jorgensen
S
Elvers
I
Trelle
MB
Menzel
T
Eskildsen
M
Jensen
ON
Helleday
T
, et al.  . 
The histone methyltransferase SET8 is required for S-phase progression
J Cell Biol
 , 
2007
, vol. 
179
 (pg. 
1337
-
1345
)
77
Tardat
M
Brustel
J
Kirsh
O
Lefevbre
C
Callanan
M
Sardet
C
Julien
E
The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells
Nat Cell Biol
 , 
2010
, vol. 
12
 (pg. 
1086
-
1093
)
78
Schotta
G
Lachner
M
Sarma
K
Ebert
A
Sengupta
R
Reuter
G
Reinberg
D
, et al.  . 
A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin
Genes Dev
 , 
2004
, vol. 
18
 (pg. 
1251
-
1262
)
79
Schotta
G
Sengupta
R
Kubicek
S
Malin
S
Kauer
M
Callen
E
Celeste
A
, et al.  . 
A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse
Genes Dev
 , 
2008
, vol. 
22
 (pg. 
2048
-
2061
)
80
Greeson
NT
Sengupta
R
Arida
AR
Jenuwein
T
Sanders
SL
Di-methyl H4 lysine 20 targets the checkpoint protein Crb2 to sites of DNA damage
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
33168
-
33174
)
81
Botuyan
MV
Lee
J
Ward
IM
Kim
JE
Thompson
JR
Chen
J
Mer
G
Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair
Cell
 , 
2006
, vol. 
127
 (pg. 
1361
-
1373
)
82
Cao
R
Wang
L
Wang
H
Xia
L
Erdjument-Bromage
H
Tempst
P
Jones
RS
, et al.  . 
Role of histone H3 lysine 27 methylation in polycomb-group silencing
Science
 , 
2002
, vol. 
298
 (pg. 
1039
-
1043
)
83
Kuzmichev
A
Nishioka
K
Erdjument-Bromage
H
Tempst
P
Reinberg
D
Histone methyltransferase activity associated with a human multiprotein complex containing the enhancer of Zeste protein
Genes Dev
 , 
2002
, vol. 
16
 (pg. 
2893
-
2905
)
84
Margueron
R
Reinberg
D
The polycomb complex PRC2 and its mark in life
Nature
 , 
2011
, vol. 
469
 (pg. 
343
-
349
)
85
Martin-Perez
D
Piris
MA
Sanchez-Beato
M
Polycomb proteins in hematologic malignancies
Blood
 , 
2010
, vol. 
116
 (pg. 
5465
-
5475
)
86
Ezhkova
E
Pasolli
HA
Parker
JS
Stokes
N
Su
IH
Hannon
G
Tarakhovsky
A
, et al.  . 
Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells
Cell
 , 
2009
, vol. 
136
 (pg. 
1122
-
1135
)
87
Wei
Y
Chen
YH
Li
LY
Lang
J
Yeh
SP
Shi
B
Yang
CC
, et al.  . 
CDK1-dependent phosphorylation of EZH2 suppresses methylation of H3K27 and promotes osteogenic differentiation of human mesenchymal stem cells
Nat Cell Biol
 , 
2011
, vol. 
13
 (pg. 
87
-
94
)
88
Kaneko
S
Li
G
Son
J
Xu
CF
Margueron
R
Neubert
TA
Reinberg
D
Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA
Genes Dev
 , 
2010
, vol. 
24
 (pg. 
2615
-
2620
)
89
Chen
S
Bohrer
LR
Rai
AN
Pan
Y
Gan
L
Zhou
X
Bagchi
A
, et al.  . 
Cyclin-dependent kinases regulate epigenetic gene silencing through phosphorylation of EZH2
Nat Cell Biol
 , 
2010
, vol. 
12
 (pg. 
1108
-
1114
)
90
Ezhkova
E
Lien
WH
Stokes
N
Pasolli
HA
Silva
JM
Fuchs
E
EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair
Genes Dev
 , 
2011
, vol. 
25
 (pg. 
485
-
498
)
91
Shen
X
Liu
Y
Hsu
YJ
Fujiwara
Y
Kim
J
Mao
X
Yuan
GC
, et al.  . 
EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency
Mol Cell
 , 
2008
, vol. 
32
 (pg. 
491
-
502
)
92
Nishioka
K
Chuikov
S
Sarma
K
Erdjument-Bromage
H
Allis
CD
Tempst
P
Reinberg
D
Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation
Genes Dev
 , 
2002
, vol. 
16
 (pg. 
479
-
489
)
93
Pradhan
S
Chin
HG
Esteve
PO
Jacobsen
SE
SET7/9 mediated methylation of non-histone proteins in mammalian cells
Epigenetics
 , 
2009
, vol. 
4
 (pg. 
383
-
387
)
94
Couture
JF
Collazo
E
Hauk
G
Trievel
RC
Structural basis for the methylation site specificity of SET7/9
Nat Struct Mol Biol
 , 
2006
, vol. 
13
 (pg. 
140
-
146
)
95
Abbondanza
C
Medici
N
Nigro
V
Rossi
V
Gallo
L
Piluso
G
Belsito
A
, et al.  . 
The retinoblastoma-interacting zinc-finger protein RIZ is a downstream effector of estrogen action
Proc Natl Acad Sci USA
 , 
2000
, vol. 
97
 (pg. 
3130
-
3135
)
96
Huang
S
Histone methyltransferases, diet nutrients and tumour suppressors
Nat Rev Cancer
 , 
2002
, vol. 
2
 (pg. 
469
-
476
)
97
Kim
KC
Geng
L
Huang
S
Inactivation of a histone methyltransferase by mutations in human cancers
Cancer Res
 , 
2003
, vol. 
63
 (pg. 
7619
-
7623
)
98
Shi
Y
Lan
F
Matson
C
Mulligan
P
Whetstine
JR
Cole
PA
Casero
RA
, et al.  . 
Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
Cell
 , 
2004
, vol. 
119
 (pg. 
941
-
953
)
99
Tsukada
Y
Fang
J
Erdjument-Bromage
H
Warren
ME
Borchers
CH
Tempst
P
Zhang
Y
Histone demethylation by a family of JmjC domain-containing proteins
Nature
 , 
2006
, vol. 
439
 (pg. 
811
-
816
)
100
Shi
Y
Whetstine
JR
Dynamic regulation of histone lysine methylation by demethylases
Mol Cell
 , 
2007
, vol. 
25
 (pg. 
1
-
14
)
101
Cloos
PA
Christensen
J
Agger
K
Helin
K
Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease
Genes Dev
 , 
2008
, vol. 
22
 (pg. 
1115
-
1140
)
102
Klose
RJ
Zhang
Y
Regulation of histone methylation by demethylimination and demethylation
Nat Rev Mol Cell Biol
 , 
2007
, vol. 
8
 (pg. 
307
-
318
)
103
Huang
J
Sengupta
R
Espejo
AB
Lee
MG
Dorsey
JA
Richter
M
Opravil
S
, et al.  . 
p53 is regulated by the lysine demethylase LSD1
Nature
 , 
2007
, vol. 
449
 (pg. 
105
-
108
)
104
Cho
HS
Suzuki
T
Dohmae
N
Hayami
S
Unoki
M
Yoshimatsu
M
Toyokawa
G
, et al.  . 
Demethylation of RB regulator MYPT1 by histone demethylase LSD1 promotes cell cycle progression in cancer cells
Cancer Res
 , 
2011
, vol. 
71
 (pg. 
655
-
660
)
105
Lee
MG
Wynder
C
Cooch
N
Shiekhattar
R
An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation
Nature
 , 
2005
, vol. 
437
 (pg. 
432
-
435
)
106
Yang
M
Gocke
CB
Luo
X
Borek
D
Tomchick
DR
Machius
M
Otwinowski
Z
, et al.  . 
Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase
Mol Cell
 , 
2006
, vol. 
23
 (pg. 
377
-
387
)
107
Metzger
E
Wissmann
M
Yin
N
Muller
JM
Schneider
R
Peters
AH
Günther
T
, et al.  . 
LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription
Nature
 , 
2005
, vol. 
437
 (pg. 
436
-
439
)
108
Wissmann
M
Yin
N
Muller
JM
Greschik
H
Fodor
BD
Jenuwein
T
Vogler
C
, et al.  . 
Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression
Nat Cell Biol
 , 
2007
, vol. 
9
 (pg. 
347
-
353
)
109
Hu
Q
Kwon
YS
Nunez
E
Cardamone
MD
Hutt
KR
Ohgi
KA
Garcia-Bassets
I
, et al.  . 
Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules
Proc Natl Acad Sci USA
 , 
2008
, vol. 
105
 (pg. 
19199
-
19204
)
110
Nicholson
TB
Chen
T
LSD1 demethylates histone and non-histone proteins
Epigenetics
 , 
2009
, vol. 
4
 (pg. 
129
-
132
)
111
Yang
Z
Jiang
J
Stewart
DM
Qi
S
Yamane
K
Li
J
Zhang
Y
, et al.  . 
AOF1 is a histone H3K4 demethylase possessing demethylase activity-independent repression function
Cell Res
 , 
2010
, vol. 
20
 (pg. 
276
-
287
)
112
Ciccone
DN
Su
H
Hevi
S
Gay
F
Lei
H
Bajko
J
Xu
G
, et al.  . 
KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints
Nature
 , 
2009
, vol. 
461
 (pg. 
415
-
418
)
113
Karytinos
A
Forneris
F
Profumo
A
Ciossani
G
Battaglioli
E
Binda
C
Mattevi
A
A novel mammalian flavin-dependent histone demethylase
J Biol Chem
 , 
2009
, vol. 
284
 (pg. 
17775
-
17782
)
114
Fang
R
Barbera
AJ
Xu
Y
Rutenberg
M
Leonor
T
Bi
Q
Lan
F
, et al.  . 
Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation
Mol Cell
 , 
2011
, vol. 
39
 (pg. 
222
-
233
)
115
van Essen
D
Zhu
Y
Saccani
S
A feed-forward circuit controlling inducible NF-kappaB target gene activation by promoter histone demethylation
Mol Cell
 , 
2011
, vol. 
39
 (pg. 
750
-
760
)
116
Frescas
D
Guardavaccaro
D
Bassermann
F
Koyama-Nasu
R
Pagano
M
JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes
Nature
 , 
2007
, vol. 
450
 (pg. 
309
-
313
)
117
He
J
Kallin
EM
Tsukada
Y
Zhang
Y
The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b)
Nat Struct Mol Biol
 , 
2008
, vol. 
15
 (pg. 
1169
-
1175
)
118
Koyama-Nasu
R
David
G
Tanese
N
The F-box protein Fbl10 is a novel transcriptional repressor of c-Jun
Nat Cell Biol
 , 
2007
, vol. 
9
 (pg. 
1074
-
1080
)
119
Tanaka
Y
Okamoto
K
Teye
K
Umata
T
Yamagiwa
N
Suto
Y
Zhang
Y
, et al.  . 
JmjC enzyme KDM2A is a regulator of rRNA transcription in response to starvation
EMBO J
 , 
2010
, vol. 
29
 (pg. 
1510
-
1522
)
120
Sanchez
C
Sanchez
I
Demmers
JA
Rodriguez
P
Strouboulis
J
Vidal
M
Proteomics analysis of Ring1B/Rnf2 interactors identifies a novel complex with the Fbxl10/Jhdm1B histone demethylase and the Bcl6 interacting corepressor
Mol Cell Proteomics
 , 
2007
, vol. 
6
 (pg. 
820
-
834
)
121
Yamane
K
Toumazou
C
Tsukada
Y
Erdjument-Bromage
H
Tempst
P
Wong
J
Zhang
Y
JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor
Cell
 , 
2006
, vol. 
125
 (pg. 
483
-
495
)
122
Okada
Y
Scott
G
Ray
MK
Mishina
Y
Zhang
Y
Histone demethylase JHDM2A is critical for Tnp1 and Prm1 transcription and spermatogenesis
Nature
 , 
2007
, vol. 
450
 (pg. 
119
-
123
)
123
Krieg
AJ
Rankin
EB
Chan
D
Razorenova
O
Fernandez
S
Giaccia
AJ
Regulation of the histone demethylase JMJD1A by hypoxia-inducible factor 1 alpha enhances hypoxic gene expression and tumor growth
Mol Cell Biol
 , 
2009
, vol. 
30
 (pg. 
344
-
353
)
124
Tateishi
K
Okada
Y
Kallin
EM
Zhang
Y
Role of Jhdm2a in regulating metabolic gene expression and obesity resistance
Nature
 , 
2009
, vol. 
458
 (pg. 
757
-
761
)
125
Whetstine
JR
Nottke
A
Lan
F
Huarte
M
Smolikov
S
Chen
Z
Spooner
E
, et al.  . 
Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases
Cell
 , 
2006
, vol. 
125
 (pg. 
467
-
481
)
126
Klose
RJ
Yamane
K
Bae
Y
Zhang
D
Erdjument-Bromage
H
Tempst
P
Wong
J
, et al.  . 
The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36
Nature
 , 
2006
, vol. 
442
 (pg. 
312
-
316
)
127
Fodor
BD
Kubicek
S
Yonezawa
M
O'Sullivan
RJ
Sengupta
R
Perez-Burgos
L
Opravil
S
, et al.  . 
Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells
Genes Dev
 , 
2006
, vol. 
20
 (pg. 
1557
-
1562
)
128
Huang
Y
Fang
J
Bedford
MT
Zhang
Y
Xu
RM
Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A
Science
 , 
2006
, vol. 
312
 (pg. 
748
-
751
)
129
Adams-Cioaba
MA
Min
J
Structure and function of histone methylation binding proteins
Biochem Cell Biol
 , 
2009
, vol. 
87
 (pg. 
93
-
105
)
130
Shin
S
Janknecht
R
Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D
Biochem Biophys Res Commun
 , 
2007
, vol. 
359
 (pg. 
742
-
746
)
131
Kawazu
M
Saso
K
Tong
KI
McQuire
T
Goto
K
Son
DO
Wakeham
A
, et al.  . 
Histone demethylase JMJD2B functions as a co-factor of estrogen receptor in breast cancer proliferation and mammary gland development
PLoS One
 , 
2011
, vol. 
6
 pg. 
e17830
 
132
Shi
L
Sun
L
Li
Q
Liang
J
Yu
W
Yi
X
Yang
X
, et al.  . 
Histone demethylase JMJD2B coordinates H3K4/H3K9 methylation and promotes hormonally responsive breast carcinogenesis
Proc Natl Acad Sci USA
 , 
2011
, vol. 
108
 (pg. 
7541
-
7546
)
133
Ponnaluri
VK
Vavilala
DT
Putty
S
Gutheil
WG
Mukherji
M
Identification of non-histone substrates for JMJD2A-C histone demethylases
Biochem Biophys Res Commun
 , 
2009
, vol. 
390
 (pg. 
280
-
284
)
134
Ponnaluri
VK
Vavilala
DT
Mukherji
M
Studies on substrate specificity of Jmjd2a-c histone demethylases
Biochem Biophys Res Commun
 , 
2011
, vol. 
405
 (pg. 
588
-
592
)
135
Xiang
Y
Zhu
Z
Han
G
Ye
X
Xu
B
Peng
Z
Ma
Y
, et al.  . 
JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer
Proc Natl Acad Sci USA
 , 
2007
, vol. 
104
 (pg. 
19226
-
19231
)
136
Christensen
J
Agger
K
Cloos
PA
Pasini
D
Rose
S
Sennels
L
Rappsilber
J
, et al.  . 
RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3
Cell
 , 
2007
, vol. 
128
 (pg. 
1063
-
1076
)
137
Iwase
S
Lan
F
Bayliss
P
de la Torre-Ubieta
L
Huarte
M
Qi
HH
Whetstine
JR
, et al.  . 
The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases
Cell
 , 
2007
, vol. 
128
 (pg. 
1077
-
1088
)
138
Klose
RJ
Yan
Q
Tothova
Z
Yamane
K
Erdjument-Bromage
H
Tempst
P
Gilliland
DG
, et al.  . 
The retinoblastoma binding protein RBP2 is an H3K4 demethylase
Cell
 , 
2007
, vol. 
128
 (pg. 
889
-
900
)
139
Yamane
K
Tateishi
K
Klose
RJ
Fang
J
Fabrizio
LA
Erdjument-Bromage
H
Taylor-Papadimitriou
J
, et al.  . 
PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation
Mol Cell
 , 
2007
, vol. 
25
 (pg. 
801
-
812
)
140
Tahiliani
M
Mei
P
Fang
R
Leonor
T
Rutenberg
M
Shimizu
F
Li
J
, et al.  . 
The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation
Nature
 , 
2007
, vol. 
447
 (pg. 
601
-
605
)
141
Lee
MG
Norman
J
Shilatifard
A
Shiekhattar
R
Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein
Cell
 , 
2007
, vol. 
128
 (pg. 
877
-
887
)
142
Wang
GG
Song
J
Wang
Z
Dormann
HL
Casadio
F
Li
H
Luo
JL
, et al.  . 
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger
Nature
 , 
2009
, vol. 
459
 (pg. 
847
-
851
)
143
Blair
LP
Cao
J
Zou
MR
Sayegh
J
Yan
Q
Epigenetic regulation by lysine demethylase 5 (KDM5) enzymes in cancer
Cancers (Basel)
 , 
2011
, vol. 
3
 (pg. 
1383
-
1404
)
144
De Santa
F
Totaro
MG
Prosperini
E
Notarbartolo
S
Testa
G
Natoli
G
The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing
Cell
 , 
2007
, vol. 
130
 (pg. 
1083
-
1094
)
145
Hong
S
Cho
YW
Yu
LR
Yu
H
Veenstra
TD
Ge
K
Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases
Proc Natl Acad Sci USA
 , 
2007
, vol. 
104
 (pg. 
18439
-
18444
)
146
Xiang
Y
Zhu
Z
Han
G
Lin
H
Xu
L
Chen
CD
JMJD3 is a histone H3K27 demethylase
Cell Res
 , 
2007
, vol. 
17
 (pg. 
850
-
857
)
147
Agger
K
Cloos
PA
Christensen
J
Pasini
D
Rose
S
Rappsilber
J
Issaeva
I
, et al.  . 
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development
Nature
 , 
2007
, vol. 
449
 (pg. 
731
-
734
)
148
Lan
F
Bayliss
PE
Rinn
JL
Whetstine
JR
Wang
JK
Chen
S
Iwase
S
, et al.  . 
A histone H3 lysine 27 demethylase regulates animal posterior development
Nature
 , 
2007
, vol. 
449
 (pg. 
689
-
694
)
149
Wang
JK
Tsai
MC
Poulin
G
Adler
AS
Chen
S
Liu
H
Shi
Y
, et al.  . 
The histone demethylase UTX enables RB-dependent cell fate control
Genes Dev
 , 
2010
, vol. 
24
 (pg. 
327
-
332
)
150
McLaughlin-Drubin
ME
Crum
CP
Munger
K
Human papillomavirus E7 oncoprotein induces KDM6A and KDM6B histone demethylase expression and causes epigenetic reprogramming
Proc Natl Acad Sci USA
 , 
2011
, vol. 
108
 (pg. 
2130
-
2135
)
151
Wen
H
Li
J
Song
T
Lu
M
Kan
PY
Lee
MG
Sha
B
, et al.  . 
Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation
J Biol Chem
 , 
2010
, vol. 
285
 (pg. 
9322
-
9326
)
152
Feng
W
Yonezawa
M
Ye
J
Jenuwein
T
Grummt
I
PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation
Nat Struct Mol Biol
 , 
2010
, vol. 
17
 (pg. 
445
-
450
)
153
Fortschegger
K
de Graaf
P
Outchkourov
NS
van Schaik
FM
Timmers
HT
Shiekhattar
R
PHF8 targets histone methylation and RNA polymerase II to activate transcription
Mol Cell Biol
 , 
2010
, vol. 
30
 (pg. 
3286
-
3298
)
154
Qiu
J
Shi
G
Jia
Y
Li
J
Wu
M
Li
J
Dong
S
, et al.  . 
The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation
Cell Res
 , 
2010
, vol. 
20
 (pg. 
908
-
918
)
155
Zhu
Z
Wang
Y
Li
X
Wang
Y
Xu
L
Wang
X
Sun
T
, et al.  . 
PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis
Cell Res
 , 
2010
, vol. 
20
 (pg. 
794
-
801
)
156
Kleine-Kohlbrecher
D
Christensen
J
Vandamme
J
Abarrategui
I
Bak
M
Tommerup
N
Shi
X
, et al.  . 
A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation
Mol Cell
 , 
2010
, vol. 
38
 (pg. 
165
-
178
)
157
Baba
A
Ohtake
F
Okuno
Y
Yokota
K
Okada
M
Imai
Y
Ni
M
, et al.  . 
PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B
Nat Cell Biol
 , 
2011
, vol. 
13
 (pg. 
669
-
676
)
158
Liu
W
Tanasa
B
Tyurina
OV
Zhou
TY
Gassmann
R
Liu
WT
Ohgi
KA
, et al.  . 
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
Nature
 , 
2010
, vol. 
466
 (pg. 
508
-
512
)
159
Qi
HH
Sarkissian
M
Hu
GQ
Wang
Z
Bhattacharjee
A
Gordon
DB
Gonzales
M
, et al.  . 
Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development
Nature
 , 
2010
, vol. 
466
 (pg. 
503
-
507
)
160
Yu
L
Wang
Y
Huang
S
Wang
J
Deng
Z
Zhang
Q
Wu
W
, et al.  . 
Structural insights into a novel histone demethylase PHF8
Cell Res
 , 
2010
, vol. 
20
 (pg. 
166
-
173
)
161
Horton
JR
Upadhyay
AK
Qi
HH
Zhang
X
Shi
Y
Cheng
X
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases
Nat Struct Mol Biol
 , 
2010
, vol. 
17
 (pg. 
38
-
43
)
162
Chen
L
Li
Z
Zwolinska
AK
Smith
MA
Cross
B
Koomen
J
Yuan
ZM
, et al.  . 
MDM2 recruitment of lysine methyltransferases regulates p53 transcriptional output
EMBO J
 , 
2010
, vol. 
29
 (pg. 
2538
-
2552
)
163
Levine
AJ
p53, the cellular gatekeeper for growth and division
Cell
 , 
1997
, vol. 
88
 (pg. 
323
-
331
)
164
Kruse
JP
Gu
W
Modes of p53 regulation
Cell
 , 
2009
, vol. 
137
 (pg. 
609
-
622
)
165
Lee
JS
Smith
E
Shilatifard
A
The language of histone crosstalk
Cell
 , 
2010
, vol. 
142
 (pg. 
682
-
685
)
166
Latham
JA
Dent
SY
Cross-regulation of histone modifications
Nat Struct Mol Biol
 , 
2007
, vol. 
14
 (pg. 
1017
-
1024
)
167
Ivanov
GS
Ivanova
T
Kurash
J
Ivanov
A
Chuikov
S
Gizatullin
F
Herrera-Medina
EM
, et al.  . 
Methylation-acetylation interplay activates p53 in response to DNA damage
Mol Cell Biol
 , 
2007
, vol. 
27
 (pg. 
6756
-
6769
)
168
Kurash
JK
Lei
H
Shen
Q
Marston
WL
Granda
BW
Fan
H
Wall
D
, et al.  . 
Methylation of p53 by Set7/9 mediates p53 acetylation and activity in vivo
Mol Cell
 , 
2008
, vol. 
29
 (pg. 
392
-
400
)
169
Xu
S
Zhong
C
Zhang
T
Ding
J
Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins
J Mol Cell Biol
 , 
2011
, vol. 
3
 (pg. 
293
-
300
)
170
Martin
C
Zhang
Y
The diverse functions of histone lysine methylation
Nat Rev Mol Cell Biol
 , 
2005
, vol. 
6
 (pg. 
838
-
849
)
171
West
LE
Roy
S
Lachmi-Weiner
K
Hayashi
R
Shi
X
Appella
E
Kutateladze
TG
, et al.  . 
The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression
J Biol Chem
 , 
2010
, vol. 
285
 (pg. 
37725
-
37732
)
172
Kachirskaia
I
Shi
X
Yamaguchi
H
Tanoue
K
Wen
H
Wang
EW
Appella
E
, et al.  . 
Role for 53BP1 Tudor domain recognition of p53 dimethylated at lysine 382 in DNA damage signaling
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
34660
-
34666
)
173
Roy
S
Musselman
CA
Kachirskaia
I
Hayashi
R
Glass
KC
Nix
JC
Gozani
O
, et al.  . 
Structural insight into p53 recognition by the 53BP1 tandem Tudor domain
J Mol Biol
 , 
2010
, vol. 
398
 (pg. 
489
-
496
)
174
Lehnertz
B
Rogalski
JC
Schulze
FM
Yi
L
Lin
S
Kast
J
Rossi
FMV
p53-dependent transcription and tumor suppression are not affected in Set7/9-deficient mice
Mol Cell
 , 
2011
, vol. 
43
 (pg. 
673
-
680
)
175
Campaner
S
Spreafico
F
Burgold
T
Doni
M
Rosato
U
Amati
B
Testa
G
The methyltransferase set7/9 (Setd7) is dispensable for the p53-mediated DNA damage response in vivo
Mol Cell
 , 
2011
, vol. 
43
 (pg. 
681
-
688
)
176
Feng
L
Lin
T
Uranishi
H
Gu
W
Xu
Y
Functional analysis of the roles of posttranslational modifications at the p53 C terminus in regulating p53 stability and activity
Mol Cell Biol
 , 
2005
, vol. 
25
 (pg. 
5389
-
5395
)
177
Krummel
KA
Lee
CJ
Toledo
F
Wahl
GM
The C-terminal lysines fine-tune P53 stress responses in a mouse model but are not required for stability control or transactivation
Proc Natl Acad Sci USA
 , 
2005
, vol. 
102
 (pg. 
10188
-
10193
)
178
Wang
H
Cao
R
Xia
L
Erdjument-Bromage
H
Borchers
C
Tempst
P
Zhang
Y
Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase
Mol Cell
 , 
2001
, vol. 
8
 (pg. 
1207
-
1217
)
179
Carr
SM
Munro
S
Kessler
B
Oppermann
U
La Thangue
NB
Interplay between lysine methylation and Cdk phosphorylation in growth control by the retinoblastoma protein
EMBO J
 , 
2011
, vol. 
30
 (pg. 
317
-
327
)
180
Ea
CK
Baltimore
D
Regulation of NF-kappaB activity through lysine monomethylation of p65
Proc Natl Acad Sci USA
 , 
2009
, vol. 
106
 (pg. 
18972
-
18977
)
181
Levy
D
Kuo
AJ
Chang
Y
Schaefer
U
Kitson
C
Cheung
P
Espejo
A
, et al.  . 
Lysine methylation of the NF-kappaB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-kappaB signaling
Nat Immunol
 , 
2011
, vol. 
12
 (pg. 
29
-
36
)
182
Sampath
SC
Marazzi
I
Yap
KL
Sampath
SC
Krutchinsky
AN
Mecklenbrauker
I
Viale
A
, et al.  . 
Methylation of a histone mimic within the histone methyltransferase G9a regulates protein complex assembly
Mol Cell
 , 
2007
, vol. 
27
 (pg. 
596
-
608
)
183
Webb
KJ
Laganowsky
A
Whitelegge
JP
Clarke
SG
Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab
J Biol Chem
 , 
2008
, vol. 
283
 (pg. 
35561
-
35568
)
184
Porras-Yakushi
TR
Whitelegge
JP
Miranda
TB
Clarke
S
A novel SET domain methyltransferase modifies ribosomal protein Rpl23ab in yeast
J Biol Chem
 , 
2005
, vol. 
280
 (pg. 
34590
-
34598
)
185
Ying
Z
Mulligan
RM
Janney
N
Houtz
RL
Rubisco small and large subunit N-methyltransferases. Bi- and mono-functional methyltransferases that methylate the small and large subunits of Rubisco
J Biol Chem
 , 
1999
, vol. 
274
 (pg. 
36750
-
36756
)
186
Rathert
P
Dhayalan
A
Ma
H
Jeltsch
A
Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins
Mol Biosyst
 , 
2008
, vol. 
4
 (pg. 
1186
-
1190
)
187
Mok
J
Kim
PM
Lam
HY
Piccirillo
S
Zhou
X
Jeschke
GR
Sheridan
DL
, et al.  . 
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs
Sci Signal
 , 
2010
, vol. 
3
 pg. 
ra12
 
188
Ong
SE
Mann
M
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
Nat Protoc
 , 
2006
, vol. 
1
 (pg. 
2650
-
2660
)
189
Oppermann
FS
Gnad
F
Olsen
JV
Hornberger
R
Greff
Z
Keri
G
Mann
M
, et al.  . 
Large-scale proteomics analysis of the human kinome
Mol Cell Proteomics
 , 
2009
, vol. 
8
 (pg. 
1751
-
1764
)
190
Olsen
JV
Blagoev
B
Gnad
F
Macek
B
Kumar
C
Mortensen
P
Mann
M
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
Cell
 , 
2006
, vol. 
127
 (pg. 
635
-
648
)
191
Zhao
S
Xu
W
Jiang
W
Yu
W
Lin
Y
Zhang
T
Yao
J
, et al.  . 
Regulation of cellular metabolism by protein lysine acetylation
Science
 , 
2010
, vol. 
327
 (pg. 
1000
-
1004
)
192
Hsia
DA
Tepper
CG
Pochampalli
MR
Hsia
EY
Izumiya
C
Huerta
SB
Wright
ME
, et al.  . 
KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation
Proc Natl Acad Sci USA
 , 
2010
, vol. 
107
 (pg. 
9671
-
9676
)
193
Jones
MA
Covington
MF
DiTacchio
L
Vollmers
C
Panda
S
Harmer
SL
Jumonji domain protein JMJD5 functions in both the plant and human circadian systems
Proc Natl Acad Sci USA
 , 
2010
, vol. 
107
 (pg. 
21623
-
21628
)