Epigenetics: Definition, Mechanisms

and Clinical Perspective

Cathérine Dupont, Ph.D.,1,2 D. Randall Armant, Ph.D.,1,3
and Carol A. Brenner, Ph.D.1,2

ABSTRACT

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A vast array of successive epigenetic modifications ensures the creation of a
healthy individual. Crucial epigenetic reprogramming events occur during germ cell
development and early embryogenesis in mammals. As highlighted by the large offspring
syndrome with in vitro conceived ovine and bovine animals, any disturbance during germ
cell development or early embryogenesis has the potential to alter epigenetic reprogram-
ming. Therefore the complete array of human assisted reproductive technology (ART),
starting from ovarian hormonal stimulation to embryo uterine transfer, could have a
profound impact on the epigenetic state of human in vitro produced individuals. Although
some investigators have suggested an increased incidence of epigenetic abnormalities in in
vitro conceived children, other researchers have refuted these allegations. To date, multiple
reasons can be hypothesized why irrefutable epigenetic alterations as a result of ART have
not been demonstrated yet.

KEYWORDS: Epigenetics, X-chromosome inactivation, imprinting, transgenerational

inheritance

DEFINITION modifications described in current literature generally

Conrad Waddington introduced the term epigenetics in comprise histone variants, posttranslational modifications
the early 1940s.1 He defined epigenetics as ‘‘the branch of of amino acids on the amino-terminal tail of histones, and
biology which studies the causal interactions between covalent modifications of DNA bases. The validity of the
genes and their products which bring the phenotype current definition of epigenetics should be seriously ques-
into being.’’2 In the original sense of this definition, tioned because the previously mentioned epigenetic mod-
epigenetics referred to all molecular pathways modulating ifications also have a crucial role in the silencing and
the expression of a genotype into a particular phenotype. expression of noncoding sequences.
Over the following years, with the rapid growth of
genetics, the meaning of the word has gradually narrowed.
Epigenetics has been defined and today is generally THE NATURE AND INHERITANCE
accepted as ‘‘the study of changes in gene function that OF EPIGENETIC MARKS
are mitotically and/or meiotically heritable and that do In addition to their importance in the commitment of
not entail a change in DNA sequence.’’3 The epigenetic cells to a particular mitotically inheritable form or

1
Departments of Obstetrics & Gynecology; 2Department of Physiol- University, School of Medicine, 275 E. Hancock St., Detroit, MI
ogy, School of Medicine, Wayne State University, Detroit, Michigan; 48201 (e-mail: [email protected]).
3
Program in Reproductive and Adult Endocrinology, Eunice Kennedy Epigenetics in Reproduction; Guest Editors, James H. Segars, Jr.,
Shriver National Institute for Child Health and Human Development, M.D., and Kjersti M. Aagaard-Tillery, M.D., Ph.D.
National Institutes of Health, Department of Health and Human Semin Reprod Med 2009;27:351–357. Copyright # 2009 by
Services, Bethesda, Maryland. Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York,
Address for correspondence and reprint requests: Carol A. Brenner, NY 10001, USA. Tel: +1(212) 584-4662.
Ph.D., Departments of Obstetrics & Gynecology and Physiology, CS DOI 10.1055/s-0029-1237423. ISSN 1526-8004.
Mott Center for Human Growth and Development, Wayne State
351
352 SEMINARS IN REPRODUCTIVE MEDICINE/VOLUME 27, NUMBER 5 2009

function, epigenetic marks have a crucial role in guar- The correlation of specific posttranslational mod-
anteeing genomic stability. Indeed, the silencing of ifications on the histones with transcriptional events has
centromeres, telomeres, and transposable elements resulted in the histone code hypothesis.35 To date, the
(TEs) ensures the correct attachment of microtubules best characterized modifications are acetylations and
to centromeres, reduces excessive recombination be- methylations of lysine residues on histones H3 and
tween repetitive elements, and prevents transposition H4. Although all acetylations of lysine residues on H3
of TEs and resulting insertional mutagenesis.4–6 and H4 have been associated with transcriptional acti-
Although covalent modifications of DNA bases vation (H3K9, H3K14, H3K18, H3K23, H4K5, H4K8,
have been described since 1948,7 it was only in 1969 H4K12, and H4K16),36–41 methylation of lysine resi-
that Griffith and Mahler suggested that these modifi- dues may be either associated with transcriptional re-
cations may modulate gene expression.8 The predom- pression (H3K9, H3K27, and H4K20) or activation
inant modification in mammalian DNA is methylation (H3K4, H3K36, and H3K79) depending on which
of cytosine,7 followed by adenine and guanine methyl- amino acid and to what extent (monomethylation, di-
ation.7,9 Although methylation of cytosine bases in methylation, or trimethylation) the residue is modi-
mammalian DNA has been primarily described in the fied.41 Although not as well documented, it has
context of CpG dinucleotides,10 evidence suggests that become clear that posttranslational modifications of

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cytosines in non-CpG sequences are also frequently other histones also have an important role in chromatin
methylated.11–13 Because the promoter regions of si- structure and gene regulation. Indeed, more recently it
lenced genes possess significantly more methylated has been reported that mutations on specific sites of
cytosines in comparison with actively transcribed genes, histones H2A and H2B modify the transcription of
this modification has been implicated in transcriptional various genes.42,43 Similarly, as for DNA methylation
repression.14,15 Methylation of cytosine in the pro- enzymes, histone-modifying enzymes may be targeted to
moter region may repress gene expression by prevent- specific DNA sequences directly19,20 or may necessitate
ing the binding of specific transcription factors16 or the interaction of intermediates such as Polycomb and
may attract mediators of chromatin remodeling, such as Trithorax group proteins and/or RNAi.44–47 In contrast
histone-modifying enzymes or other repressors of gene to DNA methylation, it is unclear how and if histone
expression.17–20 In mammals, the mitotic inheritance of modifications are correctly replicated during mitosis.
methylated DNA bases is primarily ensured by a main- Although a few investigators have claimed that histone
tenance of DNA methyltransferase (DNMT1),21–23 complexes are distributed semiconservatively over the
whereas DNA methylation enzymes DNMT3A and replicated genome,48 most researchers have refuted this
DNMT3B are mainly responsible for de novo methyl- manner of histone deposition.49 As a result, it should be
ation of unmethylated sites.24 Various studies have questioned whether covalent histone modifications and
shown that DNMT3A and DNMT3B target different histone variants are epigenetic marks according to the
sites for methylation depending on the cell type and the current definition of epigenetics.
stage of development.6,25,26 De novo methyltransfer-
ases may be directly targeted to specific DNA sequen-
ces, may necessitate the interaction with other DNA X-CHROMOSOME INACTIVATION
binding proteins or may be guided by RNA interference AND AUTOSOMAL IMPRINTING
(RNAi) in a process called RNA-directed DNA meth- During evolution, an alteration or acquisition of a sex-
ylation (RdDM).27 determining gene on one copy of a pair of chromosomes
Besides covalent modifications of DNA, histones has resulted in the emergence of sex chromosomes.
and their posttranslational modifications have also been Consequently, the sexes are generally determined by
implicated in the organization of chromatin structure the presence of a hetero- or homomorphic pair of
and regulation of gene transcription. Generally, histone allosomes. With time, as a result of reduced recombina-
classifications comprise the main histones or their var- tion events between these heteromorphic chromosomes,
iants H1, H2A, H2B, H3, and H4.28–31 The funda- vastly dissimilar sex chromosomes have arisen. This
mental building block of chromatin is the nucleosome dissimilarity between the allosomes is at the origin of a
and consists of DNA spooled around an octamer of gene dosage inequality between the two different sexes.50
histones. Each octamer contains two units of each To remediate to this imbalance, many species have
principal or variant histone H2A, H2B, H3, and H4.32 adopted gene dosage compensation mechanisms. The
Linker DNA connecting nucleosomes associates with epigenetic gene dosage compensation mechanisms of
the main form or variants of the linker histone H1. A genes located on the sex chromosomes vary with species,
variety of histone-modifying enzymes is responsible for a from simple transcriptional modulation to the entire
multiplicity of posttranslational modifications on specific silencing of one allosome.51 Although it is generally
serine, lysine, and arginine residues on the amino- accepted that therian mammals (placentals and marsu-
terminal tail of these histones.33,34 pials) equalize X-chromosome gene dosage between the
 EPIGENETICS: DEFINITION, MECHANISMS, AND CLINICAL PERSPECTIVE/DUPONT ET AL 353

sexes by inactivating one X chromosome in females, it silenced after fertilization.51 Meiotic sex chromosome
has also been suggested that transcription from the active inactivation (MSCI) during spermatogenesis supports
X chromosome is upregulated to maintain balance be- the view that the paternal X chromosome can be
tween autosomal and allosomal gene expression.52 Ini- inherited in an inactive state.61 However, it has also
tially, the observation that female mice heterozygous for been claimed that MSCI is not crucial for imprinted X-
X-chromosome-linked coat color genes displayed a mo- chromosome inactivation because autosomes that do
saic phenotype led to Mary Lyon’s hypothesis that either not undergo MSCI, but present Xist transgenes, are
the paternally or maternally derived X chromosome also preferentially silenced when paternally inherited.62
could be inactivated in female animals.53 Later inves- In opposition to the inheritance of a preinactivated X
tigations revealed that this pattern of X-chromosome chromosome, the differential remodeling of the pater-
inactivation may differ depending on the species and the nal and maternal chromatin and/or the translation of
developmental status of the conceptus. Indeed, female specific parental imprints on the X chromosomes after
offspring from placentals always possess a mixture of fertilization may be at the origin of the initial selective
cells with an inactive X chromosome from either mater- inactivation of the paternal X chromosome in female
nal or paternal origin, whereas marsupial offspring only embryos. Indeed, Xist transcription may be instigated
present inactive X chromosomes from paternal ori- on the paternally derived X-chromosome as a result of

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gin.54,55 In addition, though random X-chromosome the exchange of protamines in the paternal pronucleus
inactivation is reported in embryonic lineages from with histone variants favoring transcription.63 Alter-
mouse postimplantation embryos, the paternally inher- natively, imprinted X-chromosome inactivation has
ited X-chromosome is always preferentially silenced in also been shown to be dependent on various differential
preimplantation embryos56 and the resulting extraem- epigenetic imprints on Xist and Tsix genes acquired
bryonic lineages.57 This latter form of X-chromosome during male and female germ cell development.64,65 In
inactivation is commonly referred to as imprinted X- brief, X-chromosome inactivation in mammals has
chromosome inactivation. Although the ultimate out- originated to compensate a gene dosage inequality
come of both random and imprinted X-chromosome between the two different sexes. Because of its neces-
inactivation is the silencing of one X chromosome, sity, the establishment and maintenance of X-chromo-
studies suggest that the maintenance of epigenetic marks some inactivation seems to be controlled by a variety of
on the inactive X chromosome is markedly determined redundant epigenetic marks and mechanisms.
by whether the X chromosome underwent random or Pronuclear transfer experiments in the early
imprinted inactivation. Indeed, the silencing of im- 1980s revealed that mammalian reproduction necessi-
printed inactive X chromosomes mainly depends on tates the contribution of a paternal and maternal
histone modifications applied by Polycomb proteins genome to be successful.66,67 The preferential mono-
rather than DNA methylation, whereas DNA methyl- allelic expression of specific genes from either the
ation is a crucial factor for the maintenance of the maternal or paternal allele was believed to be at the
inactive state of randomly inactivated X chromo- origin of this phenomenon. The first imprinted genes
somes.58,59 To date no conclusive evidence exists in mammals were identified in the early 1990s.68–70
for imprinted X-chromosome inactivation in human Genomic imprinting has been observed in angiosperms
conceptuses.50 and mammals and would have independently evolved in
To permit random X-chromosome inactivation these two taxa as a result of selective pressure on specific
in the embryonic lineage of mice, a reactivation of the genes.71 Although many genes remain imprinted
initially silenced X chromosome is necessary. Random throughout the entire life of an organism, some genes
X-chromosome inactivation is controlled by a region on are imprinted in a tissue-specific or temporal manner,
the X chromosome called the X inactivation center similarly to the Xist gene. Imprinted genes are organ-
(XIC). The XIC possesses the genes Xist and Tsix, ized in clusters or domains, and their expression is
which contain noncoding RNAs that are crucial for under control of a cis-acting imprinting control ele-
inactivating and maintaining activity of specific X ment (ICE).72 Similarly to the XIC region on the
chromosomes. Indeed, transcription of Xist on the X chromosome, ICE elements on autosomes acquire
inactive X chromosome mediates its silencing, whereas differential imprints during germ cell development, de-
Tsix transcription from the active X chromosome pre- pending on their parental origin. Like X-chromosome
vents its inactivation.60 Although it remains unknown imprints, autosomal imprints in female mammals are
how X chromosomes are randomly selected for activity established during folliculogenesis, whereas imprints
or inactivity, three mechanisms have been proposed for in males are reset during fetal development.73–78 The
the selective silencing of the paternally derived X fact that the imprinted inactivation of the paternal X
chromosome during early fetal development. Concep- chromosome and autosomal genes present many molec-
tually, the paternal X chromosome can enter the oocyte ular similarities has led to the hypothesis that these
in a preinactivated condition or may be selectively phenomena have coevolved.79
354 SEMINARS IN REPRODUCTIVE MEDICINE/VOLUME 27, NUMBER 5 2009

TRANSGENERATIONAL INHERITANCE alterations is covered in detail in articles later in this

Although the maintenance, as well as the erasure, of issue. Importantly, although the whole genome is re-
acquired epigenetic marks between generations has both programmed during germ cell development and embryo-
beneficial and deleterious effects, it is unknown to what genesis, it should be noted that to date only a limited
extent epigenetic marks are maintained or erased between number of loci have been investigated. These loci gen-
generations in mammals. Because primordial germ cells erally comprise genes in which their epigenetic status
are set aside during mammalian fetal development and significantly affects a perceptible phenotype. Although a
because of epigenetic reprogramming events during germ specific clinical phenotype has not yet been associated
cell development and early embryogenesis, acquired epi- with an epigenetic change, it is it possible that pathology
genetic states are believed to be rarely passed on to may emerge from a not yet recognized epigenetic alter-
progeny.80 The erasure of epigenetic marks occurs in ation.84 An excess of epigenetic alterations could have an
female and male mammals during primordial germ cell immediate impact that precipitates pre- or postnatal
development and early embryogenesis, whereas the ac- death.
quisition of epigenetic marks takes place at different times At the other extreme, an epigenetic change might
during female and male gametogenesis. Indeed, epige- result in a perceptible alteration later in life such as
netic marks in female germ cells are established during cancer, coronary heart disease, stroke, or diabetes. An

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folliculogenesis, whereas male germ cells acquire their increased risk of heart disease, stroke, and diabetes is
epigenetic marks during fetal development.73–78 The fact associated with malnutrition in utero and low birth-
that imprints are maintained during early embryogenesis weight.85 Again, the role of nutrition and diet during
highlights that some sequences may escape reprogram- pregnancy is covered in detail in ensuing articles in this
ming events. Stella is among a group of proteins that may issue, but it must be considered whether children of
play an important role in the suppression of epigenetic ART with a low birthweight could have a predisposition
reprogramming of these specific sequences.81 The failure for these chronic phenotypes. Concerns have also been
to erase epigenetic marks during primordial germ cell raised about the epigenetic status of tumor suppressors or
development or subsequent early embryogenesis is at the fertility concerns in individuals exposed to environmen-
origin of transgenerational inheritance of epigenetic traits. tal toxins. Subsequent articles address this issue in
A clear example of a gene susceptible to transgenerational greater depth as well, but there is sufficient evidence in
inheritance is the Agouti viable yellow (Avy) allele in animals to warrant concern.
mice.82 The variable epigenetic status of an intracisternal In conclusion, there is reason to suspect that early
A particle element (IAP) located upstream from the development is vulnerable to unwanted changes in epi-
coding region of Avy in mice is responsible for the variable genetic inheritance. Animal studies have shown that
expression of this allele in adult mice. As a result of epigenetic reprogramming is a fragile process that is
incomplete erasure of epigenetic marks on IAPs, this easily modified,86–91 and such data provide compelling
variable expression is often transgenerationally inherited biologic plausibility for clinical concern. Although ani-
by offspring.82 Evidence suggests that many IAPs fail to mal models may provide some information, the results
undergo epigenetic reprogramming during germ cell may not always be representative of the epigenetic events
development.83 The high incidence of IAPs in mamma- that occur in humans. Because of the potential for
lian genomes has consequently led to the belief that this adverse health effects in offspring conceived using
type of transgenerational inheritance may be more prev- ART and in children born from altered nutritional states
alent than initially conceived. in pregnancy or exposed to environmental toxins, further
research is needed.

CLINICAL IMPLICATIONS OF EPIGENETIC

ALTERATIONS ACKNOWLEDGMENTS
Given the extent of epigenetic reprogramming that This study was supported by the Intramural Research
occurs during gametogenesis and embryogenesis and Program of the Eunice Kennedy Shriver National
the vulnerability of the process, it is not difficult to Institute of Child Health and Human Development,
understand how alteration in reprogramming could be of National Institutes of Health, DHHS (1R03HD046553,
clinical relevance. Because epigenetic reprogramming 1R21RR021881, and RO1HD045966, and the Repro-
occurs during folliculogenesis and embryogenesis, any ductive Biology and Medicine Branch, NICHD).
disturbance of the normal natural environment during
these critical phases could cause epigenetic alterations.
Accordingly, researchers have attempted to determine
REFERENCES
whether children conceived using assistive reproductive
technology (ART) carry epigenetic reprogramming de- 1. Waddington CH. The epigenotype. Endeavour 1942;1:
fects. A review of an association of ART and epigenetic 18–20
 EPIGENETICS: DEFINITION, MECHANISMS, AND CLINICAL PERSPECTIVE/DUPONT ET AL 355

2. Waddington CH. The Basic Ideas of Biology. Towards a 22. Smith SS, Kaplan BE, Sowers LC, Newman EM. Mecha-
Theoretical Biology. Edinburgh, Scotland: Edinburgh Uni- nism of human methyl-directed DNA methyltransferase and
versity Press; 1968:1–32 the fidelity of cytosine methylation. Proc Natl Acad Sci U S
3. Wu Ct, Morris JR. Genes, genetics, and epigenetics: a A 1992;89(10):4744–4748
correspondence. Science 2001;293(5532):1103–1105 23. Bestor T, Laudano A, Mattaliano R, Ingram V. Cloning and
4. Daskalos A, Nikolaidis G, Xinarianos G, et al. Hypomethy- sequencing of a cDNA encoding DNA methyltransferase of
lation of retrotransposable elements correlates with genomic mouse cells. The carboxyl-terminal domain of the mamma-
instability in non-small cell lung cancer. Int J Cancer 2009; lian enzymes is related to bacterial restriction methyltransfer-
124(1):81–87 ases. J Mol Biol 1988;203(4):971–983
5. Zaratiegui M, Irvine DV, Martienssen RA. Noncoding 24. Okano M, Xie S, Li E. Cloning and characterization of a
RNAs and gene silencing. Cell 2007;128(4):763–776 family of novel mammalian DNA (cytosine-5) methyltrans-
6. Dodge JE, Okano M, Dick F, et al. Inactivation of Dnmt3b ferases. Nat Genet 1998;19(3):219–220
in mouse embryonic fibroblasts results in DNA hypomethy- 25. Okano M, Bell DW, Haber DA, Li E. DNA methyltrans-
lation, chromosomal instability, and spontaneous immortal- ferases Dnmt3a and Dnmt3b are essential for de novo
ization. J Biol Chem 2005;280(18):17986–17991 methylation and mammalian development. Cell 1999;99(3):
7. Hotchkiss RD. The quantitative separation of purines, 247–257
pyrimidines, and nucleosides by paper chromatography. 26. Kaneda M, Okano M, Hata K, et al. Essential role for de
J Biol Chem 1948;175(1):315–332 novo DNA methyltransferase Dnmt3a in paternal and

Downloaded by: Wegner Health Science Information Center. Copyrighted material.

8. Griffith JS, Mahler HR. DNA ticketing theory of memory. maternal imprinting. Nature 2004;429(6994):900–903
Nature 1969;223(5206):580–582 27. Klose RJ, Bird AP. Genomic DNA methylation: the mark
9. Ratel D, Ravanat JL, Berger F, Wion D. N6-methyladenine: and its mediators. Trends Biochem Sci 2006;31(2):89–
the other methylated base of DNA. Bioessays 2006;28(3): 97
309–315 28. Perche PY, Robert-Nicoud M, Khochbin S, Vourc’h C.
10. Sinsheimer RL. The action of pancreatic deoxyribonuclease. Nucleosome differentiation: role of histone H2A variants [in
II. Isomeric dinucleotides. J Biol Chem 1955;215(2):579–583 French]. Med Sci (Paris) 2003;19(11):1137–1145
11. Woodcock DM, Crowther PJ, Diver WP. The majority of 29. Redon C, Pilch D, Rogakou E, Sedelnikova O, Newrock K,
methylated deoxycytidines in human DNA are not in the Bonner W. Histone H2A variants H2AX and H2AZ. Curr
CpG dinucleotide. Biochem Biophys Res Commun 1987; Opin Genet Dev 2002;12(2):162–169
145(2):888–894 30. Hake SB, Allis CD. Histone H3 variants and their potential
12. Nyce J, Liu L, Jones PA. Variable effects of DNA-synthesis role in indexing mammalian genomes: the ‘‘H3 barcode
inhibitors upon DNA methylation in mammalian cells. hypothesis’’. Proc Natl Acad Sci U S A 2006;103(17):6428–
Nucleic Acids Res 1986;14(10):4353–4367 6435
13. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, 31. Phillips DM, Johns EW. A fractionation of the histones
Jaenisch R. Non-CpG methylation is prevalent in embryonic of group F2a from calf thymus. Biochem J 1965;94:127–
stem cells and may be mediated by DNA methyltransferase 130
3a. Proc Natl Acad Sci U S A 2000;97(10):5237–5242 32. Kornberg RD. Chromatin structure: a repeating unit of
14. Naveh-Many T, Cedar H. Active gene sequences are histones and DNA. Science 1974;184(139):868–871
undermethylated. Proc Natl Acad Sci U S A 1981;78(7): 33. Kouzarides T. Chromatin modifications and their function.
4246–4250 Cell 2007;128(4):693–705
15. Waechter DE, Baserga R. Effect of methylation on expression 34. Marmorstein R, Trievel RC. Histone modifying enzymes:
of microinjected genes. Proc Natl Acad Sci U S A 1982; structures, mechanisms, and specificities. Biochim Biophys
79(4):1106–1110 Acta 2009;1789(1):58–68
16. Watt F, Molloy PL. Cytosine methylation prevents binding 35. Strahl BD, Allis CD. The language of covalent histone
to DNA of a HeLa cell transcription factor required for modifications. Nature 2000;403(6765):41–45
optimal expression of the adenovirus major late promoter. 36. Pogo BG, Allfrey VG, Mirsky AE. RNA synthesis and
Genes Dev 1988;2(9):1136–1143 histone acetylation during the course of gene activation in
17. Boyes J, Bird A. DNA methylation inhibits transcription lymphocytes. Proc Natl Acad Sci U S A 1966;55(4):805–
indirectly via a methyl-CpG binding protein. Cell 1991; 812
64(6):1123–1134 37. Allfrey VG, Faulkner R, Mirsky AE. Acetylation and
18. Hendrich B, Bird A. Identification and characterization of a methylation of histones and their possible role in the
family of mammalian methyl-CpG binding proteins. Mol regulation of RNA synthesis. Proc Natl Acad Sci U S A
Cell Biol 1998;18(11):6538–6547 1964;51:786–794
19. Jones PL, Veenstra GJ, Wade PA, et al. Methylated DNA 38. Sealy L, Chalkley R. DNA associated with hyperacetylated
and MeCP2 recruit histone deacetylase to repress tran- histone is preferentially digested by DNase I. Nucleic Acids
scription. Nat Genet 1998;19(2):187–191 Res 1978;5(6):1863–1876
20. Nan X, Ng HH, Johnson CA, et al. Transcriptional repression 39. Hong L, Schroth GP, Matthews HR, Yau P, Bradbury EM.
by the methyl-CpG-binding protein MeCP2 involves a Studies of the DNA binding properties of histone H4 amino
histone deacetylase complex. Nature 1998;393 (6683): terminus. Thermal denaturation studies reveal that acetyla-
386–389 tion markedly reduces the binding constant of the H4 ‘‘tail’’
21. Leonhardt H, Page AW, Weier HU, Bestor TH. A to DNA. J Biol Chem 1993;268(1):305–314
targeting sequence directs DNA methyltransferase to sites 40. Norton VG, Imai BS, Yau P, Bradbury EM. Histone
of DNA replication in mammalian nuclei. Cell 1992;71(5): acetylation reduces nucleosome core particle linking number
865–873 change. Cell 1989;57(3):449–457
356 SEMINARS IN REPRODUCTIVE MEDICINE/VOLUME 27, NUMBER 5 2009

41. Sims RJ III, Nishioka K, Reinberg D. Histone lysine 59. Wang J, Mager J, Chen Y, et al. Imprinted X inactivation
methylation: a signature for chromatin function. Trends maintained by a mouse Polycomb group gene. Nat Genet
Genet 2003;19(11):629–639 2001;28(4):371–375
42. Parra MA, Wyrick JJ. Regulation of gene transcription by the 60. Heard E, Disteche CM. Dosage compensation in mammals:
histone H2A N-terminal domain. Mol Cell Biol 2007; fine-tuning the expression of the X chromosome. Genes Dev
27(21):7641–7648 2006;20(14):1848–1867
43. Parra MA, Kerr D, Fahy D, Pouchnik DJ, Wyrick JJ. 61. Lifschytz E, Lindsley DL. The role of X-chromosome
Deciphering the roles of the histone H2B N-terminal inactivation during spermatogenesis (Drosophila-allocycly-
domain in genome-wide transcription. Mol Cell Biol 2006; chromosome evolution-male sterility-dosage compensation).
26(10):3842–3852 Proc Natl Acad Sci U S A 1972;69(1):182–186
44. Weinberg MS, Villeneuve LM, Ehsani A, et al. The 62. Okamoto I, Arnaud D, Le Baccon P, et al. Evidence for de
antisense strand of small interfering RNAs directs histone novo imprinted X-chromosome inactivation independent of
methylation and transcriptional gene silencing in human meiotic inactivation in mice. Nature 2005;438(7066):369–
cells. RNA 2006;12(2):256–262 373
45. Han J, Kim D, Morris KV. Promoter-associated RNA is 63. van der Heijden GW, Dieker JW, Derijck AA, et al.
required for RNA-directed transcriptional gene silencing in Asymmetry in histone H3 variants and lysine methylation
human cells. Proc Natl Acad Sci U S A 2007;104(30):12422– between paternal and maternal chromatin of the early mouse
12427 zygote. Mech Dev 2005;122(9):1008–1022

Downloaded by: Wegner Health Science Information Center. Copyrighted material.

46. Kim DH, Villeneuve LM, Morris KV, Rossi JJ. Argo- 64. Tada T, Obata Y, Tada M, et al. Imprint switching for non-
naute-1 directs siRNA-mediated transcriptional gene random X-chromosome inactivation during mouse oocyte
silencing in human cells. Nat Struct Mol Biol 2006; growth. Development 2000;127(14):3101–3105
13(9):793–797 65. Norris DP, Patel D, Kay GF, et al. Evidence that random
47. Köhler C, Villar CB. Programming of gene expression by and imprinted Xist expression is controlled by preemptive
Polycomb group proteins. Trends Cell Biol 2008;18(5):236– methylation. Cell 1994;77(1):41–51
243 66. Surani MA, Barton SC, Norris ML. Development of
48. Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y. Histone reconstituted mouse eggs suggests imprinting of the genome
H3.1 and H3.3 complexes mediate nucleosome assembly during gametogenesis. Nature 1984;308(5959):548–550
pathways dependent or independent of DNA synthesis. Cell 67. McGrath J, Solter D. Completion of mouse embryogenesis
2004;116(1):51–61 requires both the maternal and paternal genomes. Cell 1984;
49. Henikoff S, Furuyama T, Ahmad K. Histone variants, 37(1):179–183
nucleosome assembly and epigenetic inheritance. Trends 68. Bartolomei MS, Zemel S, Tilghman SM. Parental imprint-
Genet 2004;20(7):320–326 ing of the mouse H19 gene. Nature 1991;351(6322):153–
50. Payer B, Lee JT. X chromosome dosage compensation: how 155
mammals keep the balance. Annu Rev Genet 2008;42:733– 69. Barlow DP, Stöger R, Herrmann BG, Saito K, Schweifer N.
772 The mouse insulin-like growth factor type-2 receptor is
51. Huynh KD, Lee JT. X-chromosome inactivation: a hypoth- imprinted and closely linked to the Tme locus. Nature 1991;
esis linking ontogeny and phylogeny. Nat Rev Genet 349(6304):84–87
2005;6(5):410–418 70. DeChiara TM, Robertson EJ, Efstratiadis A. Parental
52. Adler DA, Rugarli EI, Lingenfelter PA, et al. Evidence of imprinting of the mouse insulin-like growth factor II gene.
evolutionary up-regulation of the single active X chromosome Cell 1991;64(4):849–859
in mammals based on Clc4 expression levels in Mus spretus 71. Wilkins JF, Haig D. What good is genomic imprinting: the
and Mus musculus. Proc Natl Acad Sci U S A 1997; function of parent-specific gene expression. Nat Rev Genet
94(17):9244–9248 2003;4(5):359–368
53. Lyon MF. Gene action in the X-chromosome of the mouse 72. Spahn L, Barlow DP. An ICE pattern crystallizes. Nat Genet
(Mus musculus L.). Nature 1961;190:372–373 2003;35(1):11–12
54. Sharman GB. Late DNA replication in the paternally derived 73. Obata Y, Kaneko-Ishino T, Koide T, et al. Disruption of
X chromosome of female kangaroos. Nature 1971;230(5291): primary imprinting during oocyte growth leads to the
231–232 modified expression of imprinted genes during embryo-
55. Cooper DW, VandeBerg JL, Sharman GB, Poole WE. genesis. Development 1998;125(8):1553–1560
Phosphoglycerate kinase polymorphism in kangaroos pro- 74. Davis TL, Yang GJ, McCarrey JR, Bartolomei MS. The
vides further evidence for paternal X inactivation. Nat New H19 methylation imprint is erased and re-established differ-
Biol 1971;230(13):155–157 entially on the parental alleles during male germ cell
56. Huynh KD, Lee JT. Inheritance of a pre-inactivated paternal development. Hum Mol Genet 2000;9(19):2885–2894
X chromosome in early mouse embryos. Nature 2003; 75. Ueda T, Abe K, Miura A, et al. The paternal methylation
426(6968):857–862 imprint of the mouse H19 locus is acquired in the gonocyte
57. Takagi N, Sasaki M. Preferential inactivation of the stage during foetal testis development. Genes Cells 2000;
paternally derived X chromosome in the extraembryonic 5(8):649–659
membranes of the mouse. Nature 1975;256(5519):640– 76. Li JY, Lees-Murdock DJ, Xu GL, Walsh CP. Timing of
642 establishment of paternal methylation imprints in the mouse.
58. Sado T, Fenner MH, Tan SS, Tam P, Shioda T, Li E. X Genomics 2004;84(6):952–960
inactivation in the mouse embryo deficient for Dnmt1: 77. Lucifero D, Mann MR, Bartolomei MS, Trasler JM. Gene-
distinct effect of hypomethylation on imprinted and random specific timing and epigenetic memory in oocyte imprinting.
X inactivation. Dev Biol 2000;225(2):294–303 Hum Mol Genet 2004;13(8):839–849
 EPIGENETICS: DEFINITION, MECHANISMS, AND CLINICAL PERSPECTIVE/DUPONT ET AL 357

78. Hiura H, Obata Y, Komiyama J, Shirai M, Kono T. Oocyte 86. Doherty AS, Mann MR, Tremblay KD, Bartolomei MS,
growth-dependent progression of maternal imprinting in Schultz RM. Differential effects of culture on imprinted H19
mice. Genes Cells 2006;11(4):353–361 expression in the preimplantation mouse embryo. Biol Reprod
79. Lee JT. Molecular links between X-inactivation and autosomal 2000;62(6):1526–1535
imprinting: X-inactivation as a driving force for the evolution 87. Li T, Vu TH, Ulaner GA, et al. IVF results in de novo DNA
of imprinting? Curr Biol 2003;13(6):R242–R254 methylation and histone methylation at an Igf2-H19
80. Dean W, Santos F, Reik W. Epigenetic reprogramming in imprinting epigenetic switch. Mol Hum Reprod 2005;11(9):
early mammalian development and following somatic nuclear 631–640
transfer. Semin Cell Dev Biol 2003;14(1):93–100 88. Khosla S, Dean W, Brown D, Reik W, Feil R. Culture of
81. Nakamura T, Arai Y, Umehara H, et al. PGC7/Stella preimplantation mouse embryos affects fetal development
protects against DNA demethylation in early embryogenesis. and the expression of imprinted genes. Biol Reprod 2001;
Nat Cell Biol 2007;9(1):64–71 64(3):918–926
82. Morgan HD, Sutherland HG, Martin DI, Whitelaw E. 89. Khosla S, Dean W, Reik W, Feil R. Culture of
Epigenetic inheritance at the agouti locus in the mouse. Nat preimplantation embryos and its long-term effects on gene
Genet 1999;23(3):314–318 expression and phenotype. Hum Reprod Update 2001;7(4):
83. Lane N, Dean W, Erhardt S, et al. Resistance of IAPs to 419–427
methylation reprogramming may provide a mechanism for 90. Wu Q, Ohsako S, Ishimura R, Suzuki JS, Tohyama C.
epigenetic inheritance in the mouse. Genesis 2003;35(2): Exposure of mouse preimplantation embryos to 2,3,7,8-

Downloaded by: Wegner Health Science Information Center. Copyrighted material.

88–93 tetrachlorodibenzo-p-dioxin (TCDD) alters the methylation
84. Maher ER, Afnan M, Barratt CL. Epigenetic risks related to status of imprinted genes H19 and Igf2. Biol Reprod 2004;
assisted reproductive technologies: epigenetics, imprinting, 70(6):1790–1797
ART and icebergs? Hum Reprod 2003;18(12):2508–2511 91. Shao WJ, Tao LY, Xie JY, Gao C, Hu JH, Zhao RQ.
85. Barker DJ. Intrauterine programming of coronary heart Exposure of preimplantation embryos to insulin alters
disease and stroke. Acta Paediatr Suppl 1997;423:178–182; expression of imprinted genes. Comp Med 2007;57(5):482–
discussion 183 486