Transcript Epigenetic modifications

Epigenetics of Human
Marie Černá
Lecture No 426-H
Interaction of
environment and genotype
external factor
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external factor
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external factor
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external factor
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external factor
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epigenetic modifications
gene pool
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gene pool
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gene pool
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gene pool
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gene pool
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Epigenetic modifications
- allow interaction of environment
with identical genotypes and by the way
formation of their various phenotypes
- modifications of gene expression which
do not involve nucleotide changes
- can be heritable
Metastable epialleles
- identical alleles
that are variably expressed
due to epigenetic modifications
that are established during life
- can be hereditary
Epigenetic modifications change
level of gene expression
Influence of environment:
- In utero
- Ex utero
Epigenetic modifications change
level of gene expression
They depend on
- environment (internal + external)
- age
- sex
Epigenetic modifications
- genome is an open system
with biological clock
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period of early pregnancy
period of medium pregnancy
period of late pregnancy
early postnatal period (until 3 years)
period of puberty (in ♀ 2 years early)
period of mode exchange (30-40 years)
Reik W, Dean W, Walter J, 2001, Science, 293, 1089-1093.
Epigenetic reprogramming in mammalian development
Epigenetic modifications
in monozygotic twins
Fraga et al., 2005, PNAS, 102, 10604-10609
in 65% pairs identical
in 35% pairs different
correlation with age and
with time spending together
Epigenetic modifications
• DNA methylation
• Histone modifications
• RNA interference
Epigenetic modifications
• Chromosomal position effects
• Polycomb and Trithorax complexes
• Prions and prion-like phenomena
Inactivation of gene expression
heterochromatin – closed chromatin
DNA methylation of CpG islands
Histone modifications
- deacetylation (H3K9)
- methylation (H3K9, H3K27, H4K20)
- sumoylation
- ubiquitination
Activation of gene expression
euchromatin – open chromatin
DNA hypomethylation of CpG islands
Histone modifications
- acetylation (H3K9)
- methylation (H3K4, H3K36, H3K79)
- phosphorylation
- ubiquitination
Mechanism of DNA methylation
Participation of protein complexes:
• DNA methyltransferases (DNMT)
- DNMT 1 – maintenance methylation
- DNMT 3A+3B – de novo methylation
• Methyl-CpG-binding protein (MeCP)
DNA methylation of CpG islands
Mechanism of histone modification
Participation of protein complexes:
• histone acetyltransferases (HAT)
• histone deacetylases (HDAC)
• histone methyltransferases (HMT)
• histone demethylases (LSD)
DNA-histone modifications
Dietary methyl supplementation
RNA interference
a natural process of gene expression
silencing, at the stage of translation or
transcription, by non-coding RNA:
1)short RNAs – obtained from digestion
of double-stranded RNAs (dsRNAs)
2)long RNAs (> 200 nucleotides)
Targets of RNA interference
short RNAs:
• inactivation of RNA from viruses
• inactivation of RNA from mobile
elements (transposons)
long RNAs:
• inactivation of X chromosome
Mechanism of RNA interference
Participation of protein complexes:
• Dicer with RNase activity
• RISC (RNA-induced silencing complex)
• RITS (RNA-induced transcriptional silencing)
• PIWI proteins
short RNAs
1)micro RNA (miRNA)
2)short interfering RNA (siRNA)
3)Piwi-interacting RNA (piRNA)
short RNAs (in cytoplasm)
x small RNAs (in nucleus et nucleolus)
micro RNA (miRNA)
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21-23 nucleotides
Endogenic
Binding to RISC
Partial recognition of complementary
sequence in 3’-UTR (nontranslated region)
• Inhibition of translation process by
binding to target mRNA
short interfering RNA (siRNA)
• 20-25 nucleotides
• Exogenic
• Binding to RISC or RITS (chromatin
modifications)
• Full recognition of complementary
sequence in coding region
• Initiation of mRNA digestion/degradation
Piwi-interacting RNA (piRNA)
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27-30 nucleotides
Exogenic
Binding to PIWI proteins
Influence of epigenetic regulation
Control of transposons silencing
Significance for diagnosis
Searching specific miRNAs
in blood and urine of patients
with a goal to obtain biomarkers for
diagnostics and progress evaluation
of disease (tumors)
In man there was described ≈ 2 500 miRNA.
Chromosomal position effects
Insulators – sequences along the DNA that
attract particular proteins (CTCF protein) for
the purpose of preventing distal enhancers
from activating or silencing genes
insulator functions:
- establish the boundaries of regulatory domains
- modify chromatin structure
- affect nuclear organization
Polycomb and Trithorax
complexes
maintain and propagate expression states
(active or silent) of homeotic genes,
HOX genes, throughout development by
the counteracting activities:
- silencing through trimethylation of H3K27
by Polycomb complexes
- activation through trimethylation of H3K4
by Trithorax complexes
Prions and prion-like
phenomena
An auto-regulatory loop – capable of
maintaining persistent cellular characteristics
the structural inheritance – the faithful
reproduction of a structure made of proteins
the regulatory inheritance – transgenerational
continuing of established function of proteins,
greatly influenced by the environment
Significance in etiology of tumors
Significance in therapy
Disease
Therapy
Physiology
Expression
Genome
Environment
Epigenetics
Definition of live system and life
Life is specific organization of matter,
energy and information
very complicated open system
• with high level of orderliness
• with capability of reproduction
• with capability of development (evolution)