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Introduction to Epigenetics
Manoj Kannan
BITS-Pilani & NCI-Frederick
Recap of some familiar terms in
genetics
Gene
Allele
Genotype
Phenotype
Gene expression
Gene silencing
Genome
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Genome expression
• Well-established paradigm of how genetic information is transcribed
and translated
• Human genome project has given plenty of data, which is still being
mined for useful information
• An estimated 140,000 proteins in the human body
• Different cells express a different subset of proteins
• Yet almost all cells have the same genomic sequence comprised of
just under 25,000 genes
• 25,000 genes  140,000 proteins?? Simple math doesn’t explain!
• Hence, it’s not just the genes, but how they are regulated that
explains the phenotype variations
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Here is a phenotype variation…
What do you think is the basis?
May be But
from different parents?
Well, age
difference…
epigenetically
Oh, okay
- mutation in the pigment causing gene?
different!
ALL THE MICE
ARE
GENETICALLY
IDENTICAL!
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What is Epigenetics?
• Study of heritable changes in gene
function that do not involve changes to the
nucleotide sequence of DNA
• When a cell undergoes mitosis or meiosis,
the epigenetic information is stably
transmitted to the subsequent generation
• Epigenetic controls add an ‘extra layer’ of
transcriptional control
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Three major epigenetic processes
we will discuss today…
• DNA Methylation
• Histone modifications
• RNA-mediated
phenomena
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DNA Methylation
Most well-studied epigenetic tag/mark; best understood
epigenetic cause of disease
Conserved across various kingdoms of life
SAM – S-adenosylmethionine
SAH – S-adenosylhomocystine
So, G, A, T, C…. and the fifth base, mC in
mammalian genome
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Distribution of DNA methylation
• In mammals, in the context of CpG dinucleotides (plants
have other types too)
• Methylated CpGs are associated with silenced DNA, eg.
Transposons, inactive X chromosome, imprinted genes
• “CpG islands”, associated with promoters of 40% of
mammalian genes, are generally free of methylation
eg. housekeeping genes, tissue-specific genes
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DNA methyltransferases (DNMTs)
2 major classes of enzymes in mammalian systems
De novo
methylases
Maintenance
methylase
Mouse knockouts of these genes tell us they
are necessary for the survival and proper
development of the organism.
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How does DNA methylation affect
gene transcription?
Unmethylated (or
hypomethylated) promoter
allows gene transcription
Methylated CpGs block
binding of TFs; hence,
transcription blocked
Me-CpG binding proteins
also preclude TF binding to
the promoter region
Other ways too…
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Role of DNA methylation
• Tight control for maintaining gene silencing (vertebrate
genes are less “leaky” compared to bacterial)
• Transcriptional silencing of transposons (‘genome
defense’ model)
• Genomic imprinting – one of the alleles of a gene is
silenced, depending on the parent of origin
• X inactivation – all but one of the X chromosomes in
female is inactivated – methylation of the inactive X copy
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Three major epigenetic processes
• DNA Methylation
• Histone modifications
• RNA-mediated
phenomena
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Structural organization of the
genome
Unless the genome is
accessible by the
transcription machinery of
the cell, the genome cannot
be functional!
Hence, the utilization of the
biological information in the
genome is dependent on
the chromatin organization.
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Structure of a nucleosome
~146 bp
DNA
Histone octamer
core
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Post-translational histone
modifications
A = acetylation
M = methylation
P = phosphorylation
U = ubiquitination
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Consequences of tail modifications
• Higher order chromatin structure is affected
eg. Addition of acetyl groups (-ve) neutralizes the positive
charge on lysine
=> affinity of the histone to bind tightly to DNA is reduced
=> chromatin becomes less compact
=> transcription of the associated gene is favored
Vice versa for deacetylation (the gene is repressed)
• Other proteins are attracted to these sites of
modifications….which, in turn, affect gene
expression
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Enzymes catalyze these covalent
tail modifications
• Histone Acetyl Transferases (HATs)
function as large, multiprotein complexes, eg. SAGA,
ADA complexes (yeast), TFTC complexes (humans);
associated with transciptional activation.
• Histone Deacetylases (HDACs)
part of multiprotein complexes, eg.Sin3, NuRD;
associated with transcriptional repression.
• Histone Methyl Transferases (HMTs)
• Histone Demethylases
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Comparing chromatin types
Transcriptionally active
chromatin/euchromatin
Transcriptionally inactive
chromatin/
heterochromatin
Chromatin conformation
Open, extended
conformation
Highly condensed
conformation
DNA CpG methylation
Relatively unmethylated,
especially at promoter
regions
Methylated, including at
promoter regions
Histone acetylation
Acetylated histones
Deacetylated histones
Histone methylation
H3-K4me3, R17me2
H3-K9me
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Crosstalk between DNA methylation
and chromatin modification
DNA
methylation
Self-reinforcing
repressive cycle
Histone
deacetylation
Histone H3-K9
methylation
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Three major epigenetic
processes
• DNA Methylation
• Histone modifications
• RNA-mediated
phenomena
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RNA interference (RNAi) causes
gene silencing
RNAi initiates heterochromatin formation in fission
yeast and DNA methylation in plants.
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Epigenetics in human disease
Association with various cancers –
stomach, kidney, colon, pancreas, liver,
uterus, lung and cervix
ICF syndrome
Fragile X syndrome
Angelman’s syndrome
HUMAN “EPIGENOME”
PROJECT
Rett Syndrome
Coffin-Lowry Syndrome
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Epigenetics….Environment
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Epigenetics….Environment
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Epigenetics….Environment
And Consciousness!
“The Biology of Belief:
Unleashing the Power of
Consciousness, Matter and
Miracles” is a recent book in
the market on epigenetics!
Disclaimer: I haven’t read the
book yet!
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References
• Genomes (3/E) – T.A. Brown
• Molecular Biology of the Cell (4/E) – Bruce
Alberts, et al.
• Human Molecular Genetics (2/E) –
Strachan & Read
• Developmental Biology (7/E) - Gilbert
• NCBI Bookshelf - free online books!
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books)
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Thank you!
Questions?
Discussion?
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If you want to read more about
Epigenetics…
• Chapter 10 of T.A. Brown’s Genomes (3/E), entitled
“Accessing the Genome” is an good place to start
• Special issue of Science 10 Aug. 2001 has a bunch of
excellent articles written by pioneers in the field. (slightly
dated, but still relevant)
• Science Functional Genomics Resources: Epigenetics
(portal hosted by the Americal journal, Science) – gives a
series of articles published in the field, and also a list of
useful websites
http://www.sciencemag.org/feature/plus/sfg/resources/res_epigenetics.dtl
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