Epigenetics

 Course work: Advanced Genetics

 Submitted by: Mughira Bin zubair

 Submitted to: Dr. tanvir burni

 EPIGENeTICS
Epigenetics refers to heritable
changes in gene expression that
occur without alteration in DNA
sequence.
These changes may be induced
spontaneously , induced by
environmental factors or as a
consequences of specific mutations.
 EPIGENETIC INHERITANCE
 Epigenetics means “above genetics”.
 There is very little background on
epigenetics because it’s a very new
field only about 50 years old !
 In the past we thought that an
embryo’s epigenome was completely
erased and rebuilt from scratch .
Cont…
 This is partially TRUE , some of the
epigenetic “tags” remain in place and
therefore pass from generation to
generation , this is called epigenetic
inheritance.
 For example:
 If you smoked your whole life the your
offspring (children) will have higher
chance of smoking.
 What is epigenome ?
 The epigenome is like the brain that tells
your cells what to become .
 Such as eye cells or muscle cells.
 It doesn’t change your genes/DNA it just
says what genes will be expressed.
 The genome is like the muscle of the
process it carries out the orders from the
epigenome.
 Epigenetic mechanisms
 The different mechanisms that control
epigenetic changes do not stand alone,
and there is a clear interconnection
and interdependency .
 There are two primary epigenetic
mechanisms :
 1) DNA methylation
 2) Histones modification.
 DNA methylation
 DNA methylation , the addition of a methyl
group to one of the basis in the
deoxyribonucleic acid chain, doesn’t change
the primary DNA sequence and it is therefore
considered to be an epigenetic modification .
 DNA methylation is generally repressive to
transcription , therefore constituting an
important mechanism for gene silencing in
embryonic development and inactivation of
defined tumor suppressor gene in human
cancer.
Cont…
 Although cytosin methylation is the most
studied modification , adenine has been
found to be methylated in prokaryotes
and plants.
 In prokaryotes ,DNA methylation is
involved in processes such as
determination in DNA host-specificity,
virulence , cell cycle regulation , and ge ne
expression.
Cont…
 In higher eukaryotes , DNA methylation is
involved in the regulation of several cellular
processes such as chromatin stability ,
imprinting , X-chromosome inactivation and
carcinogenesis.
 In mammals , DNA methylation occurs
mainly on the fifth carbon of the cytosin
base , forming what is known as 5-
methylcytidine or 5-methylcytosine.
DNA methylation
Main approaches to DNA
methylation:
 Currently , the main
approaches to study DNA
methylation are :
 a) sodium bisulfite modification.
 b) sequence-specific enzyme
digestion.
 c) capture/quantification of
methylated DNA.
 a) SODIUM BISULFITE
MODIFICATION
 Sodium bisulfite modification also known as
bisulfite conversion , is one of the most
useful tools for analyzing cytosine
methylation .
 This method is based on treating DNA with
sodium bisulfite in order to determine its
methylation pattern.
 Treatment of DA with sodium bisulfite leads
to deamination of cytosine residues and
converts them to uracil, while 5-Mc residues
remain the same.
Cont…
 The treatment will generate specific changes
in the DNA sequence that will depend on
the methylation status of individual cytosine
residue potentially providing single-
nucleotide resolution information about the
methylation status of DNA region: cytosine
residues that have been converted to uracil
will be detected as thymidine residues
whereas cytosine residues will detected
cytosines.
Sodium bisulfite
modification
 b) sequence-specific enzyme
digestion
 This method involves the use of methylation
sensitive restriction endonucleases to produce
DNA fragments based on the methylation status of
the sequence.
 In general, a methylation sensitive enzyme (i.e; an
enzyme that cannot cut methylated DNA ) and a
methylation-insensitive isoschizomer (i.e; an
enzyme which cuts the same DNA sequence
regardless of whether this is methylated or not
)are used to digest the same DNA sample.
 Comparison of sensitive versus insensitive
indicated the methylation status of cytosine in the
analyzed DNA sequences.
c) capture/quantification
of methylated DNA
 The use of methylated DNA-binding
proteins or antibodies that specifically
recognize methylated DNA is another
common method for studying methylated
DNA.
 Antibodies can be used in an ELISA-type
assay to specifically detect the percentage of
methylated or hydroxymethylated cytosine
residues in the sample, the higher the signal,
the higher percentage of methylated DNA.
 Histones modification
 Histones pack and order the DNA into
nucleosomes, the building blocks of
chromatin.
 Each nucleosome contains two subunits
each of histones H2A, H2B , H3 , H4,
known as the core histones.
 The linker histone H1 does not form part
of the nucleosome itself but seems to act
as stabilizer of the internucleosomal DNA.
Cont…
 Histones are characterized by a large
number of post-translational modifications,
which serves to allocate the genome into
“active” regions or euchromatin where
DNA is accessible for transcription , and
“inactive” regions or heterochromatin
where DNA is more compact and
therefore less accessible for transcription .
 Cont…
Atleast nine different types of histone
modifications have been described , each
catalyzed by a specific set of enzymes.
The best understood modifications are
lysine acetylation, lysine and arginine
methylation, serine/threonine/tryosine
phosphorylation , and serine/threonine
ubiquitylation.
Cont…
 It is well known that histone
modifications do not stand alone and
that there is an intense cross-talk
between them, which can occur on
the same histone (cis) , between
different histone within the same
nucleosome (trans) , or across
different nucleosome.
Histone modification
Histone modification
 Histone acetylation

 Acetylation is one of the most widely

studied histone modifications, as it was
one of the first described and linked to
transcriptional regulation.
 Acetylation on lysine residue leads to
relaxation of the chromatin structure and
allows the binding of transcription factors
and significantly increases gene
expression.
Cont…
 The enzyme responsible for
regulating of acetylation of histone
tails are histone acetyltransferases
(HAT) and deacetylases (HDAC).
 Well all histones can be acetylated
,lysine residues with H3 and H4 are
preferential target for HAT
complexes.
 Histone methylation
 Unlike acetylation, histone methylation
does not alter the charge of the modified
residues and it is therefore less likely to
directly alter nucleosomal interactions
required for chromatin folding .
 This probably explains why histone
methylation can either repress or activate
transcription depending on location.
Cont…
 Arginine methylation of histone H3 and H4
promotes transcriptional activation , whereas
lysine methylation of histone H3 and H4 is
implicated in both transcriptional activation
and represssion, depending on the methylation
site.
 For many years , histone methylation was
thought to be irreversible as it is stable mark
propagated through multiple cell divisions.
 However ,it was recently shown that, similarly
to histone acetylation , methylation is an
actively regulated and reversible process.
Histone phosphorylation
 Ithas been recently shown that all
nucleosome core histones are
phosphorylated , and that this
modification is critical as
intermediate step in chromosome
condensation during cell division ,
transcriptional regulation and DNA
damage repair .
Cont…
 Contrary to acetylation and methylation, histone
phosphorylation seems to function by establishing
interactions between other histone modifications
and serving as platform for effector proteins ,
leading to a downstream cascade of events.
 Histone H2B phosphorylation hasn’t been studied
as well as H3 and H2A phosphorylation, but
recent findings suggest that this modification
facilitates apoptosis-related chromatin
condensation , DNA fragmentation and cell death.
Overview to epigenetics
Contribution to science
work
 The new evidence for epigenetic
inheritance has had great implications for
the study of evolution .
 It extends the span of evolutionary
thinking and is leading to ideas of heredity
that include development and it is also
suggests that acquired traits can be
heritable.
 The good news
 Scientists are learning to manipulate
epigenetic marks and are making drugs
that will treat sickness by turning off the
bad genes and turning on the good ones.
 2004 –the first epigenetic drug was
approved Azacitidine, treats deadly blood
tumors/cancers etc.
 Life expectancy is expanded by 9
months+.
 Future implications
 Scientists are hoping to develop
epigenetic drugs to help people with
diabetes , cancer, Alzheimer’s ,
schizophrenia, autism, etc.
 They are hoping that further research will
help answer why one identical twin can
suffer from asthma or bipolar disorder
and the other one doesn’t .
 Or why autism is four times more likely in
a boy than a girl.