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Environmental Effects on Genomic Imprinting in Development and Disease

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Handbook of Nutrition, Diet, and Epigenetics
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Abstract

Genomic imprinting mediates the parent-of-origin-specific, mono-allelic expression of many protein-coding genes and noncoding RNAs. This paradigm for epigenetic gene regulation plays diverse roles in mammalian development, growth and behavior. Mechanistically, it involves parentally inherited DNA methylation marks that control clusters of imprinted genes. Perturbation of these epigenetic imprints affects embryonic and postnatal development and leads to complex diseases in humans, including different types of diabetes. This chapter discusses imprinted genes, with emphasis on those that control metabolism and cellular proliferation, several of which encode proteins of the insulin-like growth factor/insulin signaling pathway. Nutrition, chemical pollutants, and other environmental cues can readily perturb DNA methylation imprints, not only during development, but sometimes even in adults. Such epigenetic alterations (“epimutations”) may affect imprinted gene expression and, hence, can have deleterious effects on phenotype. In the future, clinical and environmental imprinting studies will gain from taking a broader approach that considers not only the imprinted gene loci themselves, but also similarly controlled loci located elsewhere in the genome.

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Abbreviations

ART:

Assisted Reproductive Technology

BPA:

Bisphenol A

BWS:

Beckwith-Wiedemann Syndrome

ICR:

Imprinting control region

IGF:

Insulin-like growth factor

INS:

Insulin

IUGR:

Intra-uterine growth restriction

ncRNA:

Noncoding RNA

SRS:

Silver Russell Syndrome

TNDM:

Transient neonatal diabetes mellitus

References

  • Abramowitz LK, Bartolomei MS (2012) Genomic imprinting: recognition and marking of imprinted loci. Curr Opin Genet Dev 22:72–78

    Article  CAS  Google Scholar 

  • Al Adhami H, Evano B, Le Digarcher A et al (2015) A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. Genome Res 25:353–367

    Article  Google Scholar 

  • Arima T, Kamikihara T, Hayashida T et al (2005) ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith-Wiedemann syndrome. Nucleic Acids Res 33:2650–2660

    Article  CAS  Google Scholar 

  • Barlow DP, Stoger R, Herrmann BG et al (1991) The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 349:84–87

    Article  CAS  Google Scholar 

  • Bartolomei MS, Ferguson-Smith AC (2011) Mammalian genomic imprinting. Cold Spring Harb Perspect Biol 3:a002592

    Article  CAS  Google Scholar 

  • Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351:153–155

    Article  CAS  Google Scholar 

  • Cattanach BM, Kirk M (1985) Differential activity of maternally and paternally derived chromosome regions in mice. Nature 315:496–498

    Article  CAS  Google Scholar 

  • Charalambous M, Smith FM, Bennett WR et al (2003) Disruption of the imprinted Grb10 gene leads to disproportionate overgrowth by an Igf2-independent mechanism. Proc Natl Acad Sci U S A 100:8292–8297

    Article  CAS  Google Scholar 

  • Dean W, Bowden L, Aitchison A et al (1998) Altered imprinted gene methylation and expression in completely ES cell-derived mouse fetuses: association with aberrant phenotypes. Development 125:2273–2282

    CAS  PubMed  Google Scholar 

  • DeChiara TM, Robertson EJ, Efstratiadis A (1991) Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64:849–859

    Article  CAS  Google Scholar 

  • Delaval K, Wagschal A, Feil R (2006) Epigenetic deregulation of imprinting in congenital diseases of aberrant growth. BioEssays 28:453–459

    Article  CAS  Google Scholar 

  • Deltour L, Montagutelli X, Guenet JL et al (1995) Tissue- and developmental stage-specific imprinting of the mouse proinsulin gene, Ins2. Dev Biol 168:686–688

    Article  CAS  Google Scholar 

  • Demars J, Shmela ME, Rossignol S et al (2010) Analysis of the IGF2/H19 imprinting control region uncovers new genetic defects, including mutations of OCT-binding sequences, in patients with 11p15 fetal growth disorders. Hum Mol Genet 19:803–814

    Article  CAS  Google Scholar 

  • Dias RP, Maher ER (2013) Genes, assisted reproductive technology and trans-illumination. Epigenomics 5:331–340

    Article  CAS  Google Scholar 

  • Dominguez-Salas P, Moore SE, Baker MS et al (2014) Maternal nutrition at conception modulates DNA methylation of human metastable epialleles. Nat Commun 5:3746

    Article  CAS  Google Scholar 

  • Duvillie B, Bucchini D, Tang T et al (1998) Imprinting at the mouse Ins2 locus: evidence for cis- and trans-allelic interactions. Genomics 47:52–57

    Article  CAS  Google Scholar 

  • Eggermann T, Brioude F, Russo S et al (2016) Prenatal molecular testing for Beckwith-Wiedemann and Silver-Russell syndromes: a challenge for molecular analysis and genetic counseling. Eur J Hum Genet 24:784–793

    Article  CAS  Google Scholar 

  • Eggermann T, Perez de Nanclares G, Maher ER et al (2015) Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci. Clin Epigenetics 7:123

    Article  Google Scholar 

  • El-Maarri O, Becker T, Junen J et al (2007) Gender specific differences in levels of DNA methylation at selected loci from human total blood: a tendency toward higher methylation levels in males. Hum Genet 122:505–514

    Article  CAS  Google Scholar 

  • Feil R, Fraga MF (2012) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13:97–109

    Article  CAS  Google Scholar 

  • Filipponi D, Feil R (2009) Perturbation of genomic imprinting in oligozoospermia. Epigenetics 4:27–30

    Article  CAS  Google Scholar 

  • Gabory A, Jammes H, Dandolo L (2010) The H19 locus: role of an imprinted non-coding RNA in growth and development. BioEssays 32:473–480

    Article  CAS  Google Scholar 

  • Guillemot F, Caspary T, Tilghman SM et al (1995) Genomic imprinting of Mash2, a mouse gene required for trophoblast development. Nat Genet 9:235–242

    Article  CAS  Google Scholar 

  • Hellman A, Chess A (2010) Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics Chromatin 3:11

    Article  Google Scholar 

  • Hirasawa R, Feil R (2010) Genomic imprinting and human disease. Essays Biochem 48:187–200

    Article  CAS  Google Scholar 

  • Hiura H, Okae H, Miyauchi N et al (2012) Characterization of DNA methylation errors in patients with imprinting disorders conceived by assisted reproduction technologies. Hum Reprod 27:2541–2548

    Article  CAS  Google Scholar 

  • Iglesias-Platas I, Martin-Trujillo A, Petazzi P et al (2014) Altered expression of the imprinted transcription factor PLAGL1 deregulates a network of genes in the human IUGR placenta. Hum Mol Genet 23:6275–6285

    Article  CAS  Google Scholar 

  • Ingrosso D, Cimmino A, Perna AF et al (2003) Folate treatment and unbalanced methylation and changes of allelic expression induced by hyperhomocysteinaemia in patients with uraemia. Lancet 361:1693–1699

    Article  CAS  Google Scholar 

  • Kelsey G, Feil R (2013) New insights into establishment and maintenance of DNA methylation imprints in mammals. Philos Trans R Soc Lond Ser B Biol Sci 368:20110336

    Article  Google Scholar 

  • Kerkel K, Spadola A, Yuan E et al (2008) Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 40:904–908

    Article  CAS  Google Scholar 

  • Ludwig T, Eggenschwiler J, Fisher P et al (1996) Mouse mutants lacking the type 2 IGF receptor (IGF2R) are rescued from perinatal lethality in Igf2 and Igf1r null backgrounds. Dev Biol 177:517–535

    Article  CAS  Google Scholar 

  • Mackay DJ, Callaway JL, Marks SM et al (2008) Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat Genet 40:949–951

    Article  CAS  Google Scholar 

  • Manzardo AM, Henkhaus RS, Butler MG (2012) Global DNA promoter methylation in frontal cortex of alcoholics and controls. Gene 498:5–12

    Article  CAS  Google Scholar 

  • Market Velker BA, Denomme MM, Mann MR (2012) Loss of genomic imprinting in mouse embryos with fast rates of preimplantation development in culture. Biol Reprod 86(143):1–16

    Google Scholar 

  • Marques CJ, Carvalho F, Sousa M et al (2004) Genomic imprinting in disruptive spermatogenesis. Lancet 363:1700–1702

    Article  CAS  Google Scholar 

  • Marques PI, Fernandes S, Carvalho F et al (2017) DNA methylation imprinting errors in spermatogenic cells from maturation arrest azoospermic patients. Andrology 5:451–459

    Article  CAS  Google Scholar 

  • Masemola ML, van der Merwe L, Lombard Z et al (2015) Reduced DNA methylation at the PEG3 DMR and KvDMR1 loci in children exposed to alcohol in utero: a South African Fetal Alcohol Syndrome cohort study. Front Genet 6:85

    Article  Google Scholar 

  • McGrath J, Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37:179–183

    Article  CAS  Google Scholar 

  • Monk D, Arnaud P, Apostolidou S et al (2006) Limited evolutionary conservation of imprinting in the human placenta. Proc Natl Acad Sci U S A 103:6623–6628

    Article  CAS  Google Scholar 

  • Monk D, Arnaud P, Frost J et al (2009) Reciprocal imprinting of human GRB10 in placental trophoblast and brain: evolutionary conservation of reversed allelic expression. Hum Mol Genet 18:3066–3074

    Article  CAS  Google Scholar 

  • Monnier P, Martinet C, Pontis J et al (2013) H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1. Proc Natl Acad Sci U S A 110:20693–20698

    Article  CAS  Google Scholar 

  • Moore GE, Abu-Amero SN, Bell G et al (2001) Evidence that insulin is imprinted in the human yolk sac. Diabetes 50:199–203

    Article  CAS  Google Scholar 

  • Moore GE, Ishida M, Demetriou C et al (2015) The role and interaction of imprinted genes in human fetal growth. Philos Trans R Soc Lond Ser B Biol Sci 370:20140074

    Article  CAS  Google Scholar 

  • Morita S, Horii T, Kimura M et al (2014) Paternal allele influences high fat diet-induced obesity. PLoS One 9:e85477

    Article  Google Scholar 

  • Murrell A, Heeson S, Cooper WN et al (2004) An association between variants in the IGF2 gene and Beckwith-Wiedemann syndrome: interaction between genotype and epigenotype. Hum Mol Genet 13:247–255

    Article  CAS  Google Scholar 

  • Ouko LA, Shantikumar K, Knezovich J et al (2009) Effect of alcohol consumption on CpG methylation in the differentially methylated regions of H19 and IG-DMR in male gametes: implications for fetal alcohol spectrum disorders. Alcohol Clin Exp Res 33:1615–1627

    Article  CAS  Google Scholar 

  • Park SS, Skaar DA, Jirtle RL et al (2017) Epigenetics, obesity and early-life cadmium or lead exposure. Epigenomics 9:57–75

    Article  CAS  Google Scholar 

  • Parker-Katiraee L, Carson AR, Yamada T et al (2007) Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution. PLoS Genet 3:e65

    Article  Google Scholar 

  • Peters J (2014) The role of genomic imprinting in biology and disease: an expanding view. Nat Rev Genet 15:517–530

    Article  CAS  Google Scholar 

  • Poole RL, Leith DJ, Docherty LE et al (2012) Beckwith-Wiedemann syndrome caused by maternally inherited mutation of an OCT-binding motif in the IGF2/H19-imprinting control region, ICR1. Eur J Hum Genet 20:240–243

    Article  CAS  Google Scholar 

  • Sanchez-Delgado M, Court F, Vidal E et al (2016) Human oocyte-derived methylation differences persist in the placenta revealing widespread transient imprinting. PLoS Genet 12:e1006427

    Article  Google Scholar 

  • Sandovici I, Smith NH, Nitert MD et al (2011) Maternal diet and aging alter the epigenetic control of a promoter-enhancer interaction at the Hnf4a gene in rat pancreatic islets. Proc Natl Acad Sci U S A 108:5449–5454

    Article  CAS  Google Scholar 

  • Sanli I, Feil R (2015) Chromatin mechanisms in the developmental control of imprinted gene expression. Int J Biochem Cell Biol 67:139–147

    Article  CAS  Google Scholar 

  • Sanz LA, Chamberlain S, Sabourin JC et al (2008) A mono-allelic bivalent chromatin domain controls tissue-specific imprinting at Grb10. EMBO J 27:2523–2532

    Article  CAS  Google Scholar 

  • Sferruzzi-Perri AN, Vaughan OR, Haro M et al (2013) An obesogenic diet during mouse pregnancy modifies maternal nutrient partitioning and the fetal growth trajectory. FASEB J 27:3928–3937

    Article  CAS  Google Scholar 

  • Shiura H, Nakamura K, Hikichi T et al (2009) Paternal deletion of Meg1/Grb10 DMR causes maternalization of the Meg1/Grb10 cluster in mouse proximal chromosome 11 leading to severe pre- and postnatal growth retardation. Hum Mol Genet 18:1424–1438

    Article  CAS  Google Scholar 

  • Small KS, Hedman AK, Grundberg E et al (2011) Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. Nat Genet 43:561–564

    Article  CAS  Google Scholar 

  • Stouder C, Paoloni-Giacobino A (2010) Transgenerational effects of the endocrine disruptor vinclozolin on the methylation pattern of imprinted genes in the mouse sperm. Reproduction 139:373–379

    Article  CAS  Google Scholar 

  • Stouder C, Paoloni-Giacobino A (2011) Specific transgenerational imprinting effects of the endocrine disruptor methoxychlor on male gametes. Reproduction 141:207–216

    Article  CAS  Google Scholar 

  • Stouder C, Somm E, Paoloni-Giacobino A (2011) Prenatal exposure to ethanol: a specific effect on the H19 gene in sperm. Reprod Toxicol 31:507–512

    Article  CAS  Google Scholar 

  • Surani MA, Barton SC, Norris ML (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308:548–550

    Article  CAS  Google Scholar 

  • Susiarjo M, Sasson I, Mesaros C et al (2013) Bisphenol a exposure disrupts genomic imprinting in the mouse. PLoS Genet 9:e1003401

    Article  CAS  Google Scholar 

  • Susiarjo M, Xin F, Bansal A et al (2015) Bisphenol a exposure disrupts metabolic health across multiple generations in the mouse. Endocrinology 156:2049–2058

    Article  CAS  Google Scholar 

  • Tobi EW, Goeman JJ, Monajemi R et al (2014) DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun 5:5592

    Article  CAS  Google Scholar 

  • Tobi EW, Lumey LH, Talens RP et al (2009) DNA methylation differences after exposure to prenatal famine are common and timing- and sex-specific. Hum Mol Genet 18:4046–4053

    Article  CAS  Google Scholar 

  • Umlauf D, Goto Y, Cao R et al (2004) Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36:1296–1300

    Article  CAS  Google Scholar 

  • Varrault A, Gueydan C, Delalbre A et al (2006) Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. Dev Cell 11:711–722

    Article  CAS  Google Scholar 

  • Voight BF, Scott LJ, Steinthorsdottir V et al (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 42:579–589

    Article  CAS  Google Scholar 

  • Voon HP, Hughes JR, Rode C et al (2015) ATRX plays a key role in maintaining silencing at interstitial heterochromatic loci and imprinted genes. Cell Rep 11:405–418

    Article  CAS  Google Scholar 

  • Vrooman LA, Bartolomei MS (2016) Can assisted reproductive technologies cause adult-onset disease? Evidence from human and mouse. Reprod Toxicol 68:72–84

    Google Scholar 

  • Wallace C, Smyth DJ, Maisuria-Armer M et al (2010) The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. Nat Genet 42:68–71

    Article  CAS  Google Scholar 

  • Waterland RA, Kellermayer R, Laritsky E et al (2010) Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet 6:e1001252

    Article  CAS  Google Scholar 

  • Waxman DJ, O’Connor C (2006) Growth hormone regulation of sex-dependent liver gene expression. Mol Endocrinol 20:2613–2629

    Article  CAS  Google Scholar 

  • Wutz A, Theussl HC, Dausman J et al (2001) Non-imprinted Igf2r expression decreases growth and rescues the Tme mutation in mice. Development 128:1881–1887

    CAS  PubMed  Google Scholar 

  • Xin F, Susiarjo M, Bartolomei MS (2015) Multigenerational and transgenerational effects of endocrine disrupting chemicals: a role for altered epigenetic regulation? Semin Cell Dev Biol 43:66–75

    Article  CAS  Google Scholar 

  • Zhang N, Huang W, Dong F et al (2015) Insulin gene VNTR polymorphisms -2221MspI and -23HphI are associated with type 1 diabetes and latent autoimmune diabetes in adults: a meta-analysis. Acta Diabetol 52:1143–1155

    Article  CAS  Google Scholar 

  • Zhang P, Wong C, DePinho RA et al (1998) Cooperation between the Cdk inhibitors p27(KIP1) and p57(KIP2) in the control of tissue growth and development. Genes Dev 12:3162–3167

    Article  CAS  Google Scholar 

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Pathak, R., Feil, R. (2019). Environmental Effects on Genomic Imprinting in Development and Disease. In: Patel, V., Preedy, V. (eds) Handbook of Nutrition, Diet, and Epigenetics. Springer, Cham. https://doi.org/10.1007/978-3-319-55530-0_92

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