the dynamic epigenome; an interface between nurture and nature moshe szyf department of pharmacology...

The dynamic epigenome; an interface between nurture and nature

Moshe SzyfDepartment of pharmacology and Therapeutics

McGill University, Montreal Canada

Moshe SzyfDepartment of pharmacology and Therapeutics

McGill University, Montreal Canada

OHAO SPRING SYMPOSIUMWednesday, 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

CH3

CH3

CH3

CH3

CH3 CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

MaintenanceDNA methyltransferase

DNA replicationCH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

De novo methyltransferaseDemethylase

CH3 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

XCH3 CH3

Transcription factor

Transcription factor

XAcAcAcAc AcAc

CH3 CH3

Sin3ASin3A

MECP2

SUV39

HDAC

AcAc

CHCH33 CHCH33

HP1

XFig. 3

DNA methylation silences gene expression by two mechanisms

NN

CHCH

CCNN

OO

HNHHNH

CH3CH3

CC

DNADNA

CC

NN

CHCH

CCHHNN

HNHHNH

OO

DNADNAHHOHOHCH3CH3OHOH

dMTasedMTase

DNMTDNMT

AdoMet AdoHcyAdoMet AdoHcy

The reversible methylation reactionThe reversible methylation reaction

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

environment environment

CH3

CH3

CH3

CH3

CH3

CH3

meth

ylase

dem

ethylase

active chromatin

inactive chromatin

Hypothesis: The steady state methylation pattern is a dynamicdynamic

equilibrium between methylase and demethylase activities

nutrients

toxinssocialbehavioral pathological

physiological

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

CH3

Human HEK cellsHuman HEK cells

GFP GFP

CH3

X

TSA

demethylasedemethylase

Human HEK cells

GFP

GFP

GFP

No origin of replication-no replication-no passive demethylation

HDAC inhibitors induce replication-independent active demethylation

QuickTime™ and a decompressor

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

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

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

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.QuickTime™ and a

decompressorare needed to see this picture.

QuickTime™ and a decompressor

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

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

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

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.QuickTime™ and a

decompressorare needed to see this picture.

QuickTime™ and a decompressor

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

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

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

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.QuickTime™ and a

decompressorare needed to see this picture.

CH3

CH3

CH3

demethylaseX

TSA

HAT binding

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

CH3

Ac

Ac

CH3

CH3

((++)) TTSSAA

- M H- M H - M H- M H

EcoRIEcoRI

controlcontrol

MM

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).

NN

CHCH

CCNN

OO

HNHHNHCH3CH3

CC

DNADNA

CC

NN

CHCH

CCHHNN

HNHHNH

OO

DNADNAdMTasedMTase

DNMTDNMT

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 decompressorare 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(17) REGION 16(5’ NGFI-A RE) METHYLATION TIMELINE

LOW

HIGH

Mea

n C

-Met

hyl

atio

n

0

0.2

0.4

0.6

0.8

1.0

1.2 GR (17) PROMOTER

NGFI-A

EMBRYODAY 20

BIRTHDAY 1

ADULTDAY 90

WEANINGDAY 21

PUPDAY 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-ACH3CH3

Ac Ac

Demethylase

HDAC TSA

demethylase

DNMT

SAM

X

SAM

NGFIA binding NGFIA bindingX

Detich et al. J Biol. Chem. 278, 20812-20820 (2003).SAM inhibits replication independent demethylation

NGFI-ACH3CH3

Ac Ac

Is it possible to reverse the effects of maternal care on DNA methylationand behavior in the adult rat?

(a) (b)

*

**

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

DemethylaseMBD2?

NGFI-ACH3CH3

Ac Ac

DNMT

DNA methylation and inter-individual phenotypicvariance

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 1/0Age (years) 36 ± 11 37 ± 11 33 ± 9 21PMI (hours) 23 ± 6.2 23 ± 3.7 23 ± 6.4 24pH 6.4 ± 0.2 6.6 ± 0.3 6.3 ± 0.2 6.42Childhood 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

phenotypeNon-genotoxic agents might have a profound effect on our genome

and our health icluding obesity, diabetes, cnacer autoimmune disease

AcknowledgementsAcknowledgements

• Suchin Tendulkar,• Steven Andrews• Jing-Ni Ou• Nancy Detich• Nadia Cervoni• Nada BORGHOL • Steffan Hamm George Just

MICHAEL MEANEY & IAN WEAVERSERGIY DYMOV, Patrick MacGowen Gustavo Turecki

SHAFAAT RABBANI, Bushra Ateq, Nicholai Shukeir, Pouya Pakenshan

Michael Hallet, Matt Suderman

THIS RESEARCH IS SUPPORTED BYGRANTS FROM NCIC, CIHR, HSFP & THE NICHD