CONTENTS Introduction and Definition  Examples of Epigenetic Inheritance Paramutation Parental Imprinting Stages of Mechanism Mechanism of Epigenetics DNA Methylation Histone Modification Histone Methylation Histone Phosphorylation Histone Acetylation Histone Ubiquitylation Non-coding RNA (ncRNA)-associated Gene Silencing Factors Effecting Epigenetic Inheritance

1. EPIGENETICS
Presenter: Kaneez Fatima
Roll no: 94027
Mphill Zoology (Replica)

2. CONTENTS
 Introduction and Definition
 Examples of Epigenetic Inheritance
 Paramutation
 Parental Imprinting
 Stages of Mechanism
 Mechanism of Epigenetics
 DNA Methylation
 Histone Modification
Histone Methylation
Histone Phosphorylation
Histone Acetylation
Histone Ubiquitylation
 Non-coding RNA (ncRNA)-associated
Gene Silencing
 Factors Effecting Epigenetic Inheritance

3. Introduction:  Conrad Waddington introduced the term
early 1940s
 Defined as "the causal interactions
between genes and their products which
bring the phenotype into being"
 The study of changes in gene function
that are mitotically or meiotically
heritable and that do not entail a change
in DNA sequence

4. Examples of
Epigenetic
Inheritance
 1. Paramutation:
 Certain normal alleles, called para-mutable alleles, suffer
irreversible changes after having been present in the
same genome as another class of special alleles, called
paramutagenic alleles.
 The B-I gene in corn encodes an enzyme in the pathway
of anthocyanin pigments
 Ordinary null b alleles lack these pigments, and
these b alleles are completely recessive to B-I.
 There is a special paramutagenic allele, called B′, that
confers the ability to make only a small amount of
anthocyanin pigment
 In crosses of B-I with B′ homozygotes, the resulting
heterozygotes are weakly pigmented
 However, instead, only B′ alleles appear in the next
generations, indicating that the B-I allele has been Para
mutated

5. 2. Parental
Imprinting
 In parental imprinting, certain autosomal genes have
unusual inheritance patterns
 For example, the mouse Igf2 gene is expressed in mouse
only if it was inherited from the mouse’s father
 t is said to be maternally imprinted, in as much as a copy
of the gene derived from the mother is inactive
 Conversely, the mouse H19 gene is expressed only if it was
inherited from the mother; H19 is paternally imprinted
 Furthermore, when these genes are examined at the
molecular level, no changes in their DNA sequences are
observed
 Rather, the only changes that are seen are extra methyl (–
CH3) groups present on certain bases of the DNA of the
imprinted genes

6. Stages of
Epigenetic
Mechanisms
 Epigenator:
 Triggers that change the environment of the cell
to create an epigenetic phenotype
 like nutrition, toxin, radiation, hormones etc.
 Epigenetic Initiator:
 Translates the Epigenator signal to mediate the
epigenetic effect on chromatin
 Initiator identifies location on a chromosome where
epigenetic state is to be established.
 Initiator could be a DNA-binding protein, a
noncoding RNA, or any other entity that can
define the coordinates of the chromatin structure to
be assembled

7. Cont...
 Epigenetic Maintainer:
 Signals that sustain the epigenetic chromatin
state created by initiators
 Operate at any chromosomal location to which
they are recruited by an Initiator
 Pathways includes DNA methylation, histone
modifications, histone variants, nucleosome
positioning

8. Mechanism of
Epigenetics
 DNA Methylation:
 Direct chemical modification of a cytosine C5 side-chain
that adds a -CH3 group
 Catalyzed by enzymes known as DNA methyltransferases
(DNMTs)
 Not all cytosines can be methylated; usually cytosines must
be immediately followed by a guanine in order to be
methylated
 70% of the CpG dinucleotides are methylated
 Rest are unmethylated CpG dinucleotides occur in small
clusters, known as “CpG islands”
 Types of Methylation:
 Maintenance DNMTs and de novo DNMT
 De novo DNMTs methylate previously unmethylated CpG
sites in DNA
 The maintenance DNMT isoform
methylates hemimethylated DNA, DNA which has a
methylated CpG already present on one strand but no
methyl-cytosine on the complementary strand

9. DNA Methylation

10. What are
functional
consequences of
DNA
methylation?
 Associated with suppression of gene
transcription
 Extensive DNA methylation triggers
complete silencing of the associated
gene
 Gene can be shut off functionally
 Methylation of CpGs located within gene
bodies is associated with an increase in
transcriptional activity

11. Histone
Modification
 First reported by Vincet Allfrey in early 1960s
 Histones are highly basic proteins whose function is
to organize DNA within the nucleus
 Histone modification can occur as a consequence of
DNA methylation, or can be mediated by
mechanisms that are independent of DNA
methylation
 N-terminal tails protrude from the nucleosome and
are extensively modified post-translationally
 Currently, four distinct post-translational
modifications of histone tails have been well
characterized: acetylation, methylation,
ubiquitination and phosphorylation.
 All of these modifications serve as epigenetic tags or
marks

13. Histone
acetylation
 Catalyzed by histone acetyltransferase (HAT) leading to
addition of acetyl group to lysine residue
 This nullifies the electrostatic force of attraction
 Between positively charged histone and the negatively
charged DNA resulting in relaxation of the supercoiled
DNA and transcription activation
 The mark is reversed by histone deacetylase (HDAC)
leading to transcriptional repression

14. Histone
Methylation
 It involves binding of methyl functional group to the side
chains of lysine's and arginine's
 Mediated by histone lysine methyltransferase
(HKMT) and protein arginine methyltransferase (PRMT)
 Lysine residue may be methylated multiple times
and Arginine's residues can undergo mono and di-
methylation
 PRMT are broadly classified into type I, II, III or IV
enzymes
 Type I and II enzymes are reported to regulate gene
transcription via methylation of histone proteins
 Type I PRMTs are associated with transcriptional activation
and ribosomal biosynthesis whereas Type II PRMTs
involves in transcriptional repression.
 Histone methylation can activate or retard gene
expression. For example, H3K4me3 activates transcription
on the other hand H3K9me2 and H3K27me2 acts as a
repressor

15. Histone
Phosphorylation
 Mediated by histone kinases which add phosphate
group to serine's, threonine's and tyrosine's of N-
terminal histone tails as well as linker histone H1
 The action of kinases is reversed by histone
phosphatases by removing the phosphate group
 Involved in various biological processes like
chromatin compaction during cell division, DNA
repair, transcription and apoptosis.
 Phosphorylation of H3 is best-documented mark
related to chromatin condensation in many
eukaryotic organisms
 Phosphorylation of H2A is an important histone
modification that plays a major role in DNA damage
response

16. Histone
Ubiquitylation
 Addition of ubiquitin, a 76-amino acid polypeptide,
to lysine residue of histone protein
 By orderly action of three enzymes, E1- activating,
E2-conjugating and E3-ligating enzymes
 The enzyme complexes decide both degree of
ubiquitylation (mono- or poly-) and substrate
specificity
 Two histone mono-ubiquitylation have been well-
characterized for transcriptional initiation and
elongation. Since
 Extremely large molecule induces a change in the
overall conformation of the nucleosome affecting
intra-nucleosomal interactions
 The modification is removed via the action of
deubiquitinating enzymes which are involved in
breakdown of iso-peptide bond between ubiquitin
and histone molecule

17. Non-coding
RNA-
associated
Gene
Silencing
 A non-coding RNA (ncRNA) is a functional RNA
molecule that is transcribed but not translated into
proteins
 ncRNA molecules harbor a crucial role in epigenetic
gene expression
 Account for the great difference in phenotype
between species and within human populations
 MicroRNAs (miRNA) and short interfering RNAs
(siRNA), which include less than 30 nucleotides, and
long non-coding RNAs (lncRNA), which are 200
nucleotides or longer
 Their role in epigenetics is still being determined,
evidence suggesting that ncRNAs participate in
DNA methylation and histone modifications
 siRNAs and lncRNAs both have been shown to
regulate gene expression by the formation of
heterochromatin

18. Epigenetic
Inheritance
 Epigenetic marks are erased during two phases of the
life cycle
 Firstly, just after fertilization. Secondly, in the
developing primordial germ cells
 Poor people living in inner cities, where cycles of drug
addiction, neuropsychiatric illness and other
problems often seem to recur in parents and their
children
 Laboratory mice trained to fear the smell of
acetophenone, a chemical the scent of which has
been compared to those of cherries and almonds
 He and Dias wafted the scent around a small
chamber, while giving small electric shocks to male
mice
 The animals eventually learned to associate the scent
with pain, shuddering in the presence of
acetophenone even without a shock
 This reaction was passed on to their pups

19. Effects of
environmental
chemicals
 Cadmium interact with the methyltransferase
DNA binding domain interference in
enzyme-DNA interaction, reduces genome
methylation
 Detoxification of Arsenic is by enzymatic
methylation using global DNA
hypomethylation
 Nickel enhance chromatin condensation, and
trigger de novo DNA methylation leading to
the inactivation of the gene
 Chromium reduce in-vitro H3
phosphorylation and trimethylation, and
acetylation marks in H3 and H4

20. Effects of
Nutrition on
Epigenetics
 Folate, vitamin B-12, methionine, choline (Soymilk,
broccoli)
 Betaine (Wheat Bran, Spinach, Sweet Potato, beef
etc.) can affect DNA methylation and histone
methylation through altering 1-carbon
metabolism
 Pantothenic acid is a part of CoA to form acetyl-
CoA, which is the source of acetyl group in
histone acetylation
 Genistein (soyabean, coffee) and tea catechin
affects DNA methyltransferases
 Resveratrol (grape, blueberry, raspberry,
mulberry), butyrate (released by gut bacteria),
sulforaphane (broccoli), and diallyl sulfide (garlic
and onion) inhibit HDAC and curcumin inhibits
histone acetyltransferases

21. Any Query?