Epigenetics
Petr Müller
Molecular and Cellular Pathophysiology
Human tissues are composed of differentiated cells
The daughter cells inherit the basic properties from
parental cells
All cells of the body retain complete genetic
information that remains unchanged throughout
life.
Epigenetics is the study of heritable phenotype changes that do
not involve alterations in the DNA sequence.
Epigenetics most often involves changes that affect gene
activity and expression, but the term can also be used to
describe any heritable phenotypic change.
Mechanisms:
• Covalent modifications
• RNA transcripts
• MicroRNAs
• mRNA
• sRNAs
• Prions
• Structural inheritance
• Nucleosome positioning
• Histone variants
• Genomic architecture
Epigenetics definitions and mechanisms
• process by which methyl groups are added to the
DNA molecule.
• Methylation can change the activity of a DNA
segment without changing the sequence
CpG islands are usually defined as regions with:
1) a length greater than 200bp,
2) a G+C content greater than 50%,
3) a ratio of observed to expected CpG greater than 0.6,
In mammals however, DNA methylation is almost
exclusively found in CpG dinucleotides, with the
cytosines on both strands being usually methylated.
DNA methylation
DNA methyltransferases (in mammals)
1. maintenance methylation (Maintenance methylation activity is necessary to
preserve DNA methylation after every cellular DNA replication cycle).
2. de novo methylation
DNMT1
- maintanance
DNMT3a and DNMT3b
- the de novo methyltransferases that set up DNA
methylation patterns
Model of DNMT3A activity. The DNMT3A protein complex is
associated at promoters of silent genes in a complex with
histone methyltransferase (HMT), histone deacetylase
(HDAC) and DNA methyltransferase 3L (DNMT3L). These
promoters are marked by DNA methylation, histone
deacetylation and histone 3 lysine 9 methylation (K9me3).
Detection of methylation
McrBC is an endonuclease which cleaves
DNA containing methylcytosine* on one or
both strands
1) Using methylation sensitive
restriction endonucleases
2) Using bisulfite conversion
Outline of the chemical reaction that underlies the bisulfite-catalyzed conversion of
cytosine to uracil.
DNA demethylation
• TET enzymes are a family of ten-eleven translocation (TET)
methylcytosine dioxygenases.
• They are instrumental in DNA demethylation.
Oxoguanine glycosylase (OGG1)
recruits TET enzyme
The effect of epigenetic regulation can be observed
in identical twins.
Jean-Baptiste Lamarck
• 1744 – 1829
• French biologist, first author of evolutionary
theory
• Theory of inheritance of acquired characteristics,
called Lamarckism
Epigenetics and inheritance
C. H. Waddington
• 1905 – 1975
• British developmental biologist
• proposed an evolutionary process, "genetic assimilation", as
a Darwinian mechanism that allows certain acquired
characteristic to become heritable
• Proposed imprinting and epigenetic landscape
Can epigenetic information be
passed on to the next generation ?
The term ‘‘imprinting’’ was first used by the cytogeneticist HelenCrouse in the 1960s to describe the elimination
of paternally derived X chromosomes in flies
The epigenetic imprints regarding the parental origin are established during male and
female gametogenesis, passed to the zygote through fertilization, maintained throughout
development and adult life, and erased in primordial germ cells before the new imprints are
set.
Genomic imprinting in mammals: its life cycle, molecular
mechanisms and reprogramming
Can we detect imprinting by detection of methylation in sperm or oocyte?
• post-fertilization epigenetic reprogramming
• DNA methylation is reset before implantation exept imprinted genes
• DNA methylation marks at the DMRs of imprinted genes are stable through embryogenesis
and early development, until they are reprogrammed in primordial germ cells.
In 2019, 260 imprinted
genes have been reported
in mice and 228 in
humans.
• Prader-Willi syndrome (PWS) is a complex neurodevelopmental genetic
condition due to paternal loss of imprinted genes on chromosome 15
• characterized by a range of mental and physical
• 350,000–400,000 people worldwide.
Diseases associated with impaired genomic imprinting in human
• Angelman syndromes
• Silver-Russell syndrome
• Beckwith-Weidemann syndrome
• Albright hereditary
osteodystrophy
• uniparental disomy 14
Assisted Reproductive Technology
(ART) related genomic imprinting
Under physiological conditions, proliferation and survival
genes are transcribed at a basal rate to maintain
homoeostasis.
During the transformation chromatin surrounding protooncogenes
becomes enriched for histone acetylation,
especially at enhancer regions.
This change in chromatin programming allows nucleosome
decompaction, which facilitates the recruitment of
bromodomain chromatin remodellers, such as the SWI/SNF
complex, that further open chromatin to allow the binding of
transcription factors (TF).
Epigenetics and cancer
Mutated Chromatin Regulatory Factors as Tumor Drivers in Cancer
IDH1, IDH2
• Isocitrate dehydrogenase
• Production of 2-HG -> DNA hypermethylation
• Mutated in glioblastoma and hematologic
malignancies
SWI/SNF complexes
• ATP dependent chromatin remodeling
• SMARCA4- the most frequently mutated
chromatin remodeling ATPase in cancer
• SMARCB1
• ARID1A
DNA and histone methyl transferase/demethylase
Pharmacological intervention of chromatine remodeling (in oncology)
BET inhibitors
IDH inhibitors
Histon deacetylase inhibitors
Histon methyl-transferace inhibitors inhibitors
Pharmacological intervention of chromatine remodeling (in oncology)
BET inhibitorsIDH inhibitors
Histon deacetylase inhibitors
Histon methyl-transferace inhibitors inhibitors
bromodomain is an approximately 110
amino acid protein domain that
recognizes acetylated lysine residues
IDH1 and IDH2 are both nicotinamide
adenine dinucleotide phosphate (NADP)dependent
enzymes that catalyze the
oxidative decarboxylation of isocitrate to
alpha-ketoglutarate (α-KG), while
producing NADPH.
FDA has so far approved four HDAC
inhibitors for the treatment of
cancer (romidepsin, belinostat
panobinostat, vorinostat)
Chronological age (y-axis) versus DNAm age (x-axis) across
different cells and tissues
In humans and other mammals, DNA
methylation levels can be used to
accurately estimate the age of tissues
and cell types, forming an accurate
epigenetic clock
Methylation and aging
• Ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA
methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of
glaucoma and in aged mice.
• The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2.
Changes to DNA methylation patterns over time form
the basis of ageing clocks, but whether older individuals
retain the information needed to restore these
patterns—and, if so, whether this could improve tissue
function—is not known.
Chromatine remodelation to
DNA methylation