Epigenetics - Basic Concept

BIOTECH LIVE
BASIC CONCEPT OF
EPIGENETICS
FOR BEGINNER
BIOTECH LIVE & NARENDRA YADAV
11/2/2017
THIS BOOK EXPLAINS ABOUT THE BASIC CONCEPT OF EPIGENETICS FOR THOSE WHO
WANT TO BEGIN THEIR FUTURE EDUCATION IN FIELD OF GENETICS OR EPIGENETICS TO
BE MORE PRICISE. THIS BOOK EXPLAINS ABOUT THE DEFINATION OF EPIGENETICS,
MECHANISM OF EPIGENETICS CAUSE OF CANCER DUE TO EPIGENETICS AND DRUGS OF
THE EPIGENETIC, TO REVERSE THE CAUSE BY EPIGENETIC MECHANISM.
INDEX
SR. TITLE PAGE

NO. NO.
1 INTRODUCTION 5
2 HISTORY OF EPIGENETIC 9
3 EPIGENETIC MECHANISM 10
4 DNA MODIFICATION 11
5 HISTONE MODIFICATION 19
6 CHROMATIN REMODELING 28
7 NON-CODING RNA 29
8 CANCER EPIGENETICS 30
9 EPIGENETICS DRUGS 38
10 NATURAL DRUGS (DIETARY FACTORS) 40
11 REFERENCES 43
BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 2

BIOTECH LIVE

INTRODUCTION
The total DNA content of a cell makes up the genome (eg. Nuclear genome +
Mitochondrial genome + Chloroplast genome) and this genetic blueprint builds phenotypes of
living organism (except some virus which have RNA as genetic material). One must note that,
although every cell of an individual human body contains genetically identical sequences, they
still manage to show different functional and morphological characteristics (eg. skin cell versus
hematopoietic lineages of blood cells).
One can therefore conclude that not all characteristics of living organisms can be explained by
their genes, although genetics is necessary but not sufficient to explain variations of all
phenotypes in living organisms. There is a higher level of complexity known as the epigenome
which the field of epigenetics tries to understand. This is crucial not only in our understanding of
normal functioning of the cell but also applicable in developmental diseases such as alzheimers,
neurological disorders, obesity, diabetes and cancer to name a few.
DEFINITIONS:
A single genome equivalent from a human cell (46 chromosomes) when aligned end to
end in physical distance, contains DNA approx. 2 meters long. This is tightly coiled around the
core histone proteins (pairs of H2A, H2B, H3, and H4) to form beads (nucleosome) on a string
structure. Each homologous strand of DNA binds to octamers forming histone-DNA complexes
which forms a single unit called Chromatid. These chromatids undergo further higher order
packaging (Fig 1) into what we call a Chromosome.

Figure1: Illustrations of different stages of compaction of the eukaryotic chromosome.
Histone proteins are highly basic/positively charged which allows DNA to associate with the
sugar phosphate backbone which is negatively charged. These reversible electrostatic
interactions change depending on the position of a nucleosome with respect to the
promoter/gene, and accordingly alter the accessibility of DNA binding transcription factors
and/or RNA polymerases.
The modification of chromatin (the tightly packed complex of proteins and genomic DNA) is
responsible for epigenetic regulation of gene expression. Like genetic changes, epigenetic
changes are preserved when a cell divides. A cell's epigenome is the overall epigenetic state of
a cell.
Depending on the degree of compaction chromatin can be divided into:
1. Euchromatin: Gene promoters in this state can be accessed easily by transcription factors or in
other words the gene is correlated with an active transcriptional state.

2. Heterochromatin: DNA in this state is highly compacted and is usually not transcriptionally
active. Genes in this state may be silenced permanently (constitutive heterochromatin) or may
express in some of the cells conditionally (facultative heterochromatin).
Figure 2: Chromatin organization: Euchromatin (loose or open chromatin) and heterochromatin

(tight or closed chromatin)
In summary its not the genetic mechanisms alone which decides the expression of a
gene, we need to invoke epigenetic mechanisms which regulate the expression of the gene by
making the DNA available for binding of transcription factors/RNA polymerases or
downregulate expression by not occluding the same.
The Term Epigenetics was first coined by Conrad Waddington (1905 1975), in
1940s. Many new evolving terms in biology are defined differently by researchers and
Epigenetics is no exception to that. Epigenetics, Epi = above, on top of or beside
therefore epigenetics equates to the layer of control above or on top of genetics

Depending on context, Epigenetics is defined as,
To Conrad Waddington, it was the study of epigenesis: that is, how genotypes give rise to
phenotypes during development
Arthur Riggs and colleagues defined epigenetics as the study of mitotically and/or meiotically
heritable changes in gene function that cannot be explained by changes in DNA sequence
An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome

without alterations in the DNA sequence.
Constraint that initiation of the new epigenetic state should involve a transient mechanism
separate from the one required to maintain it
More recently added to this definition is the
Epigenetics is defined as 'molecular factors and processes around DNA that regulate genome
activity independent of DNA sequence and are mitotically stable

HISTORY OF EPIGENETICS
Although the concept of Epigenetics has been around in various forms ever since the
understanding of DNA as the genetic material, several leaps and bounds in terms of concepts and
technical advances has increased the resolution at which we can molecularly understand the
process. Starting from the discovery of the first epigenetic mark as the fifth base in DNA, namely
5-methyl cytosine, our understanding and mapping of different modifications on chromatin
structure has been enhanced by the use of Chromatin Immunoprecipitation and its application to
genome wide analyses as is routinely done today.
1940s Conrad Waddington defined epigenetics as environment-gene interactions that induce

developmental phenotypes
1975 Holliday and Pugh identify DNA methylation
1988 X-chromosome inactivation and DNA methylation
1990s Imprinted genes, allelic expression and DNA methylation
1995 Histone modifications and chromatin structure
2000s Small non-coding RNAs
2005 Hybridization based Epigenome mapping and 3C technology.
2007 Massively parallel sequencing and Next-gen epigenomic approaches.

Mapping of Topologically associated domains (TADs).
2016 New RNA letter regulates gene expression.

Onwards The epitranscriptome.
Discovering a new mechanism of epigenetic inheritance.
Table 1: History of Epigenetic discoveries

EPIGENETICS MECHANISMS
Epigenetic modulation of gene expression in Mammalian systems results from

mechanism/processes such as:
1. DNA methylation: Methyl cytosine at CpG sites, heritability and imprinting.
2. Histone modification: Methylation, acetylation phosphorylation, ubiquitination
3. Histone Variants: H2A.Z, H3.3, CenH3, H2Abd etc.
4. Nucleosome positioning: Nucleosome and promoter occupancy, crystal structure and
positioning sequences
5. Higher order chromatin structure: euchromatin versus heterochromatin transitions and
chromosome packaging (loops, TADs, LARs, MARs, insulators etc)
6. Non-coding RNA: miRNA, lncRNA, X inactivation.
The best-studied epigenetic modification is the methylation of DNA at cytosine bases. Cytosine
methylation indicates gene silencing: methylated genes are not transcribed.
Histone modifications also play an important role in epigenetic regulation. Histones are highly
basic proteins that act as spools around which DNA winds in chromatin. This compacting allows
the DNA to fit into a much smaller space than it would otherwise as explained previously.
Histones possess long N-terminal tails composed mainly of basic amino-acids residues (histidine,
lysine and arginine). Post-translational epigenetic modification of the basic side-chains in histone
tails takes the form of methylation, acetylation, phosphorylation and ubiquitinylation.
DNA modifications typically correspond to long-term epigenetic memory: once methylated,

genomic DNA remains methylated through generations. Histone modifications, on the other
hand, typically provide short-term epigenetic memory and can be reversed after a few cell
division cycles.

DNA MODIFICATION
DNA METHYLATION:
DNA methylation is a major epigenetic modification which controls gene expression,

where methyl group is added to the 5th carbon atom ring of cytosine residue in eukaryotes.
Cytosine methylation is most often restricted to CpG (i.e. C followed by G) dinucleotides in
higher eukaryotes (CpG islands are generally not methylated in normal tissue), where both
cytosine residues on the opposite strands are methylated. This unique property allows the faithful
replication of the hemi-methylated state back to the original status quo of a fully methylated
dinucleotide, thereby preserving the epigenetic information transgenerationally. In addition, CpG
dinucleotides are underrepresented in vertebrate DNAs, making up 12%, and they appear to be
clustered in so-called CpG islands that are usually hypomethylated and often linked to promoter
regions of gene.
*(Replication of methylated DNA results in hemimethylated DNA in which the parent strand is
methylated while the daughter strand is unmethylated. Methylation of this hemimethylated DNA
is necessary to complete the replication of methylated DNA.)*
DNA methylation prevents transcription via several mechanisms, including inhibition of

transcription factor binding. Methylation does not affect the base-pairing of cytosine: 5-
methylcytosine still forms Watson-Crick base pairs with guanine.
DNA methylation is an enzymatic modification performed by DNA methyltransferases. Three

independent DNA methyltransferases (DNMTs) are involved in DNA methylation. In
eukaryotes, two different types of DNA methyltransferases have been characterized: de novo
methyltransferases, e.g. DNMT3a and DNMT3b (methylate unmethylated DNA) & maintenance

methyltransferases, such as DNMT1 (methylate hemimethylated DNA). The maintenance
methylation of hemimethylated DNA provides a mechanism for inheritance of a methylation
pattern through generations, making DNA methylation a stable epigenetic modification
Figure 3: Schematic representation of de novo methylation and maintenance methylation of

DNA.
MECHANISM OF CYTOSINE METHYLATION:
The mechanism of methylation of cytosine involves electrophilic attack by the cofactor

S-adenosyl-l-methionine (AdoMet; SAM), which transfers a methyl group to C(5) of cytosine,
and is converted to S-adenosyl-l-homocysteine (AdoHcy) in the process. As the C(5) atom of
cytosine is not particularly nucleophilic, some help is needed from the methyltransferase to
activate it and increase its nucleophilicity.
The mechanism of cytosine methylation is illustrated in Figure 3. DNA methyltransferases
contain a conserved cytosine residue which, on deprotonation to the thiolate anion, acts as a
strong nucleophile. The cysteine thiolate attacks the C(6) atom of cytosine in a conjugate
addition reaction, and a covalent bond is formed between the cysteine sulfur atom and the
cytosine C(6) atom. The negative charge on cytosine is stabilized by interaction with a glutamate
residue. Nucleophilic attack then takes place on the methyl group of S-adenosyl-l-methionine,
which is converted to S-adenosyl-l-homocysteine (AdoHcy). Finally, -elimination occurs across
the C(5)-C(6) bond, releasing the enzyme.

Figure 4: Mechanism of methylation of cytosine residues in DNA, catalyzed by DNA
methyltransferases.
In the mechanism of methyltransferase-catalyzed methylation of cytosine, a base is required to

deprotonate the cysteine to form the (more nucleophilic) thiolate. It is proposed that the base
involved in this reaction is a DNA phosphate group, via a bridging water molecule. Therefore,
DNA acts as both a substrate and a cofactor
(In general DNMTs catalyse the transfer of a methyl group from S-adenyl methionine (SAM) to
the fifth carbon of cytosine residue to form 5-methylcytosine (5mC). (a) DNMT3a and DNMT3b
are the de novo DNMTs and transfer methyl groups (red, Fig 5) onto naked DNA. (b) DNMT1 is
the maintenance DNMT and maintains DNA methylation pattern during replication. When DNA
undergoes semiconservative replication as depicted in Fig 5, the parental DNA strand 8 retains
the original DNA methylation pattern (grey, Fig 5). DNMT1 associates at the replication foci
and precisely replicates the original DNA methylation pattern by adding methyl groups (red)
onto the newly formed daughter strand (blue, Fig 5).

Figure 5: DNMTs catalyse the transfer of a methyl group .
ROLE OF BASE FLIPPING IN DNA METHYLATION:
Whenever a protein targets a single base within a DNA duplex, a mechanism must exist
to make the base accessible to the enzyme. For prokaryotic methyltransferases (and other DNA-
modifying enzymes), crystal structures have shown that the target cytosine swings out of the
helix completely and rotates through 180 on binding to the enzyme (Figure 4). It is thought that
this base flipping mechanism is also employed by mammalian methyltransferases.

Figure 6: Base flipping in DNA methylation.
The crystal structure of the complex between the methyltransferase from HhaI and double-
stranded DNA (blue) shows that one cytosine base (orange) is flipped out of the double helix,
and binds in the enzyme's active site.
MUTAGENESIS AND DNA REPAIR OF 5-METHYLCYTOSINE:
When cytosine is mutated to uracil by spontaneous deamination, the DNA glycosylase

enzyme UDG (uracil DNA glycosylase) reverses the damage, in a base excision repair
mechanism. When the equivalent deamination reaction occurs on 5-methylcytosine, however, the
product, thymine, is not repaired by DNA repair enzymes (and 5-methylcytosine is an order of
magnitude less susceptible to deamination than cytosine) (Figure 5). This has led to CpG
dinucleotides becoming very much rarer in the genome than would be expected statistically
(except at CpG islands, where no methylation, and therefore no mutation to thymine, occurs).

Figure 7: Deamination of cytosine and 5-methylcytosine.
Spontaneous deamination converts cytosine to uracil, and 5-methylcytosine to thymine. Uracil is
converted back to cytosine by DNA repair enzymes (UDG, a DNA glycosylase), but thymine is
not converted back to 5-methylcytosine.
Changes in DNA methylation profiles are common features of development and in a number of
human diseases, such as cancer and imprinting disorders like BeckwithWiedemann and Prader
Willi/Angelman syndromes. This suggests that DNA methylation is required for proper gene
regulation during development in differentiated tissues and has clinical relevance. DNA
methylation is also involved in X-chromosome inactivation and the allele-specific silencing of
imprinted genes.

DNA HYDROXYMETHYLATION:
If 5-methylcytosine (mC) is the 'fifth base' in the genome 5-hydroxymethylcytosine

(hmC) is the 'sixth base'. The oxidation of 5-methylcytosine (mC) to 5-hydroxymethylcytosine
(hmC) is carried out by TET enzymes, members of the 2-oxoglutarate oxygenase family. It it
proposed that this hydroxylation of 5-methylcytosine might the first step in an active pathway for
DNA demethylation.
DNA DEMETHYLATION:
Methylation of cytosine bases was initially thought to be irreversible, and no direct DNA
demethylase enzyme has been identified; but DNA demethylation is now known to be an
important process.
DNA demethylation is necessary for the reactivation of silenced genes, and in 'cleaning the
genomic slate' during embryonic development (this allows embryonic stem cells to differentiate
into any cell).
Passive DNA Demethylation:
It is easy to envisage how DNA demethylation might occur across generations, through a
loss of methylation information during DNA replication. An absence of maintenance methylation
following DNA replication will result in globally demethylated DNA.
The maintenance DNA methyltransferase DNMT1 does not recognize 5-hydroxymethylcytosine,
so a possible pathway for more specific passive methylation starts with the oxidation of 5-
methylcytosine to 5-hydroxymethylcytosine. 5-Hydroxymethylcytosine has the same base-
pairing chemistry as cytosine and 5-methylcytosine, so it will be replicated to cytosine; but no
subsequent methylation/hydroxymethylation will occur. The overall result is demethylation.
Both of these mechanisms of passive cytosine demethylation require DNA replication. Such
replication-dependent pathways are of no use if demethylation is required before the next round
of DNA replication. Despite the apparent lack of a mammalian DNA demethylase enzyme, a
pathway involving active (replication-independent) demethylaton has recently been proposed.

Active DNA Demethylation:
In plants, active DNA demethylation is achieved through base excision repair, beginning
with the hydrolysis of the N-glycosidic bond of 5-methylcytosine by a specific DNA
glycosylase. However, no demethylation pathway involving a 5-methylcytosine-specific DNA
glycosylase has been identified in mammals. If 5-methylcytosine is first converted into another
base, a base excision repair pathway might be feasible.
Following the oxidation of mC to hmC, further oxidation to 5-formylcytosine (fC) and then 5-
carboxycytosine (caC) has been observed, also catalyzed by TET enzymes. These 'seventh' and
'eighth' bases have been detected in cells, and may be important epigenetic states in their own
right. Two alternative mechanisms have been suggested for conversion of 5-carboxycytosine to
cytosine: direct decarboxylation of 5-carboxycytosine, catalyzed by an as yet unidentified
decarboxylase; or base excision repair, initiated by excision of 5-carboxycytosine by a thymine
DNA glycosylase (TDG). Another pathway has been suggested, in which enzyme-catalyzed
deamination of cytosine is followed by mismatch repair.
Figure 8: Active cytosine demethylation

Scheme showing the active demethylation of 5-methylcytosine by interactive oxidation to 5-
hydroxycytosine, 5-formylcytosine and 5-carboxycytosine, followed by decarboxylation/base
excision repair.

HISTONE MODIFICATION:
Chromatin is the state in which DNA is packaged within the cell. The nucleosome is the
fundamental unit of chromatin and it is composed of an octamer of the four core histones (H3,
H4, H2A, H2B) around which 147 base pairs of DNA are wrapped Histone modifications exert
their effects via two main mechanisms. The first involves the modification(s) directly influencing
the overall structure of chromatin, either over short or long distances. The second involves the
modification regulating (either positively or negatively) the binding of effector molecules or by
influencing the positional affinity of the nucleosome on DNA.
1. Direct structural perturbation

Histone acetylation and phosphorylation effectively reduce the positive charge of histones, and
this has the potential to disrupt electrostatic interactions between histones and DNA. This
presumably leads to a less compact chromatin structure, thereby facilitating DNA access by
protein machineries such as those involved in transcription. Notably, acetylation occurs on
numerous histone tail lysine, including H3K9, H3K14, H3K18, H4K5, H4K8 and H4K12.
(Bannister & Kouzarides, 2011). However, multiple histone acetylations are not an absolute pre-
requisite for inducing structural change histones specifically acetylated at H4K16 have a
significant negative effect on the formation of the 30 nm fibre, at least in vitro.

Figure9: Domains binding modified histones. Examples of proteins with domains that
specifically bind to modified histones as shown.
2. Regulating the binding of chromatin factors

Numerous chromatin-associated factors have been shown to specifically interact with modified
histones via many distinct domains (Fig 9). In addition, histone variants such as H3.3 and
H2A.Z, often carrying their own modification patterns, are exchanged with the canonical core
histones by dedicated chaperone and exchange machinery (Mizuguchi et al., 2004). This has
been shown to exist both as homotypic or heterotypic nucleosomes each having specific
destabilizing effects in nucleosomal contexts and thereby effects on transcription though histones
do not interact with polymerase enzymes directly, their modification can affect the way DNA
wraps around them and thereby influence which genes are expressed. Histone modifications are
necessary for recruiting cofactors and for polymerase binding, and for maintaining chromatin
stability. Most modifications of histones occur at their unstructured, alkaline N-terminal tails.
Important histone modifications include acetylation (at lysine residues) and methylation (at
lysine and arginine residues) (Figure 10).

Figure 10: Structures of important epigenetic histone modifications
HISTONE ACETYLATION:
Histone acetylation is the most widely studied epigenetic protein modification.

Acetylation of specific lysine residues in histone tails is associated with gene activation. Lysine
acetylation, catalyzed by histone acetyltransferases (HATs), neutralizes the positive charge on
the lysine residues. This charge neutralization is thought to reduce affinity between histones and

DNA, opening up access to DNA for transcription factors and polymerases, and therefore
enhancing transcription.
In histone acetylation, a conserved glutamate residue acts as a general base, activating the lysine
-amino group for nucleophilic attack on the carbonyl group of acetyl CoA. A tetrahedral
intermediate forms, and then collapses with the loss of coenzyme A (CoASH), to general acetyl
lysine (Figure 11).
Figure 11: Lysine acetylation mechanism

Mechanism of acetylation of lysine, catalyzed by histone lysine acetylases. Acetyl CoA, the
source of the acetyl group, is converted to coenzyme A (CoASH) in the reaction.
HISTONE DEACETYLATION:
Lysine acetylation is reversible: deacetylation, catalyzed by histone deacetylases (HDs or

HDACs) represses transcription. The deacetylation of acetyl lysine involves nucleophilic attack
of water on the acetyl carbonyl. The mechanism of activation of water is different for different
deacetylases enzymes. There are four classes of histone deacetylases (I-IV), that catalyze the
deacetylation of acetyl lysine via different mechanisms: classes I, II and IV use an active-site
metal-dependent mechanism (Figure 12), while class III HDACs operate using a nicotinamide
adenine dinucleotide (NAD+) dependent catalytic mechanism.

Figure 12: Lysine deacetylation mechanism
Mechanism of deacetylation of acetyl lysine by class I, II and IV histone deacetylases.
HISTONE METHYLATION:
The regulatory role of lysine methylation is complex: methylation of some lysine residues
is associated with transcription, while methylation of other lysines is associated with repression
of transcription.
Histone lysine residues undergo methylation at the N() atom, catalyzed by lysine
methyltransferases (KMTs). Histone Lysine methyltransferases catalyze mono-, di- and
trimethylation of lysine (Figure 13).
Figure 13: Lysine mono-, di- and trimethylation

Scheme showing the mono-, di- and trimethylation of lysine.

Figure 14: Lysine methylation mechanism
Mechanism of methylation of lysine by histone lysine methyltransferases (KMTs).
The source of the methyl group is S-adenosyl-l-methionine (AdoMet), which is converted to S-
adenosyl-l-homocysteine (AdoHcy) in the reaction (Figure 14).
Histones can also be methylated at arginine residues. As with lysine methylation, the regulatory
role of arginine methylation is complex.
HISTONE DEMETHYLATION:
As with acetylation, lysine methylation is reversible; and lysine demethylation, catalyzed by

lysine demethylases (KDMs), is an important epigenetic process.
The lysine demethylases fall into two broad classe: the LSD1/KDM (lysine specific
demethylase) family and the JHDM (jumonji histone demethylase) family. The mechanisms of
both classes of enzymes require an oxidative step. The mechanism of lysine demethylation
catalyzed by enzymes of the LSD1/KDM1 family is illustrated in Figure 15.

Figure 15: Lysine demethylation mechanism
Mechanism of demethylation of lysine, catalyzed by enzymes of the LSD1/KDM1 family.
Table 2: Effect of epigenetic modifications on target gene transcription.

CHROMATIN REMODELLING
Remodelers are ATP-dependent chromatin remodelling complexes which either move,

eject or restructure octamers while on DNA, i.e. in the nucleosomal context. (Teif & Rippe,
2009).
These protein complexes have a common ATPase domain and the energy from the hydrolysis of
ATP allows these remodelling complexes to reposition (slide, twist or loop) nucleosomes along
the DNA, expel histones away from DNA or facilitate exchange of histone variants, and thereby
sometimes creating nucleosome-free regions (NFRs) of DNA for gene activation. The larger the
NFR, the higher is the level of induction of gene activity since this directly effects the binding of
RNA Pol II to the promoter regions. (Wang, Allis, & Chi, 2007)
The position of nucleosomes determines the expression of the gene. If position of Nucleosome
interferes with the transcription factor binding site or transcription start site (TSS), then
ultimately it leads to the silencing of gene otherwise the TSS of the gene can be modulated and
potentially get transcribed. Chromatin remodellers are categorised into at least five families:
SWI/SNF, ISWI, NuDRD/Mi-2/CHD, INO80 and SWR1. First two remodellers being very well
studied so far, especially in the yeast model, and are responsible for a variety of chromatin
transitions involving canonical nucleosomes. The ISWI family mobilises nucleosome along the
DNA (translational only) therefore playing a role in nucleosomal spacing/positioning.
(Badenhorst, Voas, Rebay, & Wu, 2002), Whereas SWI/SNF transiently alters the structure of
nucleosome by looping or octamer eviction drastically affecting transcription rates. (Boris G &
Charles W.M. Roberts, 2011)

Figure 16: Chromatin remodelling activity alters the accessibility of nucleosomal DNA. This
involves mobilization of nucleosome position (sliding), dissociation of DNA-histone contact
(unwrapping), and eviction of histones (histone eviction). In some cases remodelling complexes
introduce histone variants into the nucleosome (histone exchange), such as H2A variant H2A.Z.

NON-CODING RNA
The mechanism of a new phenomenon of genetic interference directed by double-

stranded RNA was first discovered in 1998 by Andrew Fire and Craig Mello. It degrades mRNA
specifically and potently through the mediation of corresponding double-stranded RNA and
leads to post-transcriptional gene silencing (PTGS) both in animals and plants. Double-stranded
RNA (dsRNA) is an important regulator of gene expression in many eukaryotes. It triggers
different types of gene silencing that are collectively referred to as RNA silencing or RNA
interference. (Meister & Tuschl, 2004) Mechanism of RNAi in gene silencing: Primary miRNA
transcripts are processed to miRNA precursors in the nucleus by the RNase-III-like enzyme
Drosha. The miRNA precursor is subsequently exported to the cytoplasm by means of the export
receptor exportin-5. The miRNA precursor is further processed by Dicer to siRNA-duplex-like
intermediates. The duplex is unwound while assembling into miRNP/RISC. Mature miRNAs
bind to Ago proteins, which mediate translational repression or cleavage of target mRNAs
(Fig17) (Meister & Tuschl, 2004).

Figure 17: Mechanistic model of siRNA silencing (Meister & Tuschl, 2004).

CANCER EPIGENETICS
The discovery of the role epigenetics plays in cancer has made epigenetics an area of
huge recent interest, and understanding it has led to new cancer treatments.
Epigenetic modifications are essential in the development and function of healthy cells. Changes
in the epigenome (for example, in the methylation pattern of DNA), leading to incorrect
activation or inactivation of signalling pathways, are a hallmark of cancer. Cancer was long seen
as a genetic disease, but it has become clear recently that epigenetic factors are equally
important.
Cancer cells show genome-wide aberrations at the epigenetic level, including hypomethylation,
promoter-specific hypermethylation, histone deacetylation, down-regulation of miRNAs, and up-
regulation of certain factors of the epigenetic machinery such as PRC2/4 complex including
SirT1 and EZH2. These epigenetic changes result in global deregulation of gene expression
profiles leading to the development and progression of disease states. Activation of oncogenes or
the deactivation of tumour suppressor genes mechanism have been proposed to lead towards
carcinogenesis. Hypermethylation of the CpG islands in the promoter regions of tumour-
suppressor genes has been hypothesized as a major driving event in the origin of cancers. This
model enables us to query the role of environment in epigenetic modulations and how different
cues that finally lead to such hypomethylation and gene silencing can become the seed to pre-
cancerous stem cells (Esteller, 2005). DNA hypermethylation can also indirectly silence
additional classes of genes by silencing transcription factors and DNA repair genes. Silencing of
DNA repair genes (e.g. MLH1, BRCA1 etc.) enables cells leading to the rapid progression of
cancer.

Figure 18: During cancer formation, a large number of epigenetic modifiers are mutated or
abnormally activated. At the same time, epigenetic changes such as DNA methylation, histone
modifications and microRNAs lead to abnormal gene expression which evoke genome
instability.
DNA METHYLATION:
In normal cells, DNA methylation occurs at CpG sites, but CpG islands remain
unmethylated. In tumour cells, the level of DNA methylation at CpG sites is generally low
(hypomethylation), while CpG islands may be methylated (hypermethylation). DNA
hypomethylation leads to aberrant activation of genes.
DNA methylation effects on pathway alterations can be either direct, by affecting promoters of
tumour suppressor genes, or indirect, by silencing known inhibitors of oncogenes, such as
silencing of the secreted frizzled-related protein (SFRP) family of genes, leading to the activation

of the WNT pathway in colorectal carcinogenesis. (Aberrant WNT pathway signaling is an early
progression event in 90% of colorectal cancers).
HISTONE MODIFICATION:
Cancers show global loss of histone H4 K16 monoacetylation and H4K20 trimethylation
(Esteller, 2007). Loss of histone H3K9 acetylation and H3K4 dimethylation or trimethylation
and gain of histone H3K9 dimethylation or trimethylation and H3K27 trimethylation can be
found at specific gene promoters and can contribute to tumourigenesis by silencing critical
tumour suppressor genes (Esteller, 2007). In prostate cancer, EZH2 expression has been
correlated with aberrant H3K27 trimethylation affecting potential tumour suppressor
genes.(Kondo et al., 2008).
Table3: Histone Lysine Methylation in Cancer

Specific histone modifications are associated with tumour formation, including deacetylation of
histone 4 lysine 16 (H4K16), mediated by histone deacetylases (HDACs). It is thought that this
histone deacetylation results in the repression of tumour-suppressor genes. Cancer cells also
display changes in the methylation patterns of lysine residues including H3K9 and H3K27.
Specific histone modifications are associated with tumour formation, including deacetylation of
histone 4 lysine 16 (H4K16), mediated by histone deacetylases (HDACs). It is thought that this
histone deacetylation results in the repression of tumour-suppressor genes. Cancer cells also
display changes in the methylation patterns of lysine residues including H3K9 and H3K27.
miRNA:
Alteration in miRNA expression (down-regulated or up-regulated by epigenetic events)

led to the development of cancer (Calin & Croce, 2006). miRNAs (let-7 family) is aberrantly
down-regulated in breast and lung tumours, leading to RAS pathway oncogenic activation.
Overexpressed miRNAs include the miR-1792 cluster, which lead to development of lung and
breast cancers as well as chronic myeloid leukaemia (Yamazaki et al., 2012). Some cancers show
alteration in DICER and DROSHA expression(Merritt et al., 2008). Alteration in Dicer led to a
defective miRNA production and impaired cellular differentiation, which suggest that miRNAs
might play a role in human tumour growth (Kanellopoulou et al., 2005).

Type of Epigenetic Disruption
Cancer
Colon cancer CpG-island hypermethylation (hMLH1, p16INK4a, p14ARF,

RARB2, SFRP1, and WRN), hypermethylation
of miRNAs (miR-124a), global genomic hypomethylation,
loss of imprinting of
IGF2, mutations of histone modifiers (EP300 and HDAC2),
diminished monoacetylated and
trimethylated forms of histone H4
Breast cancer CpG-island hypermethylation (BRCA1, E-cadherin, TMS1,

and estrogen receptor), global genomic
hypomethylation
Lung cancer CpG-island hypermethylation (p16INK4a, DAPK, and

RASSF1A), global genomic hypomethylation,
genomic deletions of CBP and the chromatin-remodeling
factor BRG1
Glioma CpG-island hypermethylation (DNA-repair enzyme MGMT,

EMP3, and THBS1)
Leukemia CpG-island hypermethylation (p15INK4b, EXT1, and ID4),

translocations of histone modifiers
(CBP, MOZ, MORF, MLL1, MLL3, and NSD1)
Lymphoma CpG-island hypermethylation (p16INK4a, p73, and DNA-

repair enzyme MGMT), diminished

monoacetylated and trimethylated forms of histone H4
Bladder CpG-island hypermethylation (p16INK4a and TPEF/HPP1),

cancer hypermethylation of miRNAs
(miR-127), global genomic hypomethylation
Kidney cancer CpG-island hypermethylation (VHL), loss of imprinting of

IGF2, global genomic hypomethylation
Prostate CpG-island hypermethylation (GSTP1), gene amplification

cancer of polycomb histone methyltransferase
EZH2, aberrant modification pattern of histones H3 and H4
Esophageal CpG-island hypermethylation (p16INK4b and p14ARF),

cancer gene amplification of histone demethylase
JMJD2C/GASC1
Stomach CpG-island hypermethylation (hMLH1 and p14ARF)

cancer
Liver cancer CpG-island hypermethylation (SOCS1 and GSTP1), global

genomic hypomethylation
Ovarian CpG-island hypermethylation (BRCA1)

cancer
Table4: Epigenetic aberrations among different tumour types

EPIGENETIC DRUGS
While genetic mutations are irreversible, epigenetic modifications are, to varying

degrees, reversible. This opens up the possibility of reversing epigenetic modifications in cancer
cells to restore the cells to their healthy state. The goal of epigenetic therapy in cancer treatment
is to restore a distorted epigenome to a 'normal' epigenome.
The transition between the euchromatin and heterochromatin are regulated by the many of the
transcription activator and repressor complexes, such as PRC2 and PRC1 cellular transcription
repressor complexes, which regulated the histone modification, H3K4me (transcriptionally
active) Euchromatin state to H3K27 (transcriptionally inactive) heterochromatin state, ultimately
inhibition of the particular gene expression (Toth et al., 2013). The epigenetic anomalies can be
reversed makes them inviting targets for a new generation of drugs. The drugs can be affected at
two stage, 1. prognostic significance or diagnostic and 2. Therapeutic uses. Based on the
epigenetic variation, the different type of the drugs can be use.
Based on the mode of action of Drug, Epigenetic Drugs can be classified into two major
type:(Nebbioso, Carafa, Benedetti, & Altucci, 2012)
1) DNA methyltransferase inhibitors and
2) HDAC inhibitors (HDACi).
DNA METHYLTRANSFERASE INHIBITORS:
The rationale behind demethylation therapies is the ability of DNA methyltransferase

inhibitors to revert hyper-methylation induced gene silencing.c
(a) 5-Azacytidine or azacytidine and (b) 5-aza-2-deoxycytidine or Decitabine are indeed the
only two DNMT inhibitors (DNMTi) approved by the USA Food and Drug Administration
(FDA) and the European Medicines Agency (EMA). These nucleoside analogs, i.e., cytidine

analogs, incorporate DNA instead of deoxycytidine, covalently link the enzyme and lead to
DNMT degradation.
Azacytidine and decitabine are incorporated into the DNA of rapidly growing tumour cells
during DNA replication and, after replication, inhibit methyltransferases. This loss of
methylation leads to activation of tumour-suppressor genes, inhibiting tumour growth.
Non-nucleoside compounds that can inhibit DNA methyltransferases without being incorporated
into DNA are being pursued, but no potent inhibitors have yet been found.
Figure 19: chemical structures of decitabine (5-aza-2-deoxycytidine) and azacytibine (5-

azacytidine).
MODES OF ACTION OF THE DRUG:
Decitabine and Azacytibine a cytidine analogues that get incorporated into the DNA
covalently trap the DNMTs on the DNA and forms a complex. After DNMT binding to the C6 of
the 5-aza-CdR incorporated into the DNA, methyl group transfer will occur, but no H is present
on the N5, which precludes the resolution of the complex. As a result, further methylation of
cytosine residues is inhibited leading to a loss of DNA methylation which result into
hypomethylation of the genome and activate certain genes previously silenced.

Figure 20: Trapping mechanism of Azacytosine
HDAC INHIBITORS (HDACi):
Among current epigenetic drugs, histone deacetylase (HDAC) inhibitors induce changes
in gene expression that can lead to cell death in tumours. HDAC inhibitors include Short-chain
fatty acid, hydroxamic, and cyclic tetrapeptides. Valproic acid (VPA) is a HDAC inhibitor that
has antitumour activity at mM range (Gu et al., 2012). The restoration of histone acetylation
patterns has been shown to correlate with antitumor activity, and histone deacetylase (HDAC)
inhibitors have been investigated to this end. Suberoylanilide hydroxamic acid (SAHA;
Vorinostat; Zolinza), an inhibitor of some classes of HDACs, was approved for the treatment of
cutaneous T cell lymphoma in 2006. SAHA can bind to a zinc ion in the catalytic domain of
HDAC resulting in inhibition of the enzyme.

Figure 21: Suberoylanilide hydroxamic acid (SAHA; Vorinostat; Zolinza). Structure of
suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor
Sodium butyrate: Its a short-chain fatty acid. Sodium butyrate inhibits HDAC activity and
inhibition of HDAC activity affects the expression of only 2% of mammalian genes.

NATURAL DRUGS (DIETARY FACTORS):
Dietary factors play a role in many normal biological processes and are also involved in
the regulation of pathological progressions. Dietary factors have become agents of strong interest
in the field of epigenetics. A number of bioactive dietary components have potential to prevent
disease. Polyphenols are present in fruits and vegetables and are a vital part of the human diet.
Polyphenols include EGCG (from green tea), curcumin (from curry), resveratrol (from grapes
and berries) and Quercetin (citrus fruits and buckwheat) .
Figure 22: Illustration depicting major plants with evidence for epigenetic modifications

Curcumin:
Curcumin (major component of turmeric) is a polyphenol that present in a Curcuma
longa, and which is responsible for the yellow pigmentation of curry. Curcumin appears to have
anti-inflammatory, antioxidant, antiangiogenic and anticancer (Maheshwari, Singh, Gaddipati, &
Srimal, 2006). Curcumin inhibits DNMT activity by covalently blocking the catalytic thiolate of
C1226 of DNMT1. Curcumin exposure to genomic DNA of MV4-11 leukemia cell line induced
a decrease in global DNA methylation comparable to decitabine (Liu et al., 2009). Curcumin
also functions as a histone modifying compound and as a HDAC and HAT inhibitor.(Hardy &
Tollefsbol, 2011).
Quercetin:
Quercetin is predominantly present in citrus fruits and its a potent anti-tumour dietary
polyphenol. Quercetin have chemo-preventive activities because of its ability to reverse certain
epigenetic aberrations observed in cancers (Zheng, Wang, Yang, & Wu, 2014). Quercetin was
associated with inhibition of the HAT activity.(Link et al., 2010)
Cinnamic acid:
Cinnamic acid are natural substances. Cinnamic acids are abundant in various natural
resources. Cinnamic acids have an antibacterial and antifungal properties (Guzman, 2014).
Cinnamic acids known to have an antioxidant, anti-inflammatory and cytotoxic properties
(Pontiki, Hadjipavlou-Litina, Litinas, & Geromichalos, 2014). Cinnamic acid and its natural
analogues are unique as anticancer agents (De, Baltas, & Bedos-Belval, 2011).

Figure 23: Epigenetic mechanisms involved in carcinogenesis.

REFERENCES
Andreini, C., Bertini, I., Cavallaro, G., Holliday, G. L., & Thornton, J. M. (2008). Metal ions in
biological catalysis: From enzyme databases to general principles. Journal of Biological
Inorganic Chemistry, 13(8), 12051218. https://doi.org/10.1007/s00775-008-0404-5
Badenhorst, P., Voas, M., Rebay, I., & Wu, C. (2002). Biological functions of the ISWI
chromatin remodeling complex NURF. Genes and Development, 16(24), 31863198.
https://doi.org/10.1101/gad.1032202
Bannister, A. J., & Kouzarides, T. (2011). Regulation of chromatin by histone modifications.
Cell Research, 21(3), 381395. https://doi.org/10.1038/cr.2011.22
Berger, S. L., Kouzarides, T., Shiekhattar, R., & Shilatifard, A. (2009). An operational definition
of epigenetics. Genes and Development, 23(7), 781783.
Bestor, T., Laudano, A., Mattaliano, R., & Ingram, V. (1988). Cloning and sequencing of a
cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of
the mammalian enzymes is related to bacterial restriction methyltransferases. Journal of
Molecular Biology, 203(4), 971983. https://doi.org/10.1016/0022-2836(88)90122-2
Bird, A. (2007). Perceptions of epigenetics. Nature, 447(7143), 3968.
https://doi.org/10.1038/nature05913
Calin, G. a, & Croce, C. M. (2006). MicroRNA signatures in human cancers. Nature Reviews.
Cancer, 6(11), 85766. https://doi.org/10.1038/nrc1997
Champion, C., Guianvarch, D., Snamaud-Beaufort, C., Jurkowska, R. Z., Jeltsch, A., Ponger,
L., Guieysse-Peugeot, A. L. (2010). Mechanistic insights on the inhibition of C5 DNA
methyltransferases by zebularine. PLoS ONE, 5(8).
https://doi.org/10.1371/journal.pone.0012388
Chandrasekar, R. (2013). Alcohol and NMDA receptor: current research and future direction.
Front Mol Neurosci, 6, 14. https://doi.org/10.3389/fnmol.2013.00014
Chen, Q. W., Zhu, X. Y., Li, Y. Y., & Meng, Z. Q. (2014). Epigenetic regulation and cancer
(review). Oncol Rep, 31(2), 523532. https://doi.org/10.3892/or.2013.2913
Davie, J. R. (2003). Inhibition of histone deacetylase activity by butyrate. The Journal of
Nutrition, 133(7 Suppl), 2485S2493S. https://doi.org/10.1093/emboj/20.24.6969

De, P., Baltas, M., & Bedos-Belval, F. (2011). Cinnamic acid derivatives as anticancer agents-a
review. Current Medicinal Chemistry, 18(11), 16721703.
https://doi.org/10.2174/092986711795471347
Esteller, M. (2005). DNA methylation, epigenetics, and metastasis. Cancer metastasis.
https://doi.org/10.1007/1-4020-3642-6
Esteller, M. (2007). Cancer epigenomics: DNA methylomes and histone-modification maps.
Nature Reviews. Genetics, 8(4), 286298. https://doi.org/10.1038/nrg2005
Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Jacobsen, S. E.
(2010). Conservation and divergence of methylation patterning in plants and animals.
Proceedings of the National Academy of Sciences of the United States of America, 107(19),
868994. https://doi.org/10.1073/pnas.1002720107
Ferris, P. J., Virginia Armbrust, E., & Goodenough, U. W. (2002). Genetic structure of the
mating-type locus of Chlamydomonas reinbardtii. Genetics, 160(1), 181200.
Goldberg, A. D., Allis, C. D., & Bernstein, E. (2007). Epigenetics: A Landscape Takes Shape.
Cell. https://doi.org/10.1016/j.cell.2007.02.006
Goodenough, U. W., & Weiss, R. L. (1975). Gametic differentiation in Chlamydomonas
reinhardtii. III. Cell wall lysis and microfilament associated mating structure activation in
wild type and mutant strains. Journal of Cell Biology, 67(3), 623637.
https://doi.org/10.1083/jcb.67.3.623
Gu, S., Tian, Y., Chlenski, A., Salwen, H. R., Lu, Z., Raj, J. U., & Yang, Q. (2012). Valproic
acid shows a potent antitumour effect with alteration of DNA methylation in
neuroblastoma. Anti-Cancer Drugs, 23(10), 10541066.
https://doi.org/10.1097/CAD.0b013e32835739dd
Guzman, J. D. (2014). Natural cinnamic acids, synthetic derivatives and hybrids with
antimicrobial activity. Molecules. https://doi.org/10.3390/molecules191219292
Hallmann, A. (2011). Evolution of reproductive development in the volvocine algae. Sexual
Plant Reproduction. https://doi.org/10.1007/s00497-010-0158-4
Handy, D. E., Castro, R., & Loscalzo, J. (2011). Epigenetic modifications: Basic mechanisms
and role in cardiovascular disease. Circulation, 123(19), 21452156.
https://doi.org/10.1161/CIRCULATIONAHA.110.956839

Hardy, T. M., & Tollefsbol, T. O. (2011). Epigenetic diet: impact on the epigenome and cancer.
Epigenomics, 3(4), 503518. https://doi.org/10.2217/epi.11.71
Jin, C., Zang, C., Wei, G., Cui, K., Peng, W., Zhao, K., & Felsenfeld, G. (2009). H3.3/H2A.Z
double variant-containing nucleosomes mark nucleosome-free regions of active
promoters and other regulatory regions. Nature Genetics, 41(8), 9415.
https://doi.org/10.1038/ng.409
Kanellopoulou, C., Muljo, S. A., Kung, A. L., Ganesan, S., Drapkin, R., Jenuwein, T.,
Rajewsky, K. (2005). Dicer-deficient mouse embryonic stem cells are defective in
differentiation and centromeric silencing. Genes and Development, 19(4), 489501.
Kehres, D. G., & Maguire, M. E. (2003). Emerging themes in manganese transport, biochemistry
and pathogenesis in bacteria. FEMS Microbiology Reviews. https://doi.org/10.1016/S0168-
6445(03)00052-4
Kondo, Y., Shen, L., Cheng, A. S., Ahmed, S., Boumber, Y., Charo, C., Issa, J.-P. J. (2008).
Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter
DNA methylation. Nature Genetics, 40(6), 741750. https://doi.org/10.1038/ng.159
Kouzarides, T. (2007). Chromatin Modifications and Their Function. Cell.
https://doi.org/10.1016/j.cell.2007.02.005
Link, A., Balaguer, F., & Goel, A. (2010). Cancer chemoprevention by dietary polyphenols:
Promising role for epigenetics. Biochemical Pharmacology.
https://doi.org/10.1016/j.bcp.2010.06.036
Liu, Z., Xie, Z., Jones, W., Pavlovicz, R. E., Liu, S., Yu, J., Chan, K. K. (2009). Curcumin is
a potent DNA hypomethylation agent. Bioorganic and Medicinal Chemistry Letters, 19(3),
706709. https://doi.org/10.1016/j.bmcl.2008.12.041
Maheshwari, R. K., Singh, A. K., Gaddipati, J., & Srimal, R. C. (2006). Multiple biological
activities of curcumin: A short review. In Life Sciences (Vol. 78, pp. 20812087).
https://doi.org/10.1016/j.lfs.2005.12.007
Maul, J. E., Lilly, J. W., Cui, L., dePamphilis, C. W., Miller, W., Harris, E. H., & Stern, D. B.
(2002). The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of
repeats. The Plant Cell, 14(11), 265979. https://doi.org/10.1105/tpc.006155.present

Meister, G., & Tuschl, T. (2004). Mechanisms of gene silencing by double-stranded RNA.
Nature, 431(September), 343349. https://doi.org/10.1038/nature02873
Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, J., Witman, G. B.,
Grossman, A. R. (2010). The Chlamydomonas Genome Reveals the Evolution of Key
Animal and Plant Functions. Science, 318(5848), 245250.
https://doi.org/10.1126/science.1143609.The
Merritt, W. M., Lin, Y. G., Han, L. Y., Kamat, A. A., Spannuth, W. A., Schmandt, R., others.
(2008). Dicer, Drosha, and Outcomes in Patients with Ovarian Cancer. The New England
Journal of Medicine, 359(25), 26412650. https://doi.org/10.1056/NEJMoa0803785.Dicer
Mizuguchi, G., Shen, X., Landry, J., Wu, W.-H., Sen, S., & Wu, C. (2004). ATP-driven
exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex.
Science (New York, N.Y.), 303(5656), 3438. https://doi.org/10.1126/science.1090701
Moore, L. D., Le, T., & Fan, G. (2013). DNA methylation and its basic function.
Neuropsychopharmacology: Official Publication of the American College of
Neuropsychopharmacology, 38(1), 2338. https://doi.org/10.1038/npp.2012.112
Nebbioso, A., Carafa, V., Benedetti, R., & Altucci, L. (2012). Trials with epigenetic drugs: An
update. Molecular Oncology. https://doi.org/10.1016/j.molonc.2012.09.004
OHagan, H. M., Wang, W., Sen, S., DeStefano Shields, C., Lee, S. S., Zhang, Y. W., Baylin,
S. B. (2011). Oxidative Damage Targets Complexes Containing DNA Methyltransferases,
SIRT1, and Polycomb Members to Promoter CpG Islands. Cancer Cell, 20(5), 606619.
https://doi.org/10.1016/j.ccr.2011.09.012
Pontiki, E., Hadjipavlou-Litina, D., Litinas, K., & Geromichalos, G. (2014). Novel cinnamic acid
derivatives as antioxidant and anticancer agents: Design, synthesis and modeling studies.
Molecules, 19(7), 96559674. https://doi.org/10.3390/molecules19079655
Sager, R. (1954). NUTRITIONAL CONTROL OF SEXUALITY IN CHLAMYDOMONAS
REINHARDI. The Journal of General Physiology, 37(6), 729742.
https://doi.org/10.1085/jgp.37.6.729
Schenck, R. C., Tessier, A., & Campbell, P. G. C. (1988). The Effect of pH on Iron and
Manganese Uptake by a Green Alga. Limnology and Oceanography, 33(4), 538550.
https://doi.org/10.4319/lo.1988.33.4.0538

Shogren-Knaak, M., Ishii, H., Sun, J.-M., Pazin, M. J., Davie, J. R., & Peterson, C. L. (2006).
Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science,
311(5762), 8447. https://doi.org/10.1126/science.1124000
Skinner, M. K., & Guerrero-Bosagna, C. (2009). Environmental signals and transgenerational
epigenetics. Epigenomics, 1(1), 111117. https://doi.org/10.2217/epi.09.11
Stresemann, C., & Lyko, F. (2008). Modes of action of the DNA methyltransferase inhibitors
azacytidine and decitabine. International Journal of Cancer.
https://doi.org/10.1002/ijc.23607
Sunda, W. G., & Huntsman, S. a. (1998). Interactions among Cu2+, Zn2+, and Mn2+ in
controlling cellular Mn, Zn, and growth rate in the coastal alga Chlamydomonas. Limnology
and Oceanography, 43(6), 10551064. https://doi.org/10.4319/lo.1998.43.6.1055
Suzuki, H., Watkins, D. N., Jair, K.-W., Schuebel, K. E., Markowitz, S. D., Chen, W. D.,
Baylin, S. B. (2004). Epigenetic inactivation of SFRP genes allows constitutive WNT
signaling in colorectal cancer. Nature Genetics, 36(4), 41722.
https://doi.org/10.1038/ng1330
Teif, V. B., & Rippe, K. (2009). Predicting nucleosome positions on the DNA: Combining
intrinsic sequence preferences and remodeler activities. Nucleic Acids Research, 37(17),
56415655. https://doi.org/10.1093/nar/gkp610
Toth, Z., Brulois, K., Lee, H. R., Izumiya, Y., Tepper, C., Kung, H. J., & Jung, J. U. (2013).
Biphasic Euchromatin-to-Heterochromatin Transition on the KSHV Genome Following De
Novo Infection. PLoS Pathogens, 9(12), 114. https://doi.org/10.1371/journal.ppat.1003813
Vahrenholz, C., Riemen, G., Pratje, E., Dujon, B., & Michaelis, G. (1993). Mitochondrial DNA
of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8-kb genome
suggests mechanisms for DNA replication. Current Genetics, 24(3), 241247.
https://doi.org/10.1007/BF00351798
Vaswani S and S. Sen. (2016). Studying differential drug responses using epigenetic
phenotypes in Chlamydomonas reinhardtii.Sen lab
Wang, G. G., Allis, C. D., & Chi, P. (2007). Chromatin remodeling and cancer, part I: covalent
histone modifications. Trends in Molecular Medicine.
https://doi.org/10.1016/j.molmed.2007.07.003

Yamazaki, J., Taby, R., Vasanthakumar, A., Macrae, T., Ostler, K. R., Shen, L., Issa, J.-P. J.
(2012). Effects of TET2 mutations on DNA methylation in chronic myelomonocytic
leukemia. Epigenetics, 7(2), 2017. https://doi.org/10.4161/epi.7.2.19015
Zheng, N. G., Wang, J. L., Yang, S. L., & Wu, J. L. (2014). Aberant epigenetic alteration in
Eca9706 cells modulated by nanoliposomal quercetin combined with butyrate mediated via
epigenetic-NF-??B signaling. Asian Pacific Journal of Cancer Prevention, 15(11), 4539
4543. https://doi.org/10.7314/APJCP.2014.15.11.4539

BIOTECH LIVE


Epigenetics - Basic Concept

Uploaded by

Copyright:

Epigenetics - Basic Concept

Uploaded by

Document Information

Original Title

Copyright

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Epigenetics - Basic Concept

Uploaded by

Copyright:

What is epigenetics?

What is epigenetics?

What are some epigenetic mechanisms discussed in the text?

What are some epigenetic mechanisms discussed in the text?

BIOTECH LIVE

SR. TITLE PAGE

10 NATURAL DRUGS (DIETARY FACTORS) 40

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 2

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 3

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 5

Depending on the degree of compaction chromatin can be divided into:

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 6

Figure 2: Chromatin organization: Euchromatin (loose or open chromatin) and heterochromatin

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 7

An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome

More recently added to this definition is the

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 8

1940s Conrad Waddington defined epigenetics as environment-gene interactions that induce

1975 Holliday and Pugh identify DNA methylation

1988 X-chromosome inactivation and DNA methylation

1990s Imprinted genes, allelic expression and DNA methylation

1995 Histone modifications and chromatin structure

2000s Small non-coding RNAs

2005 Hybridization based Epigenome mapping and 3C technology.

2007 Massively parallel sequencing and Next-gen epigenomic approaches.

2016 New RNA letter regulates gene expression.

Table 1: History of Epigenetic discoveries

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 9

Epigenetic modulation of gene expression in Mammalian systems results from

DNA modifications typically correspond to long-term epigenetic memory: once methylated,

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 10

DNA methylation is a major epigenetic modification which controls gene expression,

DNA methylation prevents transcription via several mechanisms, including inhibition of

DNA methylation is an enzymatic modification performed by DNA methyltransferases. Three

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 11

Figure 3: Schematic representation of de novo methylation and maintenance methylation of

MECHANISM OF CYTOSINE METHYLATION:

The mechanism of methylation of cytosine involves electrophilic attack by the cofactor

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 12

In the mechanism of methyltransferase-catalyzed methylation of cytosine, a base is required to

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 13

ROLE OF BASE FLIPPING IN DNA METHYLATION:

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 14

MUTAGENESIS AND DNA REPAIR OF 5-METHYLCYTOSINE:

When cytosine is mutated to uracil by spontaneous deamination, the DNA glycosylase

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 15

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 16

If 5-methylcytosine (mC) is the 'fifth base' in the genome 5-hydroxymethylcytosine

Passive DNA Demethylation:

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 17

Figure 8: Active cytosine demethylation

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 18

1. Direct structural perturbation

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 19

2. Regulating the binding of chromatin factors

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 20

Histone acetylation is the most widely studied epigenetic protein modification.

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 21

Figure 11: Lysine acetylation mechanism

Lysine acetylation is reversible: deacetylation, catalyzed by histone deacetylases (HDs or

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 22

Figure 13: Lysine mono-, di- and trimethylation

BIOTECHLIVE 2016. ALL RIGHTS RESERVED Page 23