Current Perspectives on Histone Demethylases -

Original Paper

Acta Biochim Biophys

Sin 2007, 39: 81-88

doi:10.1111/j.1745-7270.2007.00272.x

Current Perspectives on

Histone Demethylases

Xiaoqing TIAN and Jingyuan

FANG*

Shanghai Institute of Digestive

Disease, Renji Hospital, Shanghai Jiaotong University School of Medicine,

Shanghai 200001, China

Received: December 6, 2006

Accepted: January 29, 2007

This work was supported by the grants from the National Basic Research

Program of China (No. 2005CB522400), Shanghai Leading Academic Discipline

Project (No. Y0205) and Shanghai Municipal Commission for Science and

Technology (No. 04DZ14006)

*Corresponding author: Tel, 86-21-63200874; Fax, 86-21-63266027; E-mail,

[email protected]

Abstract The posttranslational modification of

histones plays an important role in chromatin regulation. Histone methylation

influences constitutive heterochromatin, genomic imprinting, X-chromosome

inactivation and gene transcription. Histone demethylase catalyzes the removal

of methyl groups on lysine or arginine residues of histones. Two kinds of

histone lysine demethylases have been identified, including lysine specific

demethylase 1 and Jumonji C (JmjC) domain family proteins. These histone

demethylases are involved in the regulation of gene expression. Histone

modification is a dynamic process, and the imbalance of histone methylation has

been linked to cancers. Therefore, histone demethylases may represent a new target

for anti-cancer therapy.

Key words epigenetic modification; histone

methylation; demethylase; lysine specific demethylase 1; Jumonji C (JmjC)

protein

Epigenetic modifications such as DNA methylation and histone modification

are now recognized as additional mechanisms contributing to the non-Mendelian

inheritance of phenotypic alterations. Histone modifications include

acetylation, methylation, phosphorylation, ubiquitination, glycosylation,

sumoylation, ADP-ribosylation, and carbonylation. These different types of

histone modifications occur at multiple and specific sites, which generate

various combinations of histone modifications. It has been proposed that these

different combinations may result in distinct outcomes in terms of

chromatin-dependent functions such as gene expression [1,2]. Histone

methylation regulates fundamental processes such as heterochromatin formation,

X chromosome inactivation, genomic imprinting, transcriptional regulation and

DNA repair [3,4]. Histones may be methylated on either lysine (K) or arginine

(R) residues. Lysine side chains may be mono-, di- or tri-methylated, whereas

arginine side chains may be mono-methylated or symmetrically or asymmetrically

di-methylated [5]. Histone arginine methylation generally correlates with

transcriptional activation, while histone lysine methylation leads to either

activation or repression, which is dependent upon the particular lysine residue

[6,7]. In general, methylation at histone H3K4, H3K36, and H3K79 have been

linked to transcription activation [8–10]. In contrast,

methylation at H3K9, H3K27, and H4K20 are associated with repression of

euchromatic genes [11–16]. Even within the same lysine

residue, the biological consequence of methylation is variable, depending on

the methylation state [17–19]. Thus, methylation at

different lysine residues, degree of methylation at the same lysine residue, as

well as the location of the methylated histone within a specific gene locus,

can impact transcriptional and biological outcomes. Histone demethylase

catalyzes the removal of methyl groups on histone lysine and arginine residues.

Two kinds of histone lysine demethylases have been identified, including lysine

specific demethylase 1 (LSD1) and Jumonji C (JmjC) domain family proteins.

Peptidylarginine deiminase 4 (PAD4/PADI4) antagonizes methylation on arginine

residues by converting monomethyl-arginine in histone H3 and H4 to citrulline

[20,21]. PAD4/PADI4 is not a strict histone demethylase because the enzyme can

act on both methylated and non-methylated arginine. In addition, the reaction

does not generate arginine but citrulline. So whether PAD4/PADI4 is a histone

arginine demethylase or not is still controversial. Here we only review what is currently known about histone lysine

demethylases.

History of Several Histone

Demethylases

It was originally assumed that histone lysine methylation is an

irreversible epigenetic event. This notion arose from early studies

demonstrating that the half-life of histones and methylated lysine residues

within them were the same [22,23]. However, even at this time there was some

evidence that the removal of methyl groups takes place at low but detectable

levels [24,25]. Because histone methylation plays a large role in regulating

gene expression, research efforts have shifted to examining the process of

reversing histone methylation. Three putative mechanisms were proposed to

explain the turnover of methyl groups on histones, including removal by demethylase,

histone replacement, and clipping [26,27]. Among these mechanisms,

demethylase was considered to be the most efficient and straightforward way to

reverse histone methylation. In 1964, Paik and coworkers isolated an enzyme

(N6-methyl-lysine oxidase) from rat kidney, which removed methyl groups from

free mono- and di-methyl lysine residues [28]. The same group reported the

detection of an enzyme capable of demethylating histones [29] but could not

purify the specific protein [30]. The reversibility of methylation became

apparent when antibodies against methylated arginine or lysine residues were

used in chromatin immunoprecipitation [31]. Methylation of histone residues was

reduced under certain conditions, suggesting that methylation reversal was

possible, and that the mechanism may be dependent on an amine oxidase reaction

[5]. In one study reported in 2004, LSD1 removed methyl groups with

remarkable specificity for H3K4 (H3K4me1/2) but could not attack trimethylated

H3K4 (H3K4me3) [32]. Interestingly, LSD1 was also reported to demethylate H3K9

(H3K9me1/2) when interacting with the androgen receptor [33]. In order to

identify additional histone demethylases, Trewick speculated that the mechanism

of histone demethylation mediated by elongation protein 3 (Elp3) was similar to

that of the DNA repair demethylase AlkB [34]. AlkB is a 2-OG-Fe(II)-dependent

dioxygenase that hydroxylates the methyl groups of certain forms of DNA

methylation damage. Catalytic mechanism of AlkB is based on hydroxylation

reaction. The oxidized products are unstable and spontaneously degrade to

release formaldehyde, which results in the removal of the methyl group from DNA

[35,36]. In 2006, a JmjC family protein, JHDM1A, was purified and shown to

catalyze the turnover of H3K36 methylation (H3K36me1/2) by Tsukada [37]. The

same group purified a homologous JmjC protein, JHDM2A, which generates

unmodified H3K9 by demethylating H3K9me2 [38]. JMJD2 proteins can attack

tri-methyl lysine residues of H3K9me3 and H3K36me3 in vivo, generating H3K9me1/2

and H3K36me1/2, respectively [39–42]. The mammalian JmjC protein

family is large, and it is possible that more histone demethylases will be

discovered.

Lysine Demethylases

Mechanism and function of LSD1

LSD1, also known as KIAA0601or BHC110, is a highly conserved protein

that demethylates H3K4me1/2 but can not attack trimethylated H3K4 (H3K4me3)

[32]. The structure of LSD1 includes three domains [43]. It contains a

C-terminal amine oxidase-like (AOL) domain, which is homologus to flavin

adenine dinucleotide (FAD)-dependent oxidases [44,45]. The AOL domain includes

two subdomains, an FAD-binding subdomain and a substrate-binding subdomain

[43]. The two subdomains form a large cavity that creates a catalytic center at

their interface. K661 is a crucial residue of the catalytic center, which is

hydrogen-bonded to the N5 atom of the FAD. LSD1 is different from other

FAD-dependent oxidases. It has a highly acidic flat surface, which serves as an

additional binding site at the entrance of the catalytic cavity. The cavity is

not capable of recognizing the histone substrates with different methylation

states. [43]. This supports the opinion that the inability of LSD1 to

demethylate trimethylated histone is due to its inherent chemical rather than

sterical mechanism [43,46]. Furthermore, LSD1 requires protonated nitrogen as

the substrate for the demethylation reaction, thus trimethylated histone is not

suitable for this enzyme [32]. In addition, LSD1 also contains an N-terminal

SWIRM domain, which is important for the stability of LSD1. The SWIRM domain is

bound to the AOL domain. The interaction between these domains forms a highly

conserved cleft, which may serve as an additional histone tail-binding site

[43]. The third domain is the Tower domain, which is inserted into the AOL

domain. The Tower domain is indispensable for the histone demethylase activity

of LSD1. By interacting with other proteins, the Tower domain may regulate the

catalytic activity of LSD1 through an allosteric effect [46]. In addition, the

Tower domain directly interacts with one of the LSD1-interacting proteins,

CoREST, and functions as a molecular bridge that connects LSD1 to its

nucleosomal substrates [43]. LSD1 is a flavin-containing amine oxidase. Basically, amine oxidase

catalyzes cleavage of the a-carbon bond of the substrate to generate an imine intermediate. The

intermediate is then hydrolyzed to form an aldehyde and amine via a

nonenzymatic process. During the whole process, the cofactor FAD is reduced to

FADH and then reoxidized by oxygen to produce hydrogen peroxide [47]. The

oxidation reaction catalyzed by LSD1 depends on the cofactor FAD, and generates

an unmodified lysine (H3K4) and a formaldehyde byproduct [32] (Fig. 1).In the catalytic cycle of LSD1, oxygen molecules acting as the

electron acceptors reoxydize FADH to FAD. Forneris et al.

provided a hypothesis that ferricenium may be reduced to ferrocene instead of

oxygen as electron acceptors [48]. However, other researchers have not

supported this hypothesis. Forneris also reported that LSD1 demethylates

H3K4me1/2 in presence of a second modification on the same peptide substrate.

Acetylation of H3K9 increases the catalytic activity of LSD1, whereas

phosphorylation of Ser10 inhabits the activity [49]. This result highlighted

the complexity of cross talk between different histone modifications.

Furthermore, LSD1 is specific for H3K4me1/2, whereas the androgen receptor

alters the specificity of LSD1 from H3K4 (H3K4me1/2) to H3K9 (H3K9me1/2) and is

responsible for demethylation of the H3K9me1/2 at androgen receptor target

genes such as prostate specific antigen (PSA) or kallikrein2,

thereby acting as a transcription activator instead of a transcription

repressor [33]. Although the function of LSD1 depends on the proteins

interacting with it, the relationship between LSD1 and the androgen receptor is

still not fully understood.

LSD1 associated factors

LSD1 was found previously in multiprotein complexes [50–53]. In 2004, Shi et al. reported that the complex containing

LSD1 catalyzes two enzymatic activities: a histone deacetylase (HDAC1 or 2) and

a histone demethylase [32]. LSD1 is associated with HDAC1/2, the SANT

domain-containing corepressor CoREST, and the PHD domain-containing protein

BHC80. HDAC and LSD1 may exist in the same complex to mediate negative

regulation. The complex may first eliminate the acetyl groups from acetylated

lysine residues and then remove the methyl group from H3K4 [54]. Recently, Lee

et al. reported that HDAC inhibitors diminish H3K4 demethylation by LSD1 in

vitro, which further proved an intimate link between the histone

demethylase and deacetylase [55]. CoREST enhances the ability of LSD1 to

reverse methylation and protects LSD1 from proteasomal degradation in vivo [56].

A possible mechanism is that CoREST binds to LSD1 and tethers it to the

nucleosome, bringing the amine oxidase domain close to the H3 tail. A recent

study supports this mechanism. It showed that LSD1-CoREST forms a structure

with the catalytic domain of LSD1 and the CoREST SANT2 domain. LSD1 recognizes

the H3 tail, and CoREST SANT2 domain interacts with DNA. Mutagenesis studies

show that disruption of the SANT2-DNA interaction diminishes demethylation of

nucleosomes by LSD1. The results suggest a mechanism by which DNA binding of

CoREST facilitates the histone demethylation of nucleosomes by LSD1 [57]. BHC80

has been shown to inhibit demethylation mediated by the LSD1-CoREST complex

[58]. In addition, LSD1 is also a part of the transcription activation complex

that includes the H3K4 methyltransferase MLL1 [59]. The presence of MLL1 and

LSD1 in the same complex suggests that the balance between methylated and

unmethylated H3K4 is important for the transcription regulation of gene. To understand

the function of LSD1 completely, additional factors interacting with LSD1 need

to be identified.

Mechanism and function of JmjC

domain proteins

The JmjC domain is conserved in various organisms and predicted to be

a metalloenzyme catalytic motif. Over 100 JmjC domain-containing enzymes have

been identified [60]. Three JmjC domain subfamilies that mediate histone

demethylation reactions have been identified, including the JHDM1, JHDM2 and

JMJD2 subfamilies. The catalytic mechanisms of JmjC domain proteins are all

hydroxylation reactions. JHDM1 only demethylates di- or mono-methylated H3K36

[37]. JHDM1 was shown to be a 2-oxoglutarate (2-OG)-Fe(II)-dependent

dioxygenase. Compared with LSD1, JHDM1 depends on Fe(II) and a-ketoglutarate as

cofactors to mediate hydroxylation-based demethylation and therefore does not

require protonated nitrogen [Fig. 2(A,B)]. However, it is not clear why

JHDM1 is unable to demethylate trimethylated histones. It may be a consequence

of limited substrate recognition or restricted potential of the catalytic

pocket to accommodate a histone lysine trimethyl state [37]. The second JmjC domain-containing histone demethylase JHDM2A was

purified and found to specifically demethylate H3K9(me1/2) [38] [Fig. 2(B)].

JHDM2A is associated with the androgen receptor (AR) and contributes to

AR-mediated gene activation, probably by keeping the promoter free of H3K9

methylation [38]. So JHDM2A links its function to hormone-dependent

transcriptional activation. JMJD2 subfamily is specific trimethyl lysine demethylase. The JMJD2

subfamily consists of four members: JMJD2A, JMJD2B, JMJD2C, and JMJD2D. JMJD2

family members contain the N-terminal JmjN domain, JmjC domain, plant

homeodomain (PHD) and Tudor domains [61]. The catalytic core region of JMJD2

mainly consists of JmjN and JmjC domains. The PHD domain comprises about 60

amino acid residues and belongs to the C4HC3-type zinc-finger class. Recent

studies demonstrate that the PHD domain can specifically recognize H3K4me3 [62–65]. Different structural features of the PHD finger are crucial for

the specificity of recognition. The Tudor domain is a 60-amino acid structure

motif. Studies have shown that the Tudor domain of JMJD2A can bind to H3K4me3,

H3K9me3, H3K36me3 and H4K20me2/3 [41,66,67]. It was also suggested that the

Tudor domain of the double-stranded break-sensing protein, 53BP1, can bind to

H3K79me2 [68]. So it was believed that the PHD and Tudor domains function as

methylated histone binding domain. JMJD2A (also named JHDM3A and KIAA0677) is a lysine

trimethyl-specific histone demethylase that catalyzes the demethylation of

H3-K9me3 and H3-K36me3, converting H3-K9/36me3 to H3-K9/36me2 but not

H3-K9/36me1 to unmodified lysine [41]. JMJD2A represses transcription by

interacting with the tumor suppressor Rb, histone deacetylases (HDACs), and the

corepressor N-CoR [69–71]. Due to the importance of Rb

protein in cell cycle, JMJD2A was reported to play an important role in cell

proliferation and oncogenesis. Similar to other JmjC domain proteins,

demethylation mediated by JMJD2A requires Fe(II) and a-ketoglutarate as

cofactors [42] [Fig. 2(C)]. Absence of a-ketoglutarate or

addition of the iron chelator deferoxamine (DFO; 250 mM) completely inhibited

the demethylation activity. Recently, it was reported that the structure of the

catalytic core region of JMJD2A mainly consists of several individual domains

(JmjN and JmjC domains) and structural motifs [72]. The JmjC domain has been

shown to fold into eight b-sheets, thereby forming an enzymatically active pocket that

coordinates Fe(II) and a-ketoglutarate. Three absolutely conserved amino-acid

residues within the JmjC domain bind to the Fe(II) cofactor and two water

molecules were replaced by two oxygen atoms from a-ketoglutarate [72]. JMJD2C, also known as GASC-1, directly demethylates H3K9me3 and

H3K9me2 in vitro and produces formaldehyde and H3K9me1. Since

methylation at H3K9 is correlated with chromatin structure, GASC1 might have a

physiologically important role in controlling heterochromatin formation and

maintenance [39]. Previously, GASC1 was found to be overexpressed in esophageal

squamous carcinoma [73]. Down-regulation of GASC1 expression inhibits cell

proliferation [39]. These results suggest that over-expression of JMJD2

proteins might contribute to the development of human cancer. The functions of JMJD2D and JMJD2B are still not completely clear.

JMJD2B has been shown to demethylate H3K9me3 at pericentric heterochromatin in

mammalian cells [40]. Mass spectrometry analysis revealed JMJD2D demethylates

H3K9me2/3. In summary, JMJD2 family members are histone demethylases whose

primary substrates are H3K9me3 and H3K36me3. The activity mediated by JmjC

domain family is shown in Fig. 2. The categories and sites of known

histone demethylases are summarized in Table 1.

Perspectives

The discovery of histone demethylases provided evidence that the

process of histone methylation is reversible. A small number of histone lysine residues

(H3K4me1/2, H3K36me1/2, and H3K9me1/2/3) have been shown to be substrates for a

limited number of demethylases. It is likely that demethylases targeting other

histone lysine residues will be discovered in the near future. The functions of

specific histone methylation sites are usually associated with other histone

modifications, such as acetylation and phosphorylation. The spatial and

temporal context of histone modifications seem to be important, and the

combined effect might contribute to the final biological outcome. To date, two families of histone lysine demethylases have been

identified, but their complete biological functions are not fully understood

during human development. Moreover, several diseases are linked to aberrant

histone methylation, such as cancer [74–80]. A

recent report showed that LSD1 might serve as a novel biomarker predictive for

prostate cancer with aggressive biology [81]. Just as DNA methyltransferase

(DNMT) is associated with tumor formation [82], histone demethylases might

represent inviting drug targets. Further structural information may provide

insights that can be exploited for therapeutic applications. Currently, researchers are at the early stages of understanding the

chemistry of how histone demethylases catalyze specific reactions and exhibit

substrate-selective activity. Whether these activities are modulated by other

homologous proteins is unclear, and is a subject of intensive investigation.

Researchers are also interested in exploring what signals trigger the

demethylation reaction, and how demethylation is controlled. Also, the

identification of new demethylases is underway. It is well known that histone deacetylase inhibitors have

anticancerous functions [83]. Interestingly, just like histone deacetylase inhibitors,

histone demethylase inhibitors have been identified recently. LSD1 has close

homology to monoamine oxidases (MAO), and Pargyline, an MAO inhibitor, was

identified as an inhibitor of LSD1 [57]. Furthermore, Lee reported that the

depression treatment tranylcypromine (brand name Parnate) also resulted in a

global increase in H3K4 methylation as well as transcriptional derepression of

two LSD1 target genes [84]. These observations shed new light on the study of

histone methylation modification, and may lead to the discovery of new

therapeutic drugs. In the future, the study of MAO inhibitors by themselves and

in combination with other known inhibitors of histone demethylases will provide

important information. The initial discovery of histone demethylases took nearly half a

century. Although the functions of histone demethylases are not yet fully

characterized, these enzymes impact chromosome formation and transcription

regulation. However, more work is needed to identify novel enzymes and to further

understand the dynamic nature of histone demethylases.

References

Jenuwein T, Allis CD. Translating the histone code. Science 2001, 293:

1074–1080

Strahl BD, Allis CD. The language of covalent histone modifications.

Nature 2000, 403: 41–45

Margueron R, Trojer P, Reinberg D. The key to development: interpreting

the histone code. Curr Opin Genet Dev 2005, 15: 163–176

Lachner M, Jenuwein T. The many faces of histone lysine methylation.

Curr Opin Cell Biol. 2002, 14: 286–298

Bannister AJ, Schneider R, Kouzarides T. Histone methylation: dynamic or

static. Cell 2002, 109: 801–806

Kouzarides T. Histone methylation in transcriptional control. Curr Opin

Genet Dev 2002, 12: 198–209

Fischle W, Wang Y, Allis CD. Histone and chromatin crosstalk. Curr Opin Cell

Biol. 2003, 15: 172–183

Martin C, Zhang Y. The diverse functions of histone lysine methylation.

Nat Rev Mol Cell Biol 2005, 6: 838–849

Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP et

al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is

linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 2003,

23: 4207–4218

Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van

Leeuwen F, Gottschling DE et al. The histone modification pattern of

active genes revealed through genome-wide chromatin analysis of a higher

eukaryote. Genes Dev 2004, 18: 1263–1271

Nielsen SJ, Schneider R, Bauer UM, Bannister AJ, Morrison A, OCarroll

D, Firestein R et al. Rb targets histone H3 methylation and HP1 to

promoters. Nature 2001, 412: 561–565

Reinberg D, Chuikov S, Farnham P, Karachentsev D, Kirmizis A, Kuzmichev

A, Margueron R et al. Steps toward understanding the inheritance of

repressive methyl-lysine marks in histones. Cold Spring Harb Symp Quant Biol

2004, 69: 171–182

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, 298: 1039–1043

Peters AH, Kubicek S, Mechtler K, OSullivan RJ, Derijck AA,

Perez-Burgos L, Kohlmaier A et al. Partitioning and plasticity of

repressive histone methylation states in mammalian chromatin. Mol Cell 2003,

12: 1577–1589

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, 12: 1591–1598

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, 18: 1251–1262

Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre

NC, Schreiber SL et al. Active genes are tri-methylated at K4 of histone

H3. Nature 2002, 419: 407–411

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, 12: 475–487

Lachner M, Sengupta R, Schotta G, Jenuwein T. Trilogies of histone

lysine methylation as epigenetic landmarks of the eukaryotic genome. Cold

Spring Harb Symp Quant Biol 2004, 69: 209–218

Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T,

Yamada M, Schneider R et al. Histone deimination antagonizes arginine

methylation. Cell 2004, 118: 545–553

Wang Y, Wysocka J, Sayegh J, Lee YH, Perlin JR, Leonelli L, Sonbuchner

LS et al. Human PAD4 regulates histone arginine methylation levels via

demethylimination. Science 2004, 306: 279–283

Byvoet P, Shepherd GR, Hardin JM, Noland BJ. The distribution and

turnover of labelled methyl groups in histone fractions of cultured mammalian

cells. Arch Biochem Biophys 1972, 148: 558–567

Duerre JA, Lee CT. In vivo methylation and turnover of rat brain

histones. J Neurochem 1974, 23: 541–547

Borun TW, Pearson D, Paik WK. Studies of histone methylation during the

HeLa S-3 cell cycle. J Biol Chem 1972, 247: 4288–4298

Annunziato AT, Eason MB, Perry CA. Relationship between methylation and

acetylation of arginine-rich histones in cycling and arrested HeLa cells.

Biochemistry 1995, 34: 2916–2924

Allis CD, Bowen JK, Abraham GN, Glover CV, Gorovsky MA. Proteolytic

processing of histone H3 in chromatin: a physiologically regulated event in Tetrahymena

micronuclei. Cell 1980, 20: 55–64

Ahmad K, Henikoff S. The histone variant H3.3 marks active chromatin by

replication-independent nucleosome assembly. Mol Cell 2002, 9: 1191–1200

Kim S, Benoiton L, Paik WK. Epsilon-Alkyllsinase. Purification and

properties of the enzyme. J Biol Chem 1964, 239: 3790–3796

Paik WK, Kim S. Enzymatic demethylation of calf thymus histones. Biochem

Biophys Res Commun 1973, 51: 781–788

Paik WK, Kim S. Epsilon-alkyllysinase. New assay method, purification

and biological significance. Arch Biochem Biophys 1974, 165: 369–378

Saccani S, Natoli G. Dynamic changes in histone H3 Lys 9 methylation

occurring at tightly regulated inducible inflammatory genes. Genes Dev 2002,

16: 2219–2224

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, 119: 941–953

Metzger E, Wissmann M, Yin N, Muller JM, Schneider R, Peters AH, Gunther

T et al. LSD1 demethylates repressive histone marks to promote

androgen-receptor-dependent transcription. Nature 2005, 437: 436–439

Trewick SC, McLaughlin PJ, Allshire RC. Methylation: lost in

hydroxylation? EMBO Rep 2005, 6: 315–320

Falnes PO, Johansen RF, Seeberg E. AlkB-mediated oxidative demethylation

reverses DNA damage in Escherichia coli. Nature 2002, 419: 178182

Trewick SC, Henshaw TF, Hausinger RP, Lindahl T, Sedgwick B. Oxidative

demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature

2002, 419: 174–178

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, 439: 811–816

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, 125: 483–495

Cloos PA, Christensen J, Agger K, Maiolica A, Rappsilber J, Antal T,

Hansen KH et al. The putative oncogene GASC1 demethylates tri- and

dimethylated lysine 9 on histone H3. Nature 2006, 442: 307–311

Fodor BD, Kubicek S, Yonezawa M, OSullivan RJ, Sengupta R, Perez-Burgos

L, Opravil S et al. Jmjd2b antagonizes H3K9 trimethylation at

pericentric heterochromatin in mammalian cells. Genes Dev 2006, 20: 1557–1562

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, 442: 312–316

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, 125: 467–481

Chen Y, Yang Y, Wang F, Wan K, Yamane K, Zhang Y, Lei M. Crystal

structure of human histone lysine-specific demethylase 1 (LSD1). Proc Natl Acad

Sci USA 2006, 103: 13956–13961

Fraaije MW, Van Berkel WJH, Benen JAE, Visser J, Mattevi A. A novel

oxidoreductase family sharing a conserved FAD-binding domain. Trends Biochem

Sci 1998, 23: 206–207

Fraaije MW, Mattevi A. Flavoenzymes: diverse catalysts with recurrent

features. Trends Biochem Sci 2000, 25: 126–132

Stavropoulos P, Blobel G, Hoelz A. Crystal structure and mechanism of

human lysine-specific demethylase-1. Nat Struct Mol Biol 2006, 13: 626–632

Binda C, Mattevi A, Edmondson DE. Structure-function relationships in

flavoenzyme-dependent amine oxidations: a comparison of polyamine oxidase and

monoamine oxidase. J Biol Chem 2002, 277: 23973–23976

Forneris F, Binda C, Vanoni MA, Mattevi A, Battaglioli E. Histone

demethylation catalysed by LSD1 is a flavin-dependent oxidative process. FEBS

Lett 2005, 579: 2203–2207

Forneris F, Binda C, Vanoni MA, Battaglioli E, Mattevi A. Human histone

demethylase LSD1 reads the histone code. J Biol Chem 2005, 280: 41360–41365

Shi Y, Sawada J, Sui G, Affar el B, Whetstine JR, Lan F, Ogawa H et

al. Coordinated histone modifications mediated by a CtBP co-repressor

complex. Nature 2003, 422: 735–738

Humphrey GW, Wang Y, Russanova VR, Hirai T, Qin J, Nakatani Y, Howard

BH. Stable histone deacetylase complexes distinguished by the presence of SANT

domain proteins CoREST/kiaa0071 and Mta-L1. J Biol Chem 2001, 276: 6817–6824

Hakimi MA, Bochar DA, Chenoweth J, Lane WS, Mandel G, Shiekhattar R. A

core-BRAF35 complex containing histone deacetylase mediates repression of

neuronal-specific genes. Proc Natl Acad Sci USA 2002, 99: 7420–7425

Hakimi MA, Dong Y, Lane WS, Speicher DW, Shiekhattar R. A candidate

X-linked mental retardation gene is a component of a new family of histone

deacetylase-containing complexes. J Biol Chem 2003, 278: 7234–7239

Forneris F, Binda C, DallAglio A, Fraaije MW, Battaglioli E, Mattevi A.

A highly specific mechanism of histone H3-K4 recognition by histone demethylase

LSD1. J Biol Chem 2006, 281: 35289–35295

Lee MG, Wynder C, Bochar DA, Hakimi MA, Cooch N, Shiekhattar R.

Functional interplay between histone demethylase and deacetylase enzymes. Mol

Cell Biol 2006, 26: 6395–6402

Lee MG, Wynder C, Cooch N, Shiekhattar R. An essential role for CoREST

in nucleosomal histone 3 lysine 4 demethylation. Nature 2005, 437: 432–435

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, 23: 377–387

Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1

histone demethylase activity by its associated factors. Mol Cell 2005, 19: 857–864

Nakamura T, Mori T, Tada S, Krajewskl W, Rozovskala T, Wassell R, Dubols

G et al. ALL-1 is a histone methyltransferase that assembles a

supercomplex of proteins involved in transcriptional regulation. Mol Cell 2002,

10: 1119–1128

Clissold PM, Ponting CP. JmjC: cupin metalloenzyme-like domains in

jumonji, hairless and phospholipase A2beta. Trends Biochem Sci 2001, 26: 7–9

Holbert MA, Marmorstein R. Structure and activity of enzymes that remove

histone modifications. Curr Opin Struct Biol 2005, 15: 673–680

Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ.

Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD

finger of NURF. Nature 2006, 442: 91–95

Pena PV, Davrazou F, Shi X, Walter KL, Verkhusha VV, Gozani O, Zhao R et

al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain

of ING2. Nature 2006, 442: 100–103

Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, Kauer M et

al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with

chromatin remodeling. Nature 2006, 442: 86–90

Shi X, Hong T, Walter KL, Ewalt M, Michishita E. Huang T, Carney D et

al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene

repression. Nature 2006, 442: 96–99

Kim J, Daniel J, Espejo A, Lake A, Krishna M, Xia L, Zhang Y et al.

Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep

2006, 7: 397–403

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, 312:

748–751

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, 432: 406–411

Yoon HG, Chan DW, Huang ZQ, Li J, Fondell JD, Qin J, Wong J.

Purification and functional characterization of the human N-CoR complex: the

roles of HDAC3, TBL1 and TBLR1. EMBO J 2003, 22: 1336–1346

Gray SG, Iglesias AH, Lizcano F, Villanueva R, Camelo S, Jingu H, Teh BT

et al. Functional characterization of JMJD2A, a histone deacetylase- and

retinoblastoma-binding protein. J Biol Chem 2005, 280: 28507–28518

Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein

and is involved in repression of the human transcription factor achaete

scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol 2005, 25: 6404–6414

Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson

M et al. Structural insights into histone demethylation by JMJD2 family

members. Cell 2006, 125: 691–702

Yang ZQ, Imoto I, Fukuda Y, Pimkhaokham A, Shimada Y, Imamura M, Sugano

S et al. Identification of a novel gene, GASC1, within an amplicon at

9p2324 frequently detected in esophageal cancer cell lines. Cancer Res 2000,

60: 4735–4739

Okaka Y, Feng Q, Lin Y, Jiang Q, Li Y, Coffield VM, Su L et al.

hDOT1L links histone methylation to leukemogenesis. Cell 2005, 121: 167–178

Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta

G, Bonaldi T et al. Loss of acetylation at Lys 16 and trimethylation at

Lys 20 of histone H4 is a common hallmark of human cancer. Nat Genet 2005, 37:

391–400

Hake SB, Xiao A, Allis CD. Linking the epigenetic language of covalent

histone modifications to cancer. Br J Cancer 2004, 90: 761–769

Schneider R, Bannister AJ, Kouzarides T. Unsafe SETs: histone lysine

methyltransferases and cancer. Trends Biochem Sci 2002, 27: 396–402

Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda

MG, Ghosh D et al. The polycomb group protein EZH2 is involved in

progression of prostate cancer. Nature 2002, 419: 624–629

Jaju RJ, Fidler C, Haas OA, Strickson AJ, Watkins F, Clark K, Cross NC et

al. A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de

novo childhood acute myeloid leukemia. Blood 2001, 98: 1264–1267

Hess JL. MLL: A histone methyltransferase disrupted in leukemia. Trends

Mol Med 2004, 10: 500–507

Kahl P, Gullotti L, Heukamp LC, Wolf S, Friedrichs N, Vorreuther R,

Solleder G et al. Androgen receptor coactivators lysine-specific histone

demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate

cancer recurrence. Cancer Res 2006, 66: 11341–11347

Fang JY, Lu R, Mikovits JA, Cheng ZH, Zhu HY, Chen YX. Regulation of

hMSH2 and hMLH1 expression in the human colon cancer cell line SW1116 by DNA

methyltransferase 1. Cancer Lett 2006, 233: 124–130

Fang JY. Histone deacetylase inhibitors, anticancerous mechanism and

therapy for gastrointestinal cancers. J Gastroenterol Hepatol 2005, 20: 988–994

Lee MG, Wynder C, Schmidt DM, McCafferty DG, Shiekhattar R. Histone H3

Lysine 4 demethylation is a target of nonselective antidepressive medications.

Chem Biol 2006, 13: 563–567