1. Introduction to Epigenetics
Manoj Kannan
BITS-Pilani & NCI-Frederick

2. Recap of some familiar terms in genetics
Allele
Genotype
Phenotype
Gene expression
Gene silencing
Genome

3. 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

4. Here is a phenotype variation…
What do you think is the basis?
But epigenetically different!
ALL THE MICE ARE GENETICALLY IDENTICAL!
May be from different parents?
Well, age difference…
Oh, okay - mutation in the pigment causing gene?

5. 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

6. Three major epigenetic processes we will discuss today…
DNA Methylation
Histone modifications
RNA-mediated phenomena

7. 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

8. 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

9. 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.

10. 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…

11. 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

12. Three major epigenetic processes
DNA Methylation
Histone modifications
RNA-mediated phenomena

13. 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.

14. Structure of a nucleosome
Histone octamer core
~146 bp DNA

15. Post-translational histone modifications
A = acetylation
M = methylation
P = phosphorylation
U = ubiquitination

16. 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

17. 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

18. 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
Histone methylation
Acetylated histones
H3-K4me3, R17me2
Deacetylated histones
H3-K9me

19. Crosstalk between DNA methylation and chromatin modification
Histone deacetylation
Histone H3-K9 methylation
Self-reinforcing
repressive cycle

20. Three major epigenetic processes
DNA Methylation
Histone modifications
RNA-mediated phenomena

21. RNA interference (RNAi) causes gene silencing
RNAi initiates heterochromatin formation in fission yeast and DNA methylation in plants.

22. 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
Rett Syndrome
Coffin-Lowry Syndrome
HUMAN “EPIGENOME”
PROJECT

23. Epigenetics….Environment

24. Epigenetics….Environment

25. 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!

26. 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! (

27. Thank you! Questions? Discussion?

28. 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 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