Epigenetic programming the important first 1000days (4)

Prévia do material em texto

Acta Paediatrica. 2020;109:443–452.	 wileyonlinelibrary.com/journal/apa	 	 | 	443© 2019 Foundation Acta Pædiatrica. 
Published by John Wiley & Sons Ltd
 
Received:	8	July	2019  |  Revised:	7	September	2019  |  Accepted:	8	October	2019
DOI:	10.1111/apa.15050		
R E V I E W A R T I C L E
Epigenetic programming—The important first 1000 days
Agnes Linnér1  | Malin Almgren2
1Department	of	Women’s	and	Children’s	
Health,	Karolinska	Institutet,	Stockholm,	
Sweden
2Department	of	Clinical	Neuroscience,	 
Karolinska	Institutet,	Stockholm,	Sweden
Correspondence
Agnes	Linnér,	Department	of	Women’s	and	
Children’s	Health,	Karolinska	Institutet,	
Stockholm,	Sweden.
Email:	agnes.linner@ki.se
Abstract
The	perinatal	period	is	a	time	of	fast	physiological	change,	including	epigenetic	pro‐
gramming.	 Adverse	 events	 may	 lead	 to	 epigenetic	 changes,	 with	 implications	 for	
health	and	disease.	Our	review	covers	the	basics	of	clinical	epigenetics	and	explores	
the	 latest	 research,	 including	 the	 role	 of	 epigenetic	 processes	 in	 complex	 disease	
phenotypes,	 such	 as	 neurodevelopmental,	 neurodegenerative	 and	 immunological	
disorders.	Some	studies	suggest	that	epigenetic	alterations	are	linked	to	early	life	en‐
vironmental	stressors,	including	mode	of	delivery,	famine,	psychosocial	stress,	severe	
institutional	deprivation	and	childhood	abuse.
Conclusion: Epigenetic	modifications	due	to	perinatal	environmental	exposures	can	
lead	to	lifelong,	but	potentially	reversible,	phenotypic	alterations	and	disease.
K E Y W O R D S
deoxyribonucleic	acid	methylation,	developmental	origins	of	health	and	disease,	epigenetics,	
paediatrics,	perinatology
1  | INTRODUC TION
All	 our	 cells	 contain	 more	 or	 less	 identical	 deoxyribonucleic	 acid	
(DNA).	Yet	they	constitute	organs	each	with	specific	tasks	and	roles	
in	our	body.	The	genome	in	every	cell	is	the	same,	but	the	epigenome	
is	different	and	this	contributes	to	differences	in	protein	expression.	
During	the	last	couple	of	decades,	the	field	of	epigenetic	research	has	
grown	quickly	and	the	public	 is	becoming	aware	of	 it.	For	example,	
parents’	web	 sites	describe	how	cuddling	 can	 leave	positive	 traces	
on	your	baby's	DNA	and	talk	about	how	to	eat	methyl	donor	foods.
The	 epigenome	 refers	 to	 all	 epigenetic	marks	 on	 the	 genome,	
in	 other	 words	 the	 overall	 epigenetic	 state	 or	 functional	 genome	
of	the	cell.	Epigenetics,	which	literally	means	on	top	of	genetics,	 is	
defined	as	the	mechanisms	of	heritable,	over	cell	divisions,	specific	
cell	functions	or	phenotypes	that	do	not	directly	involve	the	primary	
DNA	sequence.	Epigenetic	mechanisms	enable	the	environment	to	
interact	with	genes,	 switching	 them	on	and	off,	 and	 this	 regulates	
the	 plasticity	 of	 the	 cell	 phenotype.	 This	 functional	 genome	with	
DNA	 transcription	 and	 ribonucleic	 acid	 (RNA)	 translation	 is	 re‐
sponsible	for	the	protein	expression	in	each	cell	and,	ultimately,	the	
phenotype.	Epigenetic	programming	is	most	active	during	foetal	life	
and	lasts	from	conception	until	the	child's	second	birthday.1	These	
first	1000	days	are	very	important.2
Epigenetics	is	a	dynamic	process	in	cell	differentiation	that	was	
first	described	by	Waddington	in	the	1950s.	He	depicted	an	epigene‐
tic	landscape	and	described	epigenetics	as	the	branch	of	biology	that	
studies	 the	causal	 interactions	between	genes	and	 their	products,	
which	brings	the	phenotype	 into	being.3	Epigenetic	marks	change,	
and	make	changes,	as	cells	differentiate	and	this	process	can	persist	
through	mitosis	 and	meiosis	 as	 cells	 divide.	 Studies	 even	describe	
transgenerational	 inheritance	 of	 phenotypes,	 but	 the	 underlying	
molecular	mechanisms	still	need	to	be	explored4	(Figure	1).
Epigenetics	is	important	during	differentiation	and	development.	
An	advantageous	environment	can	guide	healthy	development,	but	
an	adverse	environment	can	also	have	epigenetic	consequences,	by	
contributing	 to	 acute	 or	 future	 disease	 development.	 Historically,	
most	epigenetic	 studies	have	been	carried	out	 in	cancer	 research.	
In	 some	cancers,	 there	are	no	mutations,	 changes	 in	 the	DNA	se‐
quence,	but	epigenetic	aberrations	 lead	 to	detrimental	protein	ex‐
pression	and	uncontrolled	cell	division.
This	 review	 describes	 the	 epigenetics	 relevant	 to	 paediatrics,	
and	in	developmental	origins	of	health	and	disease,	but	omits	most	
of	the	cancer	epigenetics.
Abbreviations:	ART,	Assisted	reproduction	techniques;	DNA,	Deoxyribonucleic	acid;	
ICR,	Imprinting	control	regions;	RNA,	Ribonucleic	acid;	CpG,	Cytosine	guanine	pair.
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444  |     LINNÉR aNd aLMGREN
2  | T YPES OF EPIGENETIC 
MODIFIC ATIONS
The	modern	definition	of	epigenetics	 refers	 to	a	modification	that	
is	not	a	mutation	and	that	is	initiated	by	a	signal.	It	is	inherited	dur‐
ing	mitosis,	even	in	the	absence	of	this	signal,	and	that	affects	the	
regulation	of	gene	transcription	and	ultimately	protein	translation.5 
Mechanisms	can	be	pre‐	or	post‐translational,	such	as	DNA	methyla‐
tion	and	histone	modification,	respectively.	Epigenetic	modifications	
change	the	accessibility	of	DNA	for	transcription	to	RNA	in	differ‐
ent	ways.	The	most	studied	epigenetic	mechanism	is	DNA	methyla‐
tion,	as	methylation	is	stable,	DNA	is	easy	to	extract	from	cells	and	
possible	to	store.6	The	main	epigenetic	mechanisms	are	described	in	
sequential	order	(Figure	2).
2.1 | Histone modifications
The	DNA	chain	consists	of	nucleic	acids	that	are	packed	into	chro‐
matin	 and	 further	 organised	 in	 nucleosomes.	 In	 nucleosomes,	 the	
chromatin	 is	wrapped	around	a	 complex	of	 eight	histone	proteins.	
Post‐translational	modifications	of	histones	take	place	at	the	amino	
acids	lysine,	arginine	and	serine	of	histone	tails,	which	can	be	acety‐
lated,	methylated,	phosphorylated,	ubiquitinated	or	sumoylated.	The	
location	and	combination	of	the	modifications	can	lead	to	differences	
in	chromatin	structure.	Euchromatin,	more	open	chromatin,	which	is	
available	for	transcription	is	present	for	example	in	embryonic	stem	
cells.	 Heterochromatin	 is	 more	 closed	 and	 unavailable	 chromatin,	
present	 in	 differentiated	 cells.	 Change	 in	 chromatin	 structure	 can	
bring	DNA	segments	 together	and	enable	 interaction,	 for	example	
the	interaction	of	promoters	and	enhancers.	This	higher‐order	chro‐
matin	organisation	describes	how	the	chromatin	is	organised	in	three	
dimension	in	the	nucleus.	Large	organised	chromatin	lysine	K	modi‐
fications	organise	 the	 regulation	of	 gene	 regions.	 The	 role	of	 lam‐
ina‐associated	domains	 is	 similar.	Topologically	associated	domains	
contribute	to	the	unique	functions	in	cells	and	tissues	by	organising	
sequences	far	apart	in	the	DNA	in	a	domain	to	enable	interaction.6
2.2 | DNA methylation
DNA	methylation	refers	to	a	methyl	group	being	covalently	bound	to	a	
cytosine	(C)	nucleotide	on	the	5’	position	of	a	guanine	nucleotide	(G)	in	
the	DNA,	at	a	cytosine	guanine	pair	(CpG).	Methylation	of	other	nucleo‐
tides	does	occur,	but	CpG	methylation	is	the	most	common	in	mammals.	
Most	CpGs	in	mammals	are	methylated.	CpGs	are	unevenly	distributed	
with	a	higher	density	in	CpG	islands	that	are	usually	hypomethylated	
regions.	 Promoters	 are	 often	 located	 in	 CpG	 islands.	 Enhancers	 are	
other	cis‐regulatory	sequences	that	can	be	far	away	from	the	promoter	
region	on	the	DNA,	but	interact	with	the	promoter.	These	regulatory	
elements	may	also	be	methylated.	Methylated	CpG	pairs	in	regulatory	
elements	usually	 inhibit	binding	of,	for	example,	transcription	factors	
and	polymerases,	leading	to	inhibition	of	gene	expression.
Differentially	 methylated	 regions	 are	 regions	 that	 have	 differ‐
ent	methylation	 patterns	 between	 samples	 coming	 from	 different	
cells,	 tissues	and	 time	points.	Differences	between	 individuals	are	
referred	to	as	variable	methylated	regions.
Methylationcan	 be	 reversible,	meaning	 that	 genes	 can	 be	 ac‐
tivated	 or	 deactivated	 throughout	 life,	 but	 they	 can	 also	 be	 per‐
manently	 methylated	 through	 cell	 differentiation.	 However,	 DNA	
methylation	has	a	 limited	direct	effect	on	transcription	of	an	adja‐
cent	gene.7	Methylation	status	is	remembered	during	cell	divisions:	
an	 inherited	 epigenetic	 pattern.	 De	 novo	 and	 maintenance	 DNA	
methyl	transferases	are	enzymes	responsible	for	methylation	at	dif‐
ferent	stages,	for	example	the	methylation	of	a	daughter	DNA	strand	
at	the	corresponding	site	after	mitosis.6
2.3 | Non‐coding RNA
The	majority	of	the	transcribed	DNA	is	non‐coding	RNA.	Probably	
only	about	1%	of	 the	genome	 is	protein‐coding	DNA.	Non‐coding	
Key Notes
•	 Fast	 physiological	 changes	 take	 place	 during	 the	 peri‐
natal	period	and	adverse	events	may	 lead	 to	epigenetic	
changes,	with	implications	for	health	and	disease.
•	 This	review	covers	the	basics	of	clinical	epigenetics	and	
explores	the	latest	research,	including	the	role	of	epige‐
netic	processes	in	complex	disease	phenotypes.
•	 We	conclude	 that	 epigenetic	modifications	due	 to	peri‐
natal	 environmental	 exposures	 can	 lead	 to	 lifelong,	 but	
potentially	reversible,	phenotypic	alterations	and	disease.
F I G U R E 1  Epigenetic	marks	change	and	make	change	as	cells	differentiate.	They	can	persist	through	mitosis	and	meiosis	as	cells	divide	
and	organisms	develop.	Here	illustrated	by	metamorphosis	of	the	Papilio	machaon.	Picture	by	Jens	Stolt,	Fotolia,	accessed	at	https	://allyo	
uneed	isbio	logy.files.wordp	ress.com/2015/07/fotol	ia_origi	nal_38380	192_x2.jpg
https://allyouneedisbiology.files.wordpress.com/2015/07/fotolia_original_38380192_x2.jpg
https://allyouneedisbiology.files.wordpress.com/2015/07/fotolia_original_38380192_x2.jpg
     |  445LINNÉR aNd aLMGREN
RNA	can	be	 long	or	short	and	act	 in	a	housekeeping	or	regulatory	
fashion.	 Its	 role	 is	 suppressing	protein	production,	 for	example	by	
base‐pairing	and	blocking	or	degrading	RNA.	Micro	RNA	also	exists	
in	bodily	 fluids	and	 it	mediates	 intercellular	communication.	 In	ad‐
dition	to	the	more	classic	epigenetic	modulators,	DNA	methylation	
and	chromatin	modification,	 long	non‐coding	RNA	and	micro	RNA	
are	also	considered	a	part	of	the	epigenetic	machinery.	They,	in	turn,	
are	often	regulated	by	epigenetic	mechanisms.6
3  | REL ATIONSHIP BET WEEN THE 
EPIGENOME AND THE GENOME
Single‐nucleotide	 polymorphisms	 are	 differences	 in	 the	 DNA	 se‐
quence.	They	are	 important	 in	genetics,	but	also	often	mentioned	
in	 epigenetic	 research	 as	 they	 can	 affect	 the	 methylome.	 If	 sin‐
gle‐nucleotide	polymorphisms	are	associated	with,	or	affect,	DNA	
methylation	in	a	specific	locus,	they	are	referred	to	as	methylation	
quantitative	trait	 loci.	The	general	definition	of	a	quantitative	trait	
locus	 is	a	DNA	sequence	that	 is	associated	with	a	phenotype	or	a	
trait.6	A	study	by	Liu	et	al	was	the	first	to	show	that	DNA	methyla‐
tion	can	be	a	potential	mediator	of	genetic	risk.	The	authors	asso‐
ciated	the	DNA	methylation	profile	of	healthy	people	and	patients	
with	 rheumatoid	 arthritis	 with	 their	 genotypes.	 They	 found	 that	
several	differentially	methylated	positions	were	dependent	on	 the	
rheumatoid	arthritis	risk	single‐nucleotide	polymorphisms	and	they	
also	potentially	mediated	the	disease	risk	effects	of	 the	single‐nu‐
cleotide	polymorphisms.8
4  | APPROACHES IN STUDYING 
EPIGENETIC MODIFIC ATIONS
As	 a	 clinical	 researcher	 interested	 in	 epigenetics	 you	 need	 to	
consider	 which	 analyses	 are	 relevant	 and	 what	 is	 feasible	 with	
a	certain	study	population.	You	need	 to	decide	whether	you	are	
interested	 in	 a	 regulatory	 region,	 a	 specific	 gene	or	 the	genome	
as	a	whole.	The	size	of	 the	study	cohort	and	 the	budget	 for	 the	
analyses	are	of	importance.	Which	organ	are	you	interested	in	and	
is	the	tissue	available	for	sampling?	There	are	large	inter‐individual	
variations	in	epigenetic	marks.	This	means	that	large	sample	sizes	
may	be	needed	to	be	able	to	show	statistically	significant	differ‐
ences	related	to,	for	example,	an	environmental	factor.	This	is	sel‐
dom	feasible	in	clinical	studies.	Differences	in	methylation	status	
are	usually	 very	 small	 in	 population‐based	epigenetic	 studies,	 at	
around	 5%.9	 As	 we	will	 discuss	 later,	 the	methylome	 varies	 be‐
tween	cells	and	tissues.	Part	of	a	detected	variation	in	methylation	
between	individuals	can	also	be	explained	by	cell	composition	and	
F I G U R E 2  Epigenetic	mechanisms	are	important	in	cell	and	
organism	plasticity,	especially	during	gestation	and	childhood.	
DNA	methylation	can	“tag”	and	activate	or	inactivate	genes.	
Histone	modifications	can	make	DNA	more	or	less	accessible	for	
transcription	by	changing	the	chromatin	organisation.	This	has	
implications	for	health	and	disease	development
TA B L E 1  Summary	of	epigenetic	modifications	and	how	and	when	to	study	them
Epigenetic modifications Experimental methods Research applications
Global	DNA	methylation	and	
hydroxymethylation
Luminometric	methylation	assays
Methylation	sensitive	enzyme‐linked	immunosorb‐
ent	assays
To	compare	average	methylation	status	of	the	whole	
genome	in	different	cells	or	individuals,	the	amount	
of	methylation	regardless	of	the	position
Gene‐specific	DNA	methylation	
and	hydroxymethylation
Sodium	bisulphite	approach:	Bisulphite	
pyrosequencing
High	resolution	melting
Methyl‐sensitive	PCR
Restriction	enzymes	approach
Affinity	approach,	antibodies:	Methylated	DNA	
immunoprecipitation	PCR
To	study	methylation	status	in	a	locus	or	candidate	
gene	as	a	hypothesis	test	or	validation
Genome‐wide	DNA	methylation	
and	hydroxymethylation
Methylated	DNA	immunoprecipitation
Methylation	sensitive	restriction	enzyme	
sequencing
Whole‐genome	bisulphite	sequencing
DNA	methylation	microarrays
To	identify	DNA	methylation	across	parts	of	or	whole	
of	the	genome	at	variable	levels	of	resolution	down	
to	base	pair	level.	Applied	when	hypothesis‐free	
question
Histone	modifications Chromatin	immunoprecipitation	coupled	with	high‐
throughput	sequencing
Chromatin	interaction	analysis
To	characterise	and	identify	functional	elements	such	
as	transcription	factors	and	chromatin	remodelling	
proteins	in	regions	or	whole	genome.	To	study	how	
the	genome	is	distributed	in	the	nuclear	space
Abbreviations:	DNA,	deoxyribonucleic	acid;	PCR,	polymerase	chain	reaction.
446  |     LINNÉR aNd aLMGREN
heterogeneity	also	exists	between	cells	within	the	same	cell	type.	
Table	1	presents	a	summary	of	the	many	methods	available	in	epi‐
genetic	research.10
5  | EPIGENETIC S VARY BET WEEN TISSUES
In	a	clinical	study,	the	target	tissue	may	or	may	not	be	available	for	
sampling	 for	 practical	 or	 ethical	 reasons.	 For	 example,	 when	 re‐
searchers	are	 interested	 in	epigenetics	and	behaviour,	 a	 surrogate	
tissue	for	the	brain	is	needed.	As	epigenetic	modifications	guide	cells	
from	pluripotency	to	differentiated	cells,	it	is	to	be	expected	that	the	
epigenome	will	be	different	depending	on	the	tissue.	Blood	or	buc‐
cal	cells	are	the	most	frequently	used	surrogate	tissues,	but	blood	
is	made	up	of	different	cell	 types.	Different	epigenetic	patterns	 in	
whole	blood	may	be	explained	by	different	 cell	 composition	with,	
for	example,	a	dynamic	leucocyte	count	and	composition	during	the	
first	postnatal	days.11	The	most	frequently	used	tissues	in	perinatal	
research	are	cord	blood,	placenta	or	buccal	cells.	DNA	methylation	
cell	type	correction	algorithms	are	available	for	cord	blood.12	It	has	
been	suggested	that	buccal	cells	are	more	informative	than	blood	if	
studying	diseases	that	are	not	blood	based.13	In	a	study,	the	surro‐
gate	tissues	cord	blood	and	cord	tissue	were	compared	with	those	in	
25	primary	tissues	described	in	the	Roadmap	Epigenomics	Project.14 
This	 project	 showed	 that	 tissues	 could	 be	 clustered	 according	 to	
their	germinal	origin:	ectodermal,	such	as	brain	and	skin,endoder‐
mal,	 such	 as	 lung	 and	 gastrointestinal,	 and	 mesodermal,	 such	 as	
blood	and	muscle.15	Cord	blood	was	clustered	with	hematopoietic	
stem	cell	 tissues	and	cord	 tissue	was	clustered	with	mesenchymal	
stem	cell	tissues.14	Saliva	is	a	mixture	of	cells,	mainly	buccal	cells	and	
leucocytes,	 and	has	been	 shown	 to	be	 a	 fairly	 representative	 sur‐
rogate	tissue	for	the	brain.16	The	Houseman	algorithm	is	commonly	
used	 to	 estimate	 cell	 type	 contributions	 in	whole	blood	 analysis11 
and	is	often	based	on	the	cell	type	methylation	profiling	carried	out	
by	Reinius	et	al17	However,	 it	 is	 important	to	remember	that	these	
T	helper	 cells,	 cytotoxic	T	 cells,	 natural	 killer	 cells,	B	 lymphocytes	
and	monocytes	were	collected	from	six	adult	males	and	may	not	be	
representative	of	 infants.	A	methylation	 study	of	 the	 infant	blood	
cell	population	is	much	needed	for	cell	count	normalisation	analyses.
6  | IN VIVO REL ATIONSHIP BET WEEN 
EPIGENETIC S AND PHENOT YPES
Only	a	few	hereditary	diseases	can	be	defined	by	a	gene	sequence	
and	these	are	monogenic	diseases.	Environmental	factors	can	con‐
tribute	to	as	much	as	80%	of	disease	risk.	Ageing,	diet	and	smoking	
are	environmental	 factors	 that	all	 contribute	 to	disease,	partly	via	
epigenetic	mechanisms.	Metabolic	disorders	and	obesity	are	partly	
caused	by	lifestyle	and	partly	due	to	genomes.	For	example,	there	is	
a	great	difference	in	how	individuals	react	to	same	diet.18	However,	
disease	development	takes	time	and	we	still	know	very	little	about	
the	epigenetic	marks	in	most	non‐communicable	diseases	that	have	
a	 long	pre‐symptomatic	period.	This	means	 that	we	can	often	say	
something	 about	 correlation,	 but	 it	 is	 harder	 to	 draw	 conclusions	
about	causation.
DNA	 methylation	 and	 other	 epigenetic	 modifications	 contrib‐
ute	 to	different	phenotypes	 and	disease	development	 in	monozy‐
gotic	 twins,	 since	 their	 genetic	 contribution	 is	 virtually	 the	 same.	
Epigenomes	of	twins	are	similar	at	birth	but	more	differences	appear	
over	time.19	Hence,	twin	studies	are	valuable	for	establishing	the	im‐
pact	 of	 environmental	 factors	 on	 diseases	where	 genotype	 risk	 is	
only	part	of	the	aetiology.
Most	 genes	 are	 inherited	 from	both	 parents.	 In	 the	 1980s	 re‐
searchers	 discovered	 that	maternal	 and	paternal	 genomes	did	 not	
contribute	equally	to	mouse	zygotes	and	loss	of	maternal	or	paternal	
genomes	resulted	in	different	phenotypes.20	As	far	as	we	know,	in	
about	100	genes,	one	of	the	alleles	 is	 inactivated	by	DNA	methyl‐
ation	and,	or,	histone	modification.	This	leads	to	expression	of	just	
the	 maternal	 or	 paternal	 alleles	 and	 is	 called	 genomic	 imprinting.	
Prader–Willi	is	a	syndrome	where	feeding	difficulties	and	hypotony	
are	 seen	 in	 the	newborn	period	 followed	by	developmental	delay,	
increased	appetite	and	obesity.	In	Angelman	syndrome,	poor	feeding	
and	growth	is	seen	in	the	newborn	period	and	later	in	life	motor	and	
cognitive	disabilities	can	be	severe.	Prader–Willi	and	Angelman	syn‐
dromes	are	both	caused	by	a	defect	on	different	parts	of	the	same	
region	of	chromosome	15.	Deletions	are	the	most	common	mecha‐
nisms.	The	lack	of	active	paternal	genes	when	the	maternal	allele	is	
inactivated	by	DNA	methylation	causes	the	Prader–Willi	phenotype.	
In	Angelman	syndrome,	the	phenotype	results	from	silencing	of	the	
paternal	allele	of	15q11.2	by	methylation	 in	 the	absence	of	active	
maternal	genes.21	 In	Rett	syndrome,	a	mutation	on	the	X	chromo‐
some	at	 the	gene	 for	methyl	CpG	binding	protein	 (MECP2)	affects	
the	binding	to	methylated	DNA	generally	and	hence	the	expression	
of	a	number	of	genes	involved	in	nerve	cell	development	and	func‐
tion.	Rett	 syndrome	 is	more	 common	 in	 girls.	After	 normal	 devel‐
opment	during	the	first	months	 in	 life,	 infants	display	a	regression	
in	motor	and	interaction	development	and	go	on	to	develop	severe	
motor,	cognitive	and	communicative	handicaps.21
Insulin‐like	 growth	 factor	 2	 (IGF2)	 is	 a	 growth	 factor	 during	
gestation.	 The	 IGF2	 gene	 is	 highly	 active	 during	 embryogenesis,	
but	 is	also	active	 to	a	certain	extent	 in	adulthood.	Ohlsson	et	al	
showed	that	the	same	imprinting	pattern	of	IGF2	was	seen	in	hu‐
mans	as	previous	shown	in	mice	studies,	suggesting	that	imprint‐
ing	 is	 an	 evolutionarily	 conserved	 mechanism	 in	 mammals.	H19 
is	 a	 long	non‐coding	RNA,	which	 acts	 as	 a	 cell	 growth	 inhibitor.	
An	 imprinting	control	 region	 (ICR)	upstream	 from	 the	 IGF2	 gene	
is	 differently	 methylated	 on	 the	 maternal	 and	 paternal	 alleles.	
On	the	paternal	allele,	the	methylated	ICR	silences	the	H19	gene,	
which	 indirectly	 leads	 to	 transcription	of	 the	 IGF2	promoter.	On	
the	maternal	allele,	the	unmethylated	ICR	activates	transcription	
of	 the	H19	 gene.	 The	mechanism	 is	 that	 the	 region	 is	 bound	 by	
an	insulator,	which	prevents	looping	that	would	otherwise	enable	
enhancer‐promoter	interaction	and	IGF2	transcription.	This	leads	
to	active	gene	 transcription	of	paternal	alleles,	but	no	 transcrip‐
tion	 of	 maternal	 alleles.22	 Beckwith–Wiedemann	 syndrome	 is	
     |  447LINNÉR aNd aLMGREN
characterised	 by	 accelerated	 foetal	 growth	 and	macrosomy	 and	
an	increased	risk	of	solid	tumours	in	childhood.21	Imprinting	of	the	
IGF2	gene	has	 implications	 for	Beckwith–Wiedemann	syndrome,	
as	5%	have	 increased	methylation	 in	 the	H19	 ICR	on	 the	mater‐
nal	 allele.	This	 leads	 to	decreased	 transcription	of	 the	H19	 gene	
and	increased	transcription	of	IGF2.	However,	methylation	distur‐
bances	 in	 ICRs	and	decreased	methylation	of	 three	other	genes,	
DKN1C, KCNQ1 and KCNQ1OT,	 are	 more	 common	 in	 Beckwith–
Wiedemann	syndrome.	These	ultimately	 lead	 to	cell	 growth	due	
to	lack	of	inhibition.21
A	simple	animal	model,	 the	viable	yellow	Agouti	mouse	model,	
shows	that	environmental	factors	such	as	diet	can	change	the	phe‐
notype	of	 the	offspring	by	DNA	methylation.	The	Agouti	gene	en‐
codes	either	black	eumelanin	or	yellow	pheomelanin	depending	on	
its	methylation	status.	This	results	 in	the	yellow	agouti	phenotype	
or	 the	darker	pseudo	agouti	 phenotype.	When	a	 retrotransposon,	
a	 genetic	 element	 that	 can	 amplify	 itself	 in	 a	 genome,	 is	 inserted	
upstream	of	the	Agouti	gene,	an	epiallele	 is	created.	This	regulates	
the	gene	by	a	cryptic	promoter	in	an	ectopic	way,	which	means	that	
it	is	transcribed	in	all	the	cells	in	the	body	as	well	as	in	the	hair	folli‐
cles.	The	degree	of	methylation	in	the	retrotransposon	is	correlated	
to	obesity,	diabetes	and	tumours.	One	study	showed	that	when	the	
female	pregnant	Agouti	mouse	was	fed	a	diet	low	in	methyl	donors,	
such	as	 folate,	vitamin	B12,	methionine	and	choline,	her	offspring	
had	a	yellow	coat	and	were	obese.20	This	model	was	the	first	to	de‐
scribe	a	direct	mechanism	for	the	effect	of	maternal	nutrition	on	dis‐
ease	development	in	offspring.
7  | EPIGENETIC CLOCK
As	cells	differentiate	there	is	a	cumulative	effect,	as	the	epigenetic	
maintenance	system	linearly	increases	global	methylation	age	with	
cell	cycles.23	This	has	been	studied	in	several	tissues	and	the	accu‐
racy	with	which	biological	age,	and	to	a	lesser	extent	chronological	
age,	can	be	predicted	by	epigenetic	age	was	very	high	across	tis‐
sues.	Horvath	generated	an	epigenetic	clock	by	studying	methyla‐
tion	at	353	loci	in	51	different	tissues.	Interestingly,	although	the	
epigenomes	were	 highly	 tissue	 specific,	 epigenetic	 age	was	 uni‐
form	across	tissues.	Although	cancer	cells	are	immortal,	epigenetic	
age	acceleration	was	generally	high.	Where	it	was	not,	several	dif‐
ferent	mutations	were	 usually	 found.23	One	 study	 reported	 that	
breast	 tissue	 and	endometrium	were	 exceptions	 to	 the	 accuracy	
of	 the	 epigenetic	 clock,	 possibly	 because	 of	 the	 high	 levels	 of	
oestrogen.24
If	 chronological	 age	can	be	predicted	by	methylation	patterns,	
can	 they	 also	 predict	 gestational	 age?	 A	 Norwegian	 birth	 cohortfound	 that	 methylation	 patterns	 after	 birth	 predicted	 gestational	
age	when	ultrasound	dating	was	used,	but	the	correlations	were	not	
so	strong	when	the	last	menstrual	period	was	used.25	Other	groups	
have	replicated	the	findings.	It	is	suggested	that,	in	the	future,	ges‐
tational	age	could	be	assessed	from	epigenetic	patterns	whenever	
the	dates	are	unsure.	A	study	by	Knight	et	al	successfully	estimated	
epigenetic	gestational	age	from	DNA	methylation	in	cord	blood	and	
blood	spots,	using	148	CpG	sites.	There	was	some	overlap	between	
this	study	and	the	study	by	Horvath.	The	Knight	et	al26	study	investi‐
gated	methylation	data	from	1434	neonates	in	15	different	cohorts,	
ranging	 from	24	 to	 42	weeks	 of	 gestation.	 Suarez	 et	 al	 also	 used	
this	data	and	associated	maternal	antenatal	depression	with	 lower	
epigenetic	gestational	age,	which	was	subsequently	associated	with	
a	developmental	disadvantage	for	boys.27	Hence,	epigenetic	gesta‐
tional	age	may	have	potential	as	a	biomarker	for	disease	later	in	life.
8  | DE VELOPMENTAL ORIGINS OF 
HE ALTH AND DISE A SE
The	developmental	origins	of	health	and	disease	were	first	described	
by	Barker	and	Osmond	in	the	1980s28	and	it	has	gone	on	to	become	
a	growing	field	of	research.	The	theory	is	that	adult	health	and	dis‐
ease	can	be	explained	by	early	 life	experiences,	either	 in	utero,	as	
an	infant	or	as	a	young	child.	The	early	environment	includes	nutri‐
tion,	toxins	and	exposure	to	psychological	and	physiological	factors	
or	stressors.	This	indicates	programming	by	epigenetic	mechanisms,	
possibly	in	stem	cells,	although	there	is	little	evidence	on	the	molec‐
ular	level.	The	consequences	of	the	state	of	mother‐child	dyads	have	
been	discussed	more,	but	paternal	factors	have	also	been	studied	to	
some	extent.	For	example,	one	study	found	that	methylation	marks	
in	 sperm	cells	were	associated	with	autism	 in	 the	offspring.29	The	
role	of	early	life	in	the	development	of	non‐communicable	diseases	
has	been	studied	the	most.	The	implications	for	behaviour	and	well‐
being	 have	 also	 been	 described.	 Examples	 of	 both	 are	mentioned	
below.
The	Överkalix	study	followed	birth	cohorts	from	1890,	1905	and	
1920	and	collected	historical	data	on	parents’	and	grandparents’	ac‐
cess	 to	 food.	 This	 study	 found	 that	 the	 risk	 of	 diabetes	mortality	
was	higher	if	a	paternal	grandfather	had	had	food	in	excess	during	
the	pre‐puberty	slow	growth	period.	If	food	was	scarce	for	a	pater‐
nal	grandfather,	 the	risk	of	cardiovascular	disease	 in	 the	adult	off‐
spring	was	low.30	Children	born	after	the	Dutch	famine	in	1944‐1945	
showed	an	increased	prevalence	of	cardiovascular	disease	and	can‐
cer	later	in	life.31	These	examples	suggest	intergenerational	effects	
of	 environmental	 factors	 and	 unfavourable	 programming	 during	
embryogenesis.	The	mechanisms	are	not	known,	but	children	born	
after	the	Dutch	famine	had	less	methylation	of	the	IGF2	gene	than	
their	 unexposed	 siblings.32	 Poor	 nutrition	 in	 early	 pregnancy	 has	
also	been	associated	with	an	increased	risk	of	schizophrenia	in	the	
offspring.33
9  | INTERGENER ATIONAL TR ANSMISSION
Biologists	as	early	as	Lamarck	(1744‐1829)	proposed	that	acquired	
traits	could	be	passed	on	to	the	next	generation.34	Intergenerational	
transmission	of	epigenetic	marks	means	transmission	from	an	index	
person	 to	 the	 offspring.	 Another	 example	 of	 intergenerational	
448  |     LINNÉR aNd aLMGREN
transmission	 than	 those	 mentioned	 above,	 is	 the	 Veenendaal	 et	
al	 study	 that	 found	 that	 the	 offspring	 of	 prenatally	 undernour‐
ished	 fathers	 had	 higher	 birth	 weights.31	 Epigenetic	 information	
can	 also	 be	 transferred	 transgenerationally,	 through	 a	 generation.	
Transgenerational	epigenetic	transmission	is	defined	as	a	mark	being	
inherited	from	an	ancestor	that	persists	in	three	generations	for	fe‐
males	and	two	generations	for	males.35	(Figure	3)	The	mechanisms	of	
epigenetic	transmission	are	poorly	understood.	In	intergenerational	
reprogramming,	demethylation	is	followed	by	remethylation,	first	in	
the	gametocytes	and	then	again	during	embryogenesis.	Methylation	
is	 very	prolific	 during	 implantation,	 except	 in	CpG	 islands,	 leading	
to	expression	of	housekeeping	genes.	 In	the	post‐implantation	pe‐
riod,	the	pattern	is	more	stable	and	stage	and	tissue	type‐specific.36 
Non‐coding	micro	RNAs	may	play	a	role	in	the	epigenetic	memory	
between	 generations.	 There	 has	 not	 been	much	 research	 on	 how	
histone	modifications	and	higher‐order	chromatin	structure	modifi‐
cations	are	remembered	between	generations.
10  | A SSISTED REPRODUC TION AND 
EPIGENETIC S
There	is	a	higher	incidence	of	diseases	involving	imprinted	genes	
in	children	born	after	assisted	reproduction	techniques	(ART)	and	
they	often	have	a	 low	birth	weight.37	As	described	above,	 there	
is	 important	 epigenetic	 programming	 during	 gametogenesis	 and	
the	 early	 period,	with	 demethylation	 and	methylation	 coming	 in	
waves.	 Global	 demethylation	 in	 the	 zygote	 and	 during	 the	 blas‐
tocyst	stage	is	later	followed	by	methylation	during	implantation.	
In	 in	 vitro	 fertilisation,	 DNA	methylation	 is	 affected	 by	 ovarian	
stimulation	leading	to	superovulation,	collection	of	the	immature	
oocyte,	 handling	 of	 the	 spermatocyte	 and	 the	 culturing	method	
used.	 Culturing,	 in	 particular,	 provides	 an	 environment	 that	 is	
very	different	 to	 the	environment	 in	 the	oviduct,	 including	 tem‐
perature,	light,	oxygen	concentration,	culture	media	and	plastics.	
Culturing	of	oocytes	 is	more	strongly	associated	with	epigenetic	
alterations	than	culturing	of	spermatocytes,	as	ependymal	sperm	
have	completed	reprogramming.	Imprinted	alleles,	where	there	is	
normally	a	memory	of	paternal	or	maternal	origin	surviving	dem‐
ethylation	during	gametogenesis,	are	disturbed	to	a	higher	extent	
in	ART.	Animal	studies	have	shown	epigenetic	modifications	as	a	
result	 of	 each	 of	 these	 steps.	As	 a	 result,	 alterations	 are	mainly	
seen	in	imprinted	genes.38	Imprinting	disorders	are	also	more	com‐
mon	 in	 the	 offspring	 of	 subfertile	 parents.	 A	 systematic	 review	
confirmed	a	higher	prevalence	of	imprinting	disorders	in	children	
conceived	after	in	vitro	fertilisation	than	spontaneously,	although	
there	was	no	difference	in	DNA	methylation	in	selected	genes.39 
In	children	born	after	spontaneous	vs	assisted	reproduction	there	
was	 both	 an	 intra‐	 and	 an	 inter‐individual	 variation	 in	 the	 IGF2/
H19	differently	methylated	region.	This	resulted	in	more	variance	
in	methylation	and	more	aberrant	maternal	methylation	in	the	ART	
group.	Since	IGF2	is	an	 important	foetal	growth	factor,	methyla‐
tion	aberrations	partly	explain	why	children	born	after	ART	have	
lower	birth	weights.	However,	 no	differences	 in	 transcription	of	
the	IGF2	gene	were	seen.37
11  | ROLE OF THE MICROBIOME
Microbiota	 refers	 to	 colonising	 bacteria.	 Their	 perturbations	 have	
been	 associated	with,	 for	 example,	 obesity	 later	 in	 life.	 Studies	 in	
F I G U R E 3  Epigenetic	marks	can	be	inherited	by	
(intergenerational)	or	through	(transgenerational)	the	next	
generation,	in	a	sense	making	the	environment	inheritable.	A	If	
a	pregnant	woman	(F0)	is	exposed	to	an	environmental	stressor,	
her	son	or	daughter	(F1;	green),	and	his	or	her	germ	cells	that	will	
form	the	F2	generation	(yellow)	are	also	directly	exposed,	and	this	
might	result	in	intergenerational	effects.	The	third	generation	(F3;	
blue)	is	the	first	generation	that	could	represent	transgenerational	
epigenetic	inheritance.	B	If	a	man	or	a	woman	(F0)	and	their	germ	
cells,	representing	the	F1	generation	(yellow),	are	directly	exposed	
to	an	environmental	stressor,	the	F2	offspring	(blue)	is	the	first	
generation	that	could	represent	transgenerational	epigenetic	
inheritance.	Picture	from	“Transgenerational	and	intergenerational	
epigenetic	inheritance	in	allergic	diseases”	by	Morkve	Knudsen	et	al	
in	the	Journal	of	Allergyand	Clinical	Immunology	2018,	accessed	at	
https	://doi.org/10.1016/j.jaci.2018.07.007
https://doi.org/10.1016/j.jaci.2018.07.007
     |  449LINNÉR aNd aLMGREN
mice	have	shown	that	lean	or	obese	microbiota	can	be	transferred	
between	individuals	and	lead	to	a	change	in	phenotypes.40	Different	
types	 of	 microbiomes	may	 also	 be	 associated	 with	 type	 1	 diabe‐
tes,	allergies,	inflammatory	bowel	disease	and	rheumatoid	arthritis,	
partly	via	epigenetic	mechanisms	modulating	 formation	of	 the	 im‐
mune	system.	Patients	with	inflammatory	bowel	disease	have	been	
reported	to	have	a	different	microbiome	compared	to	healthy	con‐
trols.41	The	 relation	of	 the	microbiome	with	 the	gut	and	 the	brain	
is	 referred	 to	as	 the	microbiome‐gut‐brain	axis.	Studies	 in	 rodents	
have	showed	more	anxious	behaviour	in	germ‐free	rats.	In	humans,	
microbiota	and	the	microbiome‐gut‐brain	axis	probably	plays	a	role	
in	mental	health,	especially	in	autism	spectrum	disorders.42	The	link	
may	be	 increased	gut	permeability,	specifically	a	 leaky	gut	that	al‐
lows	metabolites	 from	 bacteria	 across	 the	 gut	 barrier,	 which	may	
affect	neurodevelopment.	 It	was	earlier	 thought	 that	 the	amniotic	
fluid	was	 sterile	 and	 that	 colonisation	with	 bacteria	 started	 post‐
partum,	but	we	now	know	that	this	not	the	case.	Formation	of	the	
microbiome	begins	in	utero	and	the	resulting	disturbances	may	lead	
to	changes	in	the	foetal	epigenetic	programming.	One	study	found	
that	 the	prevalence	of	 atopic	dermatitis	was	 significantly	 lower	 at	
the	age	of	seven	if	the	children's	mothers	had	been	given	probiotics	
or	prebiotics	during	pregnancy.	Formation	of	the	microbiome	con‐
tinues	after	birth	and	is	influenced	by	the	type	of	delivery,	nutrition,	
antibiotic	treatment	and	skin‐to‐skin	care.	During	the	first	3	years	of	
life,	there	is	a	high	turnover	of	the	types	of	colonising	bacteria,	after	
which	the	microbiome	is	more	stable.43
12  | IN UTERO AND PERINATAL STRESS 
E XPOSURE
Many	animal	and	human	studies	describe	epigenetic	effects,	some	
with	 clinical	 correlates,	 after	 an	 adverse	 in	 utero	 environment	 of	
some	kind.	One	study	reported	that	term	infants	showed	hypometh‐
ylation	of	the	nuclear	receptor	subfamily	3	group	C	member	1	glu‐
cocorticoid	receptor	gene	(NR3C1)	if	their	mother	had	a	depression	
during	late	pregnancy.	At	3	months	of	age,	they	had	increased	excre‐
tion	of	salivary	cortisol	following	a	stressful	daily	care	procedure.44
Many	 studies	 have	 shown	 differentially	 methylated	 regions	 in	
the	offspring	of	smoking	mothers.	A	meta‐analysis	was	carried	out	
on	13	birth	cohorts	that	explored	smoking	during	pregnancy	to	iden‐
tify	epigenetic	marks,	mainly	in	newborn	infants	but	also	including	
older	children.	Methylation	status	differed	in	about	3000	CpGs	out	
of	which	half	were	 less	and	half	more	methylated	 than	 in	 the	off‐
spring	of	non‐smoking	mothers.	Some	were	also	related	to	a	change	
in	gene	expression	in	genes	previously	known	to	be	related	to	ma‐
ternal	smoking.45
Delivery	 by	Caesarean	 section	has	 been	 associated	with	 the	 in‐
creased	 risk	 of	 conditions	 like	 allergies,	 coeliac	 disease,46	 obesity,47 
type	1	diabetes,48	cancers49	and	autism.50	While	the	underlying	causes	
are	currently	unknown,	perinatal	epigenetic	alterations	of	the	genome	
have	been	suggested	to	be	a	potential	risk	for	later	disease.51	The	hy‐
pothesis	is	that	mode	of	delivery	affects	the	epigenetic	state	of	stem	
cells	 in	 newborn	 infants,	 thereby	 influencing	 their	 plasticity	 and	 re‐
sponsiveness	later	in	life.	There	is	an	enormous	stress	on	a	baby	during	
labour,	which	exceeds	that	of	any	other	critical	life‐event.52	However,	
this	stress	is	needed	so	that	the	baby	can	adapt	and	survive	during	the	
transition	from	foetal	to	neonatal	life.	A	study	found	differently	meth‐
ylated	regions	in	haematopoietic	stem	cells	of	cord	blood	from	children	
delivered	vaginally	compared	to	those	delivered	by	elective	Caesarean	
sections.	Interestingly,	the	level	of	DNA	methylation	increased	in	line	
with	the	duration	of	labour	for	three	loci.51	Further	investigations	are	
needed	to	find	out	how	long	these	alterations	remain	and	their	poten‐
tial	implications	for	later	life	disease.
13  | PRETERM BEHAVIOUR AL 
EPIGENETIC S
Preterm	birth	greatly	changes	the	conditions	as	compared	to	being	
born	at	term.	Instead	of	staying	with	the	mother,	usually	in	a	home	
environment	within	 the	 first	 couple	 of	 days,	 being	 born	 too	 soon	
brings	with	it	a	need	for	neonatal	care	that	is	stressful.	A	systematic	
review	by	Provenzi	et	al	summarised	nine	papers	that	described	the	
epigenetic	consequences	of	early	adverse	experiences	by	preterm	
infants.53	These	are	described	briefly	in	this	section.	Preterm	infants	
of	depressed	mothers	had	increased	methylation	of	the	maternally	
expressed	 3	 (MEG3)	 gene,	which	 encodes	 non‐coding	 RNA	 and	 is	
possibly	correlated	to	foetal	and	placental	growth.	The	mesoderm‐
specific	transcript	(MEST)	gene,	which	is	involved	in	the	maintenance	
of	mesodermal	cells,	has	been	shown	to	have	a	role	in	stress	regula‐
tion	in	offspring	exposed	to	stress	and	was	methylated	to	a	higher	
extent	 following	 preterm	 birth.	 The	 glucocorticoid	 receptor	 gene	
NR3C1	 and	serotonin	 transporter	genes	SLC7A5 and SLC1A2 were 
hypomethylated	in	preterm	infants	during	the	neonatal	period,	while	
SLC6A4,	another	serotonin	transporter	gene,	was	hypermethylated.	
Stress	 related	 to	 the	 neonatal	 intensive	 care	 unit	 correlated	 to	 a	
higher	extent	of	methylation.	Painful	procedures,	such	as	venipunc‐
tures,	were	associated	with	hypermethylation	of	 the	SLC6A4	 gene	
in	 the	 neonatal	 period,	 but	 the	 opposite	 effect	 was	 seen	 later	 at	
7	years	of	age.	Epigenetic	modifications	related	to	prematurity	were	
associated	with	a	number	of	developmental	outcomes.	Behavioural	
problems	in	7‐year‐old	children	were	related	to	hypermethylation	of	
the	SLC6A4	gene.	Poor	stress	regulation	was	seen	with	hypermethyl‐
ated	SLC6A4.	Brain	white	matter	shape	and	integrity	was	related	to	
increased	DNA	methylation.53
14  | PARENTAL BEHAVIOUR
The	first	evidence	of	epigenetic	consequences	of	an	adverse	early	
environment	came	 from	a	study	 in	 rodents.	Pups	born	 to	high‐	or	
low‐licking	 rat	 dams,	 representing	 more	 or	 less	 caring	 mothers,	
showed	differences	in	methylation	patterns	within	the	exon	17 pro‐
moter	 of	NR3C1.	 They	 also	 demonstrated	 a	 histone	 modification	
leading	to	different	expression	of	the	glucocorticoid	receptor	in	the	
450  |     LINNÉR aNd aLMGREN
hippocampus.	Pups	with	high‐licking	mothers	had	 less	methylated	
NR3C1	the	first	week	of	life,	higher	expression	of	the	glucocorticoid	
receptor	and	more	activated	feedback	 inhibition	of	the	corticotro‐
pin‐releasing	 hormone	 in	 the	 hypothalamus‐pituitary‐adrenal	 axis,	
which	 led	 to	 better	 cortisol	 regulation.	 Their	 behaviour	 indicated	
better	stress	tolerance	as	adults	than	the	pups	of	low‐licking	moth‐
ers.	Importantly,	the	hypermethylation	or	hypomethylation	could	be	
reversed	by	cross‐fostering	with	high‐	or	low‐licking	dams	or	phar‐
macologically	using	an	epigenetic	drug.54
A	Canadian	study	published	in	2017	aimed	to	replicate	the	lick‐
ing	and	grooming	study,	but	 in	a	human	context.55	The	amount	of	
physical	contact	between	parents	and	term	or	moderately	preterm	
infants	 was	 self‐reported	 in	 a	 parental	 diary.	 This	 also	 described	
the	 infant's	 behaviour	 during	 a	 4‐day	 period	 at	 5	 weeks	 of	 age.	
About	1000	dyads	were	screened	and	a	third	completed	daily	dia‐
ries.	Dyads	were	divided	 into	high	and	 low	contact	groups,	with	a	
difference	of	6	hours	of	contact	between	the	groups.	At	4‐5	years	
of	age,	buccal	swabs	were	collected	for	DNA	methylation	analysis	
from	94	of	the	children.	No	difference	in	methylation	patterns	was	
seen	 for	 four	 candidate	 genes,	 each	with	 a	 role	 in	 social	 bonding,	
stress	regulation	and	development	and	previously	studied	in	similar	
animals,some	of	them	mentioned	above:	NR3C1,	OPRM1 and OXTR 
and BDNF.	However,	 there	was	a	difference	 in	methylation	at	 five	
other	loci,	differently	methylated	regions.	The	epigenetic	age	of	the	
infants	with	high	distress	and	a	low	level	of	contact	was	lower	than	
their	chronological	age.	These	findings	imply	that	early	parent‐infant	
contact	may	 leave	 lasting	epigenetic	marks,	but	the	study	was	too	
underpowered	to	draw	conclusions.
15  | EPIGENETIC S IN PAEDIATRIC S
This	 review,	which	 is	 aimed	 at	 paediatricians,	 has	 described	 how	
epigenetic	mechanisms	are	mainly	active	prenatally.	Disturbances	
during	foetal	life	have	greater	consequence	than	disturbances	expe‐
rienced	later	in	life.	Little	is	known	about	the	timing	of	disturbances	
and	their	relation	to	epigenetic	marks	found	in	childhood	and	dis‐
ease.	Published	studies	and	ongoing	research	about	epigenetics	in	
paediatrics	beyond	the	neonatal	period	deal	with	asthma	and	aller‐
gies,	diabetes,	obesity,	acute	myeloid	leukaemia	and	behavioural	or	
neuropsychiatric	diagnoses.	A	strong	association	has	been	demon‐
strated	between	birth	weight	and	DNA	methylation	and	between	
birth	weight	and	health	outcomes.56	However,	we	still	need	to	ex‐
plore	whether	DNA	methylation	is	a	cause	or	consequence	of,	for	
example,	low	birth	weight.	The	Mechanisms	of	the	Development	of	
Allergy	project	reported	that	in	children	with	asthma,	DNA	meth‐
ylation	at	CpG	pairs	associated	with	eosinophil	and	cytotoxic	T	cell	
activation	was	reduced.	No	differences	were	seen	in	cord	blood.57 
The	Pregnancy	 and	Childhood	Epigenetics	Consortium	 found	dif‐
ferentially	methylated	loci	 in	newborn	infants	and	these	were	po‐
tential	biomarkers	for	developing	asthma	at	a	later	stage.58
The	Avon	Longitudinal	 Study	of	Parents	 and	Children,	which	
was	carried	out	in	England,	looked	at	the	correlation	between	epi‐
genetic	marks	at	birth	and	short‐	and	long‐term	conduct	problems.	
Several	of	these	marks	were	in	loci,	suggesting	that	prenatal	expo‐
sures,	such	as	maternal	smoking,	stress	or	psychopathology,	were	
not	 linked	to	any	methylated	quantitative	 loci.	No	differences	 in	
epigenetic	marks	were	seen	between	childhood	conduct	problems	
and	 those	persisting	 later	 in	 life.59	 In	 a	 study	by	Kumsta	et	 al60,	
methylation	 of	 the	 oxytocin	 receptor	 gene	 was	 associated	 with	
differential	 activation	 of	 parts	 of	 the	 brain	 active	 in	 social	 per‐
ception,	related	to	autism	and	unemotional	traits	and	regulated	by	
psychosocial	stress.
16  | DISCUSSION
The	epigenetics	revolution	started	in	the	2000s	and,	at	the	time,	
we	 believed	 that	 epigenetics	 was	 able	 to	 explain	 it	 all.	 Since	
then	 it	 has	been	 argued	 that	 it	 is	 not	 as	 simple	 as	 a	 functional	
genome	being	 shaped	by	genes	being	 switched	on	 and	off	 and	
remembered	through	mitosis	or	even	transgenerationally.	Gene	
transcription	requires	a	complicated	machinery	with	presence	of,	
for	 example,	 transcription	 factors	 and	 cis‐regulatory	 elements	
within	the	DNA.	Epigenetics	also	requires	a	maintenance	system	
that	 is	more	or	 less	active	during	different	periods	in	 life	and	it	
should	 only	 be	 considered	 a	 part	 of	 the	 puzzle.	 However,	 the	
knowledge	that	genes	and	environments	interact	is	important	in	
optimising	obstetric	practice,	such	as	assisted	reproductive	tech‐
niques	and	neonatal	 care.	The	biological	pathways	 that	predis‐
pose	the	foetus	and	newborn	infant	to	diseases	in	adulthood	are	
multifactorial.	Early	alterations	in	stem	cells,	in	set	points	of	reg‐
ulatory	systems	and	in	organ	growth	and	structure,	are	involved.	
These	processes,	which	are	controlled	by	gene	expression,	may	
be	modified	for	life	by	gene	and	environment	interactions	in	the	
foetal	 and	 neonatal	 period.	 Early	 life	 epigenetic	 modifications	
are,	 therefore,	 a	 target	 for	mechanistic	 research	 in	 the	 field	of	
developmental	 origins	 of	 health	 and	 disease.	 Several	 common	
diseases	are	now	considered	to	have	a	developmental	origin.	In	
this	 context,	 epigenetic	 studies	 of	 newborn	 infants	 and	 young	
children,	 who	 are	 exposed	 to	 different	 stressors,	 may	 provide	
important	 information	 about	 pathophysiological	 mechanisms.	
Such	studies	can	 identify	early	 risk	 factors	 that	are	modifiable,	
laying	the	grounds	for	preventive	strategies	and	improved	public	
health.
17  | CONCLUSION
Epigenetic	modifications	due	to	perinatal	environmental	exposures	
can	lead	to	lifelong,	but	potentially	reversible,	phenotypic	alterations	
and	disease.
     |  451LINNÉR aNd aLMGREN
ACKNOWLEDG EMENTS
We	are	grateful	to	Professor	Tomas	Ekström	at	the	Dept	of	Clinical	
Neuroscience,	Medical	Epigenetics,	for	sharing	his	great	knowledge	
of	the	field.
CONFLIC T OF INTERE S T
The	authors	have	no	conflicts	of	interest	to	declare.
ORCID
Agnes Linnér https://orcid.org/0000‐0002‐2934‐2771 
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 Agnes Linnér Malin Almgren
How to cite this article:	Linnér	A,	Almgren	M.	Epigenetic	
programming—The	important	first	1000	days.	Acta Paediatr. 
2020;109:443–452. https	://doi.org/10.1111/apa.15050	
https://doi.org/10.1111/apa.15050