nurture and nature

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7 Νοε 2013 (πριν από 3 χρόνια και 7 μήνες)

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The dynamic epigenome; an interface between
nurture and nature





Moshe Szyf

Department of pharmacology and Therapeutics

McGill University, Montreal Canada

OHAO SPRING SYMPOSIUM

Wednesday, March 26, 2008

Toronto ON

The programming of the genome is controlled by
the epigenome

The epigenome is composed of two components:

1) the

chromatin

which is associated with the DNA and

2)

DNA methylation

which is part of the covalent
structure of the genome and is therefore a stable long
-
term signal

DNA methylation is an interface between the
dynamic environment and the static genome

The dynamic epigenome and its
implications

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3

Maintenance

DNA methyltransferase

DNA replication

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3

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3

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3

CH
3

CH
3

De novo

methyltransferase

Demethylase

CH
3

CH

(DNMT3a, 3b and DNMT1?)

(DNMT1)

DNA methylation reactions

Anders H. Lund et al. Genes Dev. 2004; 18: 2315
-
2335

Covalent modifications of the N
-
terminal tail of the canonical
core histones






X

CH
3

CH
3

Transcription


factor

Transcription


factor



X

Ac

Ac

Ac

CH
3

CH
3


Sin3A

MECP2

SUV39

HDAC

Ac

CH
3

CH
3

HP1



X

Fig. 3

DNA methylation silences gene expression by two mechanisms

N

CH

C

N

O

HNH

CH3

C

DNA

C

N

CH

C
H

N

HNH

O

DNA

H
OH

CH3
OH

dMTase

DNMT

AdoMet AdoHcy

The reversible methylation reaction

The environment is dynamic, the chromatin is
dynamic, would DNA methylation remain static
throughout life?

environment

environment

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3

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3

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3

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3

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3

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3

methylase

demethylase

active chromatin

inactive chromatin

Hypothesis: The steady state methylation pattern is a



dynamic



equilibrium between methylase and demethylase activities

nutrients

toxins

social

behavioral

pathological

physiological

Methylated DNA is actively demethylated in
a replication independent manner upon
induction of histone acetylation by TSA

CH
3



Human HEK cells




Human HEK cells

CH
3

X

TSA

demethylase




Human HEK cells

No origin of replication
-
no
replication
-
no passive
demethylation


HDAC inhibitors induce replication
-
independent active
demethylation

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decom pr essor
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decom pr essor
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
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decom pr essor
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3
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3
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3
demethylase
X
TSA
HAT binding
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decom pr essor
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
Q uickTim e™ and a
decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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decom pr essor
ar e needed t o see t his pict ur e.
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CH
3
Ac
Ac
Ac
Ac
Ac
Ac
Ac
demethylase
CH
3
CH
3
(
(
+
+
)
)


T
T
S
S
A
A
- M H
- M H
- M H
- M H
EcoRI
EcoRI
control
control
M
M
U
U
(529bp)
(529bp)
- R1 D1 X
- R1 D1 X
Cervoni et al.,
J. Biol. Chem

276,

40788 (2001)

Cervoni et al.,

J. Biol. Chem
.
277
, 25026 (2002)

Detich et al.,
J Biol. Chem
.

278
, 27586 (2003).



N

CH

C

N

O

HNH

CH3

C

DNA

C

N

CH

C
H

N

HNH

O

DNA

dMTase

DNMT

Is there
in vivo

evidence for a
dynamic methylation pattern in
postmitotic tissue?

LOW LG

HIGH LG

Glucocorticoid receptor gene

GR GENE

GR RECEPTORS

GR GENE









GR RECEPTORS

Environmental programming of gene activity

STRESS RESPONSE

STRESS RESPONSE

PUP (Day 1
-
6)

ADULT (Day 90)

QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
MECHANISM

How are the long
-
term effects of maternal care on gene
expression in the offspring maintained into adulthood?

How are these differences transmitted across generations?

HIPPOCAMPAL GR(1
7
) REGION 16

(5’ NGFI
-
A RE) METHYLATION TIMELINE

LOW

HIGH

Mean C
-
Methylation

0

0.2

0.4

0.6

0.8

1.0

1.2

GR (1
7
) PROMOTER

NGFI
-
A

EMBRYO

DAY 20

BIRTH

DAY 1

ADULT

DAY 90

WEANING

DAY 21

PUP

DAY 6

Age

*

*

*

In the adult (day 90) rat hippocampal GR
gene expression of Low LG
-
ABN offspring
is
reversed

by TSA

DNMT

NGFI
-
A

X

High LG




Low LG

NGFI
-
A

CH
3

CH
3

Ac

Ac

Demethylase

HDAC

TSA

demethylase

DNMT

SAM

X

SAM

NGFIA binding

NGFIA binding

X

Detich et al.
J Biol. Chem
.
278
, 20812
-
20820 (2003).


SAM inhibits replication independent demethylation


NGFI
-
A

CH
3

CH
3

Ac

Ac

Is it possible to reverse the effects of maternal care on DNA methylation

and behavior in the adult rat?


0
10
20
30
40
50
60
70
80
90
100
110
Low LG-ABN
High LG-ABN
Maternal care
Time spent in inner field (min)
Vehicle
TSA
Methionine
(a)

(b)

0
50
100
150
200
250
300
350
400
Low LG-ABN
High LG-ABN
Maternal care
Total number of squares crossed
Vehicle
TSA
Methionine
*

**

Methionine treatment reverses Open Field Behavior of Adult (Day
-
90)



Male Offspring of High LG
-
ABN maternal care

PKA

Behavioural gene programming

5
-
HT

cAMP

NGFI
-
A

HAT

Demethylase

MBD2?

DNMT

DNA methylation and inter
-
individual phenotypic

variance


Working hypothesis:


environment



epigenetic changes




inter
-
individual epigenetic variation



gene expression programming


Phenotypic variation


.


Suicide study and control
group

Male/Female
13/0
5/0
11/0
1/0
Age (years)
36 ± 11
37 ± 11
33 ± 9
21
PMI (hours)
23 ± 6.2
23 ± 3.7
23 ± 6.4
24
pH
6.4 ± 0.2
6.6 ± 0.3
6.3 ± 0.2
6.42
Childhood Abuse/Neglect
13/13 100%
0/5 0%
0/11 0%
0/1 0%
Mood
9/13 69%
5/5 100%
3/11 27%
0/1 0%
Alcohol/drug dependence
9/13 69%
3/5 60%
5/11 46%
0/1 0%
Anxiety
3/13 23%
0/5 0%
1/11 9%
1/1 100%
The values are mean ± SD.
(n = 13)
(n = 5)
(n = 11)
(n = 1)
Suicide
Additional Suicide
Control
Additional Control
Methylation of the GR locus and its
chromosomal neighborhood in suicide
completers


Genome wide organization of differentially
methylated promoters

What are the implications of a life
-
long
dynamic epigenome?

chemical

social

Signaling pathways

Epigenome

phenotype

Non
-
genotoxic agents might have a profound effect on our genome
and our health icluding obesity, diabetes, cnacer autoimmune
disease

Acknowledgements


Suchin Tendulkar,



Steven Andrews


Jing
-
Ni Ou


Nancy Detich


Nadia Cervoni


Nada BORGHOL


Steffan Hamm
George Just


MICHAEL MEANEY

& IAN WEAVER

SERGIY DYMOV, Patrick MacGowen


Gustavo Turecki


SHAFAAT RABBANI,
Bushra Ateq,

Nicholai Shukeir, Pouya Pakenshan


Michael Hallet,

Matt Suderman

THIS RESEARCH IS SUPPORTED BY

GRANTS FROM NCIC, CIHR, HSFP & THE NICHD