Systems Biology in Toxicology and Environmental …...48 Systems Biology in Toxicology and...

43Systems Biology in Toxicology and Environmental Healthhttp://dx.doi.org/10.1016/B978-0-12-801564-3.00003-1

Copyright © 2015 Elsevier Inc. All rights reserved.

CHAPTER 3

Systems Biology and the EpigenomeMichele M. Taylor, Susan K. Murphy

ContentsIntroduction 43DNA Methylation 44Molecular Basis of DNA Methylation 44Posttranslational Histone Modifications 46Chromatin 50References 52

INTRODUCTIONEpigenetics is a continually evolving, emergent branch of biology initially defined by Conrad Waddington in 1942 as the mechanism by which genes bring about pheno-type [1]. This definition was expanded in 1987 by Robin Holliday to include patterns of DNA methylation that result in corresponding gene activity [2]. Currently, epi-genetics can be defined as the study of heritable changes in gene expression that are not attributable to alterations of the genome sequence. Epigenetics has been accepted as a biological function for many years. During development, the zygote starts in a totipotent state from which the dividing cells progressively differentiate into a myriad of cell types of subsequently narrower potential. This allows for vastly different pheno-types of cells in an individual, all of which carry an identical genome (an eye cell is different than a neural or skin cell). The genome is the complete set of genes or genetic material present in a cell. The genome includes both genes and noncoding sequences of the DNA. The epigenome includes both the histone-associated chroma-tin assembly (histones, DNA binding proteins, and the DNA) along with the patterns of genomic DNA methylation, thereby conferring the three-dimensional structure and compaction of the genomic material inside the cell nucleus. DNA methylation and histone modifications are the most extensively studied epigenetic modifications. In this chapter, we present an overview of currently understood epigenetic mecha-nisms as they relate to the regulation of single genes and larger chromosomal domains within the entirety of the epigenome.

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DNA METHYLATIONFirst recognized in 1948 and now commonly referred to as the “fifth base” of DNA [3], 5-methylcytosine (5-mC) generated considerable interest and debate as researchers sought to realize its biological significance (for a review, see Ref. [4]). It is now well estab-lished that DNA methylation imparts both short- and long-term effects on gene expres-sion [5,6]. Specifically, DNA methylation can elicit long-term epigenetic silencing of particular sequences in somatic cells such as transposons, imprinted genes, and pluripo-tency-associated genes [5]. DNA methylation is an integral part of numerous cellular processes, including embryonic development, genomic imprinting, preservation of chro-mosome stability, and X chromosome inactivation [7–10]. Researchers have gained insight about DNA methylation, including the mechanisms by which it occurs and pref-erential target sequences. In-depth characterization of DNA methylation (and histone modifications) has also come from the results of the Human Roadmap Epigenomics project that has utilized high-throughput sequencing technologies to define epigenomic information across different tissue types and at different life stages in humans [11].

Given its fundamental role in transcriptional regulation, it follows that perturbation of these epigenetic marks or the enzymatic machinery that adds or removes these marks may lead to complications including developmental disorders or cancer [12]. Indeed, two independent research laboratories linked DNA methylation status and cancer in seminal papers published in 1983 [13,14]. Feinburg and Vogelstein first reported reduced DNA methylation of specific genes in human colon cancer cells compared with normal tissue [14]. Months later, Gama-Sosa et al. showed global reductions in 5-mC content of DNA obtained from various human malignancies, particularly metastases [13]. These preliminary studies paved the way for increased awareness of the importance of DNA methylation in cancer and portended the role it plays in other disorders and diseases.

MOLECULAR BASIS OF DNA METHYLATIONDNA methylation is the process by which the covalent addition of a methyl group (-CH3) to the 5′ carbon of a cytosine moiety generates 5-mC. DNA methylation pre-dominantly occurs in the context of cytosines that precede guanines, also known as 5′-CpG-3′ dinucleotides, or CpG sites [15]. It has also been shown to occur in CpA, CpC and CpT sequences in mammalian cells [16–18], and in fact, approximately 25% of all DNA methylation in embryonic stem cells is in nonCpG context [10]. CpGs are highly underrepresented in the genome, yet 70% of these are methylated. The remaining are unmethylated and often found in “CpG islands.” CpG islands are regions of the genome that are at least 200 base pairs in length with greater than 50% G and C contents and a ratio of observed to expected CpG frequency of at least 0.6 [16]. CpG islands are enriched in the 5′ promoter and/or exon regions of genes. Nearly 60% of human pro-moters are characterized by a high CpG content [19]. However, CpG density by itself

Systems Biology and the Epigenome 45

does not influence gene expression. Instead, regulation of transcription often depends on DNA methylation status. In general, promoter-associated CpG islands are unmethylated at transcriptionally active genes; in contrast, methylation is typically associated with gene silencing [12,15,16]. The first demonstration that gene silencing occurs in diploid somatic cells by methylation (separate from X chromosome inactivation) was at the reti-noblastoma tumor suppressor gene [12]. Since then, many other tumor suppressor genes have also been found to be subjected to silencing by epigenetic mechanisms [16].

The methylation reaction that adds the 5′ cytosine moiety is catalyzed by a class of enzymes called DNA methyltransferases (DNMTs). These enzymes transfer a methyl group to the 5′ position of the cytosine ring, taking it from the universal methyl group donor S-adenosylmethionine (SAM) (Figure 1).

There are five members of the DNMT family, including DNMT1, DNMT2, DNMT3a, DNMT3b, and DNMT3L [20]. DNMT1, DNMT3a, and DNMT3b inter-act with cytosine nucleotides to generate the global methylation pattern, or methylome.

Figure 1 Schematic of epigenetic modifications. DNA strands are wrapped around histone octamers, forming nucleosomes that organize into chromatin. Chromatin forms the building blocks of a chromo-some. Reversible histone modifications occur at multiple amino acid residues via methylation, acetyla-tion, phosphorylation, ubiquitination, and sumoylation. DNA methyltransferases (DNMTs) transfer a methyl group from the methyl group donor, S-adenosylmethionine (SAM), to the 5′ position of the cytosine ring.


These enzymes are further classified as either de novo (DNMT3a and DNMT3b) or maintenance (DNMT1) enzymes. DNMT2 and DNMT3L do not function as cytosine methyltransferases [16]. Possessing homology to DNMT3a and DNMT3b, DNMT3L stimulates de novo DNA methylation activity via DNMT3a by increasing the binding affinity to SAM [21] and also mediates transcriptional gene repression by recruiting his-tone deacetylase 1 (discussed below) [22–24]. DNMT2 does not possess the N-terminal regulatory domain that the other DNMTs share. It is thought to be involved in DNA damage response and repair [25].

DNMT1 is responsible for bestowing the methylation pattern of the parental template DNA strand to the newly synthesized DNA daughter strand as DNA replication occurs, prior to cell division. This ensures that both resulting cells have the same methylome [16]. This activity is essential for proper cell function and for the maintenance of methylation status across somatic cell division. De novo DNA methylation during embryogenesis and germ cell development is carried out by DNMT3a and DNMT3b [26].

It was discovered that 5-mC can be oxidized by ten-eleven translocation (TET) pro-teins to form 5-hydroxymethylcytosine (5-hmC), prompting a paradigm shift in our current understanding of the mechanism by which DNA methylation is reversed. 5-hmC, which is structurally similar to 5-mC, was initially discovered in cerebellar neurons as well as in embryonic stem cells [27–29]. Other mechanisms that replace 5-mC with unmethylated cytosine have also been identified and involve the activity of the TET enzymes to form 5-hmC, the deamination of 5-mC or 5-hmC through the activation induced deaminase proteins, and finally base excision repair by the DNA glycosylase family of enzymes [30]. 5-mC can also be converted by the TET proteins to 5-carboxyl-cytosine and 5-formylcytosine in the process of DNA demethylation [31]. The distinct roles of DNMT family members have been the focus of continued research and the discovery of potential multifunctionality and/or epigenetic crosstalk among them has been reported [32]. In fact, it has been demonstrated that DNMT3A and DNMT3B can function in vitro as both DNA methyltransferases and dehydroxymethylases [33].

POSTTRANSLATIONAL HISTONE MODIFICATIONSPosttranslational histone modifications are another type of epigenetic modification (Figure 2).

The amino terminal tails of the four core histones, H2A, H2B, H3, and H4, are labile and receptive to a number of modifications, including acetylation, methylation, phos-phorylation, ubiquitination, and sumoylation [34,35]. Histones are tightly packaged in globular cores with N-terminal unstructured tails that protrude outward and these tails are targets of histone-modifying enzymes [36]. When fully extended, the N termini of histone tails can extend well beyond the super helical duplicate turns of DNA of the nucleosome [36]. The histone tails are exceedingly rich in lysine residues that are highly


positively charged at physiological pH [37]. The positive charge associated with lysine allows it to bind tightly to the negatively charged DNA, which condenses nucleosomes and forms a closed chromatin structure that is inaccessible to transcription factors. His-tone modifications, a form of posttranslational modification (PTM), are essential for controlling both chromatin structure and function which then impacts DNA-associated processes such as transcription [38] and chromosomal organization [35,36,39]. The two most prevalent PTMs are acetylation and methylation of lysine residues at histone tails along euchromatin and heterochromatin [39]. Histone lysine acetylation is catalyzed by histone acetyltransferases (HATs) and the presence of the acetyl groups neutralizes the positive charge of the histone tail that in turn decreases the affinity of the histones for the negatively charged DNA. This loosens the association between the histones and DNA, thus facilitating access of transcription factors to promoter regions and consequently increasing transcriptional activity [40–43]. A positive relationship between locus-specific acetylation and transcriptional activity has been previously demonstrated [44–46].

Histone acetylation was the first epigenetic modification to be correlated with tran-scriptional regulation [35,47–50]. However, it was not until the discovery that coactiva-tor complexes could function as HATs that a definitive link between chromatin function and acetylation was established [51–53]. Gene activation versus transcriptional repression is accomplished through alternation between HAT and histone deacetylase (HDAC)

Figure 2 Nucleosome structure and sites of histone tail modification.


activities, respectively [54]. These enzymes typically function within large multiprotein complexes that regulate chromatin in highly specific ways. HATs transfer the acetyl group from acetyl-coenzyme A (CoA) to the amino group of lysine residues with CoA as the resultant product [43]. Research suggests that lysine acetylation also provides a site for protein–protein interactions such as the acetyl lysine-binding bromodomain [55–58], resulting in a transcriptionally permissive euchromatin conformation. There are three main families of HATs that have a conserved acetyl-CoA binding site: the Gcn5-related N-acetyltransferases (GNATs), MYST, and p300/CBP [59,60]. The GNAT family members are characterized by the presence of a bromodomain that acetylates lysine resi-dues on histones H2B, H3, and H4 [61]. The MYST family, named for the four members MOZ, Ybf 2 (Sas3), Sas2, and Tip60, acetylate lysine residues on histones H2A, H3, and H4. Lysines on all four histones are substrates for acetylation by p300/CBP.

The reverse reaction, catalyzed by HDACs or lysine deacetylases (KDACs), increases the positive charge on histone tails and hinders the transcriptional potential of the under-lying gene via tight binding to the negatively charged backbone of the DNA. In fact, it is well known in a variety of biological systems that transcriptionally repressed loci are associated with deacetylated histones [62–64]. There are many HDACs that make up four different groups according to function and sequence homology to yeast proteins. The two primary groups, 1 and 2, contain members that are considered classical zinc-dependent histone deacetylases. Group 1 includes HDACs 1, 2, 3, and 8. HDACs 1, 2, and 8 are local-ized primarily in the nucleus, while HDAC3 is found in the cytoplasm, nucleus, and is also membrane-associated. Group 2 HDACs (HDAC 4, 5, 6, 7, 9, and 10) are transported in and out of the nucleus in response to specific signals [65,66]. Lysine deacetylation by these two groups of HDACs plays an integral role in transcriptional inactivation [67].

Histone methylation has been described as the central, distinguishing, epigenetic pat-tern related to gene activity [34,68,69]. In contrast to histone hyperacetylation, which is positively correlated with actively transcribed genes [70], histone methylation is associ-ated with transcriptional activation, inactivation, and silencing of genomic regions depending on the target amino acid [39,71]. It has been correlated with cellular func-tions such as DNA replication and DNA repair. Among these, transcriptional activation and repression are the most studied [67]. Histones are exclusively methylated on either lysine (K) or arginine (R) residues of the H3 and H4 histone tails [72]. However, histone methylation is most commonly observed on lysine residues (Figure 2). Methylation modifies chromatin conformation, not by altering the charge of lysine residues, as in histone acetylation, but by promoting or restricting the docking of chromatin associated proteins and transcription factors. In general, there is an enrichment of histone methylation in activated gene regions, particularly at the well-studied K4, K36, or K79 [38,69,73–75]. On the other hand, enrichment of methylation at lysine residues K9, K20, or K27 has been implicated in gene inactivation or silencing [34,35,76]. Lysine and arginine residues each contain amino groups that confer basic, hydrophobic characteristics. Lysine


is able to be mono-, di-, or trimethylated while arginine may be both monomethylated and symmetrically or asymmetrically dimethylated. Methyl group attachment to either residue requires distinct enzymes along with various substrates and cofactors. Methyla-tion of arginine residues involves a complex, including protein arginine methyltransfer-ase while lysine methylation requires a specific histone methyltransferase.

Histone methyltransferases are a class of enzymes that transfer methyl groups from SAM onto lysine or arginine residues of the H3 and H4 histones. Many of the covalent modifications that occur on the histone tails are enzymatically reversible. For instance, phosphorylation and acetylation of residues can be reversed by phosphatases and deacet-ylases, respectively. This allows the cell to quickly respond to alterations within the cel-lular milieu by rapidly changing the gene regulatory machinery. However, histone methylation was previously considered enzymatically irreversible. First discovered in the 1960s, the methylation of histone lysine residues had been considered static because the half-life approximated that of the histones themselves [77–79]. Discovery of the histone demethylase lysine-specific demethylase 1 (LSD1) in 2004 [80] provided the first dem-onstration that the methylation of histone lysine residues is in fact dynamic. Since then, several important lysine residues on both core and linker histones have been cataloged as methylation sites and the enzymes that catalyze the addition or removal of methyl groups have been identified [81]. Two enzyme families, lysine methyltransferases (KMTs) and demethylases (KDMs) regulate histone lysine methylation status. KMTs are now known to also target nonhistone substrates (for a review, see Refs [82,83]).

There are two main classes of KDMs that both employ oxidative mechanisms, LSDs, the flavin-dependent subfamily and the 2-oxoglutarate-(2OG) dependent JmjC sub-family [84,85]. LSD demethylases can demethylate mono- and dimethylated lysine resi-dues. The JmjC subfamily of demethylases can demethylate mono-, di-, and trimethylated histone lysine residues.

The abundance of lysine and arginine residues on histone tails combined with the numerous potential combinatorial methylation patterns offers enormous regulatory potential. Given that histone demethylases are involved in normal and pathological cel-lular processes, their discovery has already had a notable impact on the field of epi-genetics. Indeed, now that it has been established that histone methylation is reversible, researchers have been inspired to broaden the search for other demethylases [29], which offer promising therapeutic targets or epigenetic treatments to explore.

Histone phosphorylation is another form of posttranslation modification involved in transcription regulation as well as chromatin compaction (for a review, see Ref. [86]). Each of the four nucleosomal histone tails has acceptor sites which can be phosphory-lated by protein kinases and dephosphorylated by phosphatases. Phosphorylation at ser-ine, threonine, and tyrosine residues constitutes the signature or “histone code” which is deciphered by reader proteins that contain distinct binding motifs specific for each modi-fication [87,88]. Several phosphorylated histones are involved with gene expression,


particularly regulation of proliferative genes. For instance, phosphorylation at H3S10 and H2BS32 has been correlated with regulation of epidermal growth factor gene transcrip-tion and linked to expression of protooncogenes c-fos, c-jun, and c-myc [89–91]. Further, phosphorylation of H3S10 has been associated with H3 acetylation, strongly implicating such modifications in transcription activation [92]. Histone phosphorylation also plays a role in chromatin compaction. Originally discovered to be associated with chromosome compaction during mitosis and meiosis, H3 phosphorylation is also involved in chroma-tin relaxation and regulation of gene expression [93–95].

Several other posttranslation modifications of histone tails, including propionylation, sumoylation, and ubiquitination are also known and crosstalk between different types of histone modifications act to converge in a combinatorial manner to fine-tune gene expression according to changing environmental signals.

CHROMATINChromatin refers to the complex assemblage of DNA as well as histone proteins that organize the genome. The genome is approximately 2 m long. Yet remarkably, these large amounts of DNA are packaged inside the nucleus of cells, the average diameter of which is only 6 µm. Spooling of DNA around histone proteins creates nucleosomes, the basic functioning unit of chromatin (Figure 2). This is the first of many stages of compaction that fits the DNA into the nucleus in an organized manner. Nucleosomes consist of approximately 147 base pairs of DNA wrapped around a core that contains two copies each of histones H2A, H2B, H3, and H4. The linker histone H1 associates with DNA between nucleosomes, stabilizing it and facilitating the assembly of higher order chroma-tin structure. While core histones are required for chromatin and chromosome assembly, linker histones are not [96,97]. Binding of linker histones prompts slight rearrangement of the core histone interactions. Consequently, their removal represents a likely entry point for destabilizing both the local and higher order chromatin structures and altering core histone-DNA interactions [43]. Despite the requirement for substantial genome compaction, genes and regulatory regions must be accessible for transcription, and pro-cesses such as replication and repair must be allowed to occur. Therefore, genome orga-nization is tightly regulated, cell-type specific and labile. Chromatin regulation ensures correct spatial and temporal gene activation at multiple levels. Those mechanisms of regu-lation that are transmitted through cell divisions are termed epigenetic. DNA itself can undergo modification as was described earlier, and so can the amino acids in the N-terminal tails of the histone proteins that protrude outward from the core nucleosome. Molecular modification of the histone tails can directly affect the chromatin packaging state and act as docking sites for writer or reader proteins that preferentially bind a spe-cific sequence of DNA within the chromatin, in the first of many stages of compaction.

In a dividing cell, chromatin exists as transcriptionally inactive heterochromatin or transcriptionally permissive euchromatin (Table 1) [34,39].


As depicted in Figure 3, heterochromatin exists in a closed conformation where DNA is condensed and tightly wrapped around the associated histones and is inac-cessible to transcription factors and chromatin-associated proteins [39]. Conversely, euchromatin exists in an open, relaxed conformation in which the DNA is accessi-ble [39,98,99]. The gene regions within heterochromatin consist primarily of repeti-tive elements as well as repressed genes that are involved in morphogenesis, differentiation (imprinting or X chromosome inactivation) [50,100], or chromo-somal stability [98,99,101].

Figure 3 Schematic representation of the dynamic, reversible changes in chromatin organization which impact gene expression. (A) Genes are poised for expression (turned on) when chromatin is open and (B) they are repressed (turned off ) when chromatin is condensed.

Table 1 Epigenetic Modifications Determine Chromatin Conformation Status. DNA Methylation and Histone Modifications Impart Either Gene Silencing or Activation

Heterochromatin Euchromatin

Chromatin features

DNA sequence Repetitive elements Gene rich

Structure Condensed, closed, inaccessible

Less condensed, open, accessible

Activity DNA expression silenced

Active DNA expression

Epigenetic markers

DNA methylation Hypermethylated Hypomethylated

Histone acetylation Hypoacetylated at H3 and H4

Hyperacetylated at H3 and H4

Histone methylation H3K27me2, H3K27me3, H3K9me2, H3K9me3

H3K4me2, H3K4me3, H3K9me1


Chromosomal territories include heterochromatin, chromatin loops, and other higher-order chromatin fibers that incorporate interchromosomal domains interspersed throughout. It is well known that gene expression is controlled by cis regulatory elements located in the same region of the chromosome [102]. However, interchromosomal inter-actions also regulate gene activity via trans regulators [103,104]. Moreover, these inter-chromosomal interactions may also occur with the central portions of chromosomal territories, such as euchromatin loops migrate and interact at the surface of nearby ter-ritories [105,106]. In addition, long-range interactions between chromosomal regions that are separated by more than 105 base pairs have also been studied using two novel techniques, chromosome conformation capture and RNA-TRAP [107,108,109]. These findings have made it increasingly apparent that nuclear architecture and chromatin geography factor in the regulation of gene expression offer new insights into the com-plexity of gene regulation [107]. Indeed, the function of chromatin extends beyond DNA compaction and regulation of genetic information. The dynamics of epigenetic modifica-tions and chromatin states guide the specifics of gene regulation as well as the overall structure and thus function of the genome, orchestrating cellular behavior to bring about phenotype [34,39,110], much as Conrad Waddington had envisioned in the 1940s.

REFERENCES [1] Waddington CH. Endeavour 1942;1:18–20. [2] Holliday R. The inheritance of epigenetic defects. Science 1987;238:163–70. [3] Doerfler W, Toth M, Kochanek S, Achten S, Freisem-Rabien U, Behn-Krappa A, et al. Eukaryotic

DNA methylation: facts and problems. FEBS Lett 1990;268:329–33. [4] Weissbach A. A chronicle of DNA methylation (1948–1975). EXS 1993;64:1–10. [5] Li G, Reinberg D. Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev

2011;21:175–86. [6] Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science 2010;330:612–6. [7] Efstratiadis A. Parental imprinting of autosomal mammalian genes. Curr Opin Genet Dev 1994;4:265–80. [8] Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993;366:362–5. [9] Hackett JA, Surani MA. DNA methylation dynamics during the mammalian life cycle. Philos Trans

R Soc Lond B Biol Sci 2013;368:20110328. [10] Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA

methylomes at base resolution show widespread epigenomic differences. Nature 2009;462:315–22. [11] Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of

111 reference human epigenomes. Nature 2015;518:317–30. [12] Esteller M. Epigenetics in cancer. N Engl J Med 2008;358:1148–59. [13] Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, et al. The

5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 1983;11:6883–94. [14] Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their

normal counterparts. Nature 1983;301:89–92. [15] Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol 2010;28:1057–68. [16] Kulis M, Esteller M. DNA methylation and cancer. Adv Genet 2010;70:27–56. [17] Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is

prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000;97:5237–42.

[18] Pinney SE. Mammalian non-CpG methylation: stem cells and beyond. Biology (Basel) 2014;3:739–51.


[19] Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006;103:1412–7.

[20] Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. Chembiochem 2011;12:206–22.

[21] Kareta MS, Botello ZM, Ennis JJ, Chou C, Chedin F. Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J Biol Chem 2006;281:25893–902.

[22] Chedin F, Lieber MR, Hsieh CL. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci USA 2002;99:16916–21.

[23] Deplus R, Brenner C, Burgers WA, Putmans P, Kouzarides T, de Launoit Y, et al. Dnmt3L is a transcriptional repressor that recruits histone deacetylase. Nucleic Acids Res 2002;30:3831–8.

[24] Aapola U, Liiv I, Peterson P. Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity. Nucleic Acids Res 2002;30:3602–8.

[25] Subramaniam D, Thombre R, Dhar A, Anant S. DNA methyltransferases: a novel target for prevention and therapy. Front Oncol 2014;4:80.

[26] Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010;11:204–20.

[27] Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009;324:930–5.

[28] Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009;324:929–30.

[29] Kriaucionis S, Tahiliani M. Expanding the epigenetic landscape: novel modifications of cytosine in genomic DNA. Cold Spring Harb Perspect Biol 2014;6:a018630.

[30] Li CJ. DNA demethylation pathways: recent insights. Genet Epigenet 2013;5:43–9. [31] Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine

to 5-formylcytosine and 5-carboxylcytosine. Science 2011;333:1300–3. [32] Murr R. Interplay between different epigenetic modifications and mechanisms. Adv Genet

2010;70:101–41. [33] Chen CC, Wang KY, Shen CK. The mammalian de novo DNA methyltransferases DNMT3A and

DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases. J Biol Chem 2012;287: 33116–21.

[34] Kouzarides T. Chromatin modifications and their function. Cell 2007;128:693–705. [35] Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by

linked binding modules. Nat Rev Mol Cell Biol 2007;8:983–94. [36] Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome

core particle at 2.8 Å resolution. Nature 1997;389:251–60. [37] Urnov FD, Wolffe AP. Above and within the genome: epigenetics past and present. J Mammary

Gland Biol Neoplasia 2001;6:153–67. [38] Koch CM, Andrews RM, Flicek P, Dillon SC, Karaoz U, Clelland GK, et al. The landscape of histone

modifications across 1% of the human genome in five human cell lines. Genome Res 2007;17:691–707. [39] Jenuwein T, Allis CD. Translating the histone code. Science 2001;293:1074–80. [40] Vermaak D, Steinbach OC, Dimitrov S, Rupp RA, Wolffe AP. The globular domain of histone H1 is

sufficient to direct specific gene repression in early Xenopus embryos. Curr Biol 1998;8:533–6. [41] Rothbart SB, Strahl BD. Interpreting the language of histone and DNA modifications. Biochim

Biophys Acta 2014;1839:627–43. [42] Cheung WL, Briggs SD, Allis CD. Acetylation and chromosomal functions. Curr Opin Cell Biol

2000;12:326–33. [43] Wolffe AP, Hayes JJ. Chromatin disruption and modification. Nucleic Acids Res 1999;27:711–20. [44] Hebbes TR, Thorne AW, Crane-Robinson C. A direct link between core histone acetylation and

transcriptionally active chromatin. EMBO J 1988;7:1395–402. [45] Bone JR, Lavender J, Richman R, Palmer MJ, Turner BM, Kuroda MI. Acetylated histone H4 on the

male X chromosome is associated with dosage compensation in Drosophila. Genes Dev 1994;8:96–104. [46] Hebbes TR, Clayton AL, Thorne AW, Crane-Robinson C. Core histone hyperacetylation co-maps

with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. EMBO J 1994;13:1823–30.


[47] Grunstein M. Histone acetylation in chromat in structure and transcription. Nature 1997;389: 349–52.

[48] Brownell JE, Allis CD. Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr Opin Genet Dev 1996;6:176–84.

[49] Wade PA, Wolffe AP. Histone acetyltransferases in control. Curr Biol 1997;7:R82–4. [50] Feinberg AP, Tycko B. The history of cancer epigenetics. Nat Rev Cancer 2004;4:143–53. [51] Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SY, et al. Tetrahymena histone

acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 1996;84:843–51.

[52] Ogryzko VV, Schiltz RL, Russanova V, Howard BH, Nakatani Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 1996;87:953–9.

[53] Kuo MH, Zhou J, Jambeck P, Churchill ME, Allis CD. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev 1998;12:627–39.

[54] Yang XJ, Seto E. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 2008;9:206–18.

[55] Yang XJ. Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 2004;26:1076–87.

[56] Mujtaba S, Zeng L, Zhou MM. Structure and acetyl-lysine recognition of the bromodomain. Oncogene 2007;26:5521–7.

[57] Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, Zhou MM. Structure and ligand of a histone acetyltransferase bromodomain. Nature 1999;399:491–6.

[58] Dyson MH, Rose S, Mahadevan LC. Acetyllysine-binding and function of bromodomain-containing proteins in chromatin. Front Biosci 2001;6:D853–65.

[59] Roth SY, Denu JM, Allis CD. Histone acetyltransferases. Annu Rev Biochem 2001;70:81–120. [60] Marmorstein R, Roth SY. Histone acetyltransferases: function, structure, and catalysis. Curr Opin

Genet Dev 2001;11:155–61. [61] Lee KK, Workman JL. Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell

Biol 2007;8:284–95. [62] Jeppesen P, Turner BM. The inactive X chromosome in female mammals is distinguished by a lack of

histone H4 acetylation, a cytogenetic marker for gene expression. Cell 1993;74:281–9. [63] Braunstein M, Rose AB, Holmes SG, Allis CD, Broach JR. Transcriptional silencing in yeast is associated

with reduced nucleosome acetylation. Genes Dev 1993;7:592–604. [64] Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M. Transcriptional repression by UME6

involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 1998;392:831–5. [65] de Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB. Histone deacetylases

(HDACs): characterization of the classical HDAC family. Biochem J 2003;370:737–49. [66] Longworth MS, Laimins LA. Histone deacetylase 3 localizes to the plasma membrane and is a

substrate of Src. Oncogene 2006;25:4495–500. [67] Zhang G, Pradhan S. Mammalian epigenetic mechanisms. IUBMB Life 2014;66:240–56. [68] Berger SL. The complex language of chromatin regulation during transcription. Nature 2007;447:407–12. [69] Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription

initiation at most promoters in human cells. Cell 2007;130:77–88. [70] Roh TY, Cuddapah S, Zhao K. Active chromatin domains are defined by acetylation islands revealed

by genome-wide mapping. Genes Dev 2005;19:542–52. [71] Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, et al. Identification

and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799–816.

[72] Wood A, Shilatifard A. Posttranslational modifications of histones by methylation. In: Ronald CC, Joan Weliky C, editors. Advances in protein chemistry, vol. 67. Academic Press; 2004. p. 201–22.

[73] Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007;39:311–8.

[74] Edmunds JW, Mahadevan LC, Clayton AL. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J 2008;27:406–20.


[75] Steger DJ, Lefterova MI, Ying L, Stonestrom AJ, Schupp M, Zhuo D, et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol Cell Biol 2008;28:2825–39.

[76] Moving AHEAD with an international human epigenome project. Nature 2008;454:711–5. [77] Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol

2010;20:662–71. [78] Allfrey VG, Mirsky AE. Structural modifications of histones and their possible role in the regulation

of RNA synthesis. Science 1964;144:559. [79] Murray K. The occurrence of epsilon-N-methyl lysine in histones. Biochemistry 1964;3:10–5. [80] Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, et al. Histone demethylation mediated

by the nuclear amine oxidase homolog LSD1. Cell 2004;119:941–53. [81] Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev

Genet 2012;13:343–57. [82] Moore KE, Gozani O. An unexpected journey: lysine methylation across the proteome. Biochim

Biophys Acta 2014;1839:1395–403. [83] Clarke SG. Protein methylation at the surface and buried deep: thinking outside the histone

box. Trends Biochem Sci 2013;38:243–52. [84] Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ. Targeting

histone lysine demethylases–progress, challenges, and the future. Biochim Biophys Acta 2014;1839:1416–32.

[85] Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harb Perspect Biol 2013;5. [86] Rossetto D, Avvakumov N, Cote J. Histone phosphorylation: a chromatin modification involved in

diverse nuclear events. Epigenetics 2012;7:1098–108. [87] Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret

histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 2007;14:1025–40. [88] Yun M, Wu J, Workman JL, Li B. Readers of histone modifications. Cell Res 2011;21:564–78. [89] Lau AT, Lee SY, Xu YM, Zheng D, Cho YY, Zhu F, et al. Phosphorylation of histone H2B serine 32

is linked to cell transformation. J Biol Chem 2011;286:26628–37. [90] Chadee DN, Hendzel MJ, Tylipski CP, Allis CD, Bazett-Jones DP, Wright JA, et al. Increased Ser-10

phosphorylation of histone H3 in mitogen-stimulated and oncogene-transformed mouse fibroblasts. J Biol Chem 1999;274:24914–20.

[91] Choi HS, Choi BY, Cho YY, Mizuno H, Kang BS, Bode AM, et al. Phosphorylation of histone H3 at serine 10 is indispensable for neoplastic cell transformation. Cancer Res 2005;65:5818–27.

[92] Lo WS, Trievel RC, Rojas JR, Duggan L, Hsu JY, Allis CD, et al. Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol Cell 2000;5:917–26.

[93] Wei Y, Mizzen CA, Cook RG, Gorovsky MA, Allis CD. Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc Natl Acad Sci USA 1998;95:7480–4.

[94] Sauve DM, Anderson HJ, Ray JM, James WM, Roberge M. Phosphorylation-induced rearrangement of the histone H3 NH2-terminal domain during mitotic chromosome condensation. J Cell Biol 1999;145:225–35.

[95] de la Barre AE, Gerson V, Gout S, Creaven M, Allis CD, Dimitrov S. Core histone N-termini play an essential role in mitotic chromosome condensation. EMBO J 2000;19:379–91.

[96] Shen X, Yu L, Weir JW, Gorovsky MA. Linker histones are not essential and affect chromatin condensation in vivo. Cell 1995;82:47–56.

[97] Dasso M, Dimitrov S, Wolffe AP. Nuclear assembly is independent of linker histones. Proc Natl Acad Sci USA 1994;91:12477–81.

[98] Talbert PB, Henikoff S. Spreading of silent chromatin: inaction at a distance. Nat Rev Genet 2006;7:793–803.

[99] Huang J, Fan T, Yan Q, Zhu H, Fox S, Issaq HJ, et al. Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res 2004;32:5019–28.

[100] Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007;447:425–32.


[101] Muegge K. Lsh, a guardian of heterochromatin at repeat elements. Biochem Cell Biol 2005;83:548–54. [102] Spector DL. The dynamics of chromosome organization and gene regulation. Annu Rev Biochem

2003;72:573–608. [103] Spilianakis CG, Flavell RA. Molecular biology. Managing associations between different chromosomes.

Science 2006;312:207–8. [104] Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. Interchromosomal associations between

alternatively expressed loci. Nature 2005;435:637–45. [105] Cremer T, Kreth G, Koester H, Fink RH, Heintzmann R, Cremer M, et al. Chromosome territories,

interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr 2000;10:179–212.

[106] Branco MR, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 2006;4:e138.

[107] Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001;2:292–301.

[108] Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002;295:1306–11.

[109] Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet 2002;32:623–6.

[110] Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007;128:707–19.

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