Epigenetics of Human

Marie Černá

Lecture No 426-H

Interaction of environment and genotype

gene pool1 gene pool

2

gene pool3

gene pool4

gene pool5

external factor 1

external factor 2

external factor 3

external factor 4

external factor 5

epigenetic modifications

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• 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 modificationsin 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

• DNA methylation

• Histone modifications

• RNA interference

Epigenetic modifications

Epigenetic modifications

• Chromosomal position effects

• Polycomb and Trithorax complexes

• Prions and prion-like phenomena

Inactivation of gene expressionheterochromatin – closed chromatin

DNA methylation of CpG islands

Histone modifications

- deacetylation (H3K9)

- methylation (H3K9, H3K27, H4K20)

- sumoylation

- ubiquitination

Activation of gene expressioneuchromatin – 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)

• 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)

• 27-30 nucleotides

• Exogenic

• Binding to PIWI proteins

• Influence of epigenetic regulation

• Control of transposons silencing

Significance for diagnosis

Searching specific miRNAsin blood and urine of patientswith a goal to obtain biomarkers fordiagnostics and progress evaluationof 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

EpigeneticsEnvironment

Expression

Genome

Physiology

Disease

Therapy

Significance in therapy

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)