Epigenetics definition, history of epigenetics, molecular basis of epigenetics, epigenetic modification, tools to study epigenetics, disease linked with epigenetics, DNA methylation demethylation and enzymes regulating DNA methylation

1. Epigenetics and DNA Methylation
Presented by- Partha Chattopadhyay
Department of Biotechnology
National Institute of Pharmaceutical Education and Research-
Guwahati

2. What is Epigenetics?
• What began as broad research focused on combining genetics
and developmental biology by well-respected scientists including
Conrad H. Waddington and Ernst Hadorn during the mid-twentieth
century (1942) has evolved into the field we currently refer to as
“epigenetics”.
• The term “Epigenetics” means “Above Genetics” as the nucleotide sequence is
unaltered.
• Reversible heritable chemical modification of DNA or histone or non-histone
protein that does not alter DNA sequence itself but it affects how cell reads the
genes.
• Epigenetic change is a regular and natural occurrence but it can also be influenced
by several factors including age, environment/lifestyle and disease state etc.
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4. Epigenetic Modification
• Epigenetic modifications can manifest as commonly as the manner in which cells
terminally differentiate to end up as skin cells, liver cells, brain cells, etc. Or,
epigenetic change can have more damaging effects that can result in diseases like
cancer.
• At least three systems including DNA methylation,
histone modification and non-coding RNA (ncRNA)-
associated gene silencing are currently considered
to initiate and sustain epigenetic change.
• The renewed interest in epigenetics has led to new
findings about the relationship between epigenetic
changes and a host of disorders including various
cancers, mental retardation associated disorders.
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5. Molecular Basis of Epigenetics
• Methylation of cytosines at CpG
dinucleotides (red lollipops) recruits
methyl-DNA binding proteins, of which
MeCP2 is a specific example. All proteins
that bind to methylated DNA have both a
methyl-DNA binding domain (MBD) and a
transcription-regulatory domain (TRD). The
TRD recruits adapter proteins such as Sin3A
which, in turn, recruit histone deacetylases
(HDACs). The HDACs alter chromatin structure locally through removing acetyl
groups (Ac) from histone core proteins (gray spheres), leading to compaction of
chromatin and transcriptional suppression.
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6. Environment, Lifestyle and Epigenetics
• Human epidemiological studies have provided evidence that prenatal and early
postnatal environmental factors influence the adult risk of developing various
chronic diseases and behavioral disorders
• Research has also shown that a mother’s exposure
to pollution could impact her child’s asthma susceptibility
and her intake of vitamin D could change DNA
methylation that influences placenta functioning.
• Air pollution could alter methyl tags on DNA and
increase one’s risk for neurodegenerative disease.
Interestingly, B vitamins may protect against harmful
epigenetic effect of pollution and may be able to
combat the harmful effects that particular matter
has on the body.
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7. • An epigenetic diet may guide people toward the optimal
food regimen as scientific studies reveal the underlying
mechanisms and impact that different foods have on the
epigenome and health.
• Researchers have found that a ketogenic diet– consuming
high amounts of fat, adequate protein, and low
carbohydrates increases an epigenetic agent
naturally produced by the body.
• Studies have shown that children born during the period
of the Dutch famine from 1944-1945 have increased rates
of coronary heart disease and obesity after maternal
exposure to famine during early pregnancy compared to
those not exposed to famine.
Environment, Lifestyle and Epigenetics cont…
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8. • DNA Methylation Analysis
1. Bisulfite Conversion- Sodium bisulfite convert unmethylated cytosine to uracil while
methylated cytosine are left unmodified.
2. High Resolution Meta Analysis- Qualitative analysis of DNA fragment’s melt curve
following PCR amplification.
3. Methylated DNA Immunoprecipitation- MeDIP involves isolation of DNA from cells and
using antibody specially designed for methylated DNA, the methylated regions are
detected.
• Analysis of DNA/Protein Interaction- Interaction between DNA and protein is
studied by chromatin immunoprecipitation using highly specific antibodies directed
against DNA binding proteins.
• Chromatin Accessibility and Conformation Assay- By investigating nuclease
accessibility of chromatin, the native chromatin state can be identified.
• EpiQ Chromatin Analysis Kit- It is a real time qPCR assay kit for quantitative
assessment of chromatin accessibility.
Tools to Study Epigenetics
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9. Epigenetic Disease
• Epigenetic changes are linked to several disorders that result in intellectual
disabilities such as ATR-X, Fragile X, Rett, Beckwith-Weidman (BWS), Prader-
Willi and Angelman syndromes.
• DNA methylation patterns may cause abnormal expression of cancer associated
genes. DNA hypomethylation can activate oncogenes and initiate chromosome
instability.
• Patients with lupus whose T cells exhibit
decreased DNA methyltransferase activity
and hypomethylated DNA.
• Epigenetic research has also shown that
there is joint-specific DNA methylation
and transcriptome signatures in
rheumatoid arthritis.
• Epigenetic errors also play a role in the
causation of complex adult psychiatric,
autistic, and neurodegenerative disorders.
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10. • Several reports have associated schizophrenia and
mood disorders with DNA rearrangements that include
the DNMT genes.
• A role for aberrant methylation mediated by folate
levels has been suggested as a factor in Alzheimer’s
disease.
• Autism has been linked to the region on chromosome 15
that is responsible for Prader-Willi syndrome and
Angelman syndrome.
• In addition to epigenetic alterations, specific mutations
affecting components of the epigenetic pathway have
been identified that are responsible for several syndromes
like Rett syndrome, ICF etc.
Epigenetic Disease cont…
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11. • DNA methylation is an epigenetic mechanism that occurs by the addition of a
methyl (CH3) group to DNA, thereby often modifying the function of the genes
and affecting gene expression.
• These methyl groups project into the major groove of DNA and inhibit
transcription.
• The addition of methyl groups is controlled at several different levels in cells and
is carried out by a family of enzymes called DNA methyltransferases (DNMTs).
• Three DNMTs (DNMT1, DNMT3a and DNMT3b) are
required for establishment and maintenance of DNA
methylation patterns.
• DNMT1 appears to be responsible for the maintenance
of established patterns of DNA methylation, while
DNMT3a and 3b seem to mediate establishment of new or
de novo DNA methylation patterns.
DNA Methylation
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12. • Diseased cells such as cancer cells may be different in that DNMT1 alone is not
responsible for maintaining normal gene hypermethylation (an increase in global
DNA methylation) and both DNMTs 1 and 3b may cooperate for this function.
• In human DNA, 5-methylcytosine is found in approximately 1.5% of genomic DNA.
• In the bulk of genomic DNA, most CpG sites are heavily methylated while CpG in
germ-line tissues and located near promoters of normal somatic cells, remain
unmethylated.
• DNA Demethylation is the removal of a methyl group from DNA. This mechanism
is equally as important and coupled with DNA methylation.
• The demethylation process is necessary for epigenetic reprogramming of genes
and is also directly involved in many important disease mechanisms such as tumor
progression.
DNA Methylation cont…
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13. References
1. Lister R. et al. Human DNA methylomes at base resolution show widespread epigenomic
differences. Nature 462, 315-322 (2009).
2. Sweatt JD, Nestler EJ, Meaney MJ, Akbarian S. An Overview of the Molecular Basis of
Epigenetics. Chapter 1 - Epigenetic Regulation in the Nervous System 1-31, Elsevier education,
2013, South Asian Edition.
3. http://www.bio-rad.com/en-us/applications-technologies/epigenetics-
analysis?ID=LUSNNRCZF#2 (accessed on 16/9/2018)
4. Egger G. et al. Epigenetics in human disease and prospects for epigenetic therapy. Nature 429,
457-463 (2004).
5. Brouwer J.R. A Crash Course in Epigenetics Part 1: An intro to epigenetics. Bitesize Bio. 94
(1681-776 (2012).
6. Painter RC, Roseboom TJ, Bleker OP. Prenatal exposure to the Dutch famine and disease in later
life: an overview. Reproductive Toxicology 20, 345-352 (2005).
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14. Thank You!!!