Mammalian Genome

, Volume 22, Issue 11–12, pp 722–735 | Cite as

Hypomethylation of functional retrotransposon-derived genes in the human placenta

  • Erin C. Macaulay
  • Robert J. Weeks
  • Simon Andrews
  • Ian M. MorisonEmail author


DNA hypomethylation is assumed to be a feature of the mammalian placenta; however, its role in regulating placental gene expression is not well defined. In this study, MeDIP and Sequenom MassARRAY were used to identify hypomethylated gene promoters in the human placenta. Among the genes identified, the hypomethylation of an alternative promoter for KCNH5 was found to be restricted to the placenta and chorion. Complete methylation of this promoter correlates with a silenced KCNH5 transcript in embryonic tissues, including the amnion. Unusually, this hypomethylated promoter and the alternative first exon are derived from a SINE (AluY) retrotransposon. Examination of additional retrotransposon-derived gene promoters in the placenta confirmed that retrotransposon hypomethylation permits the placenta-specific expression of these genes. Furthermore, the lineage-specific methylation displayed by KCNH5, INSL4, and ERVWE1 revealed that dichotomous methylation establishes differential retrotransposon silencing between the extra-embryonic and embryonic lineages. The hypomethylation of the retrotransposons that regulate these genes, each of which arose during recent primate evolution, is consistent with these genes having functional roles that are unique to the invasive haemochorial placentas of humans and recent primates.


Promoter Methylation Primitive Endoderm Aviva System Biology Placental Gene Expression Adult Somatic Tissue 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank the women who donated their pregnancy tissues to this study. We acknowledge funding from the University of Otago and the National Research Centre for Growth and Development.

Supplementary material

335_2011_9355_MOESM1_ESM.pdf (121 kb)
Supplementary material 1 (PDF 121 kb)
335_2011_9355_MOESM2_ESM.pdf (164 kb)
Supplementary material 2 (PDF 164 kb)
335_2011_9355_MOESM3_ESM.pdf (95 kb)
Supplementary material 3 (PDF 96 kb)
335_2011_9355_MOESM4_ESM.pdf (119 kb)
Supplementary material 4 (PDF 120 kb)
335_2011_9355_MOESM5_ESM.doc (341 kb)
Supplementary material 5 (DOC 341 kb)


  1. Agapitov AV, Haynes WG (2002) Role of endothelin in cardiovascular disease. J Renin Angiotensin Aldosterone Syst 3:1–15PubMedCrossRefGoogle Scholar
  2. Arai H, Nakao K, Takaya K, Hosoda K, Ogawa Y, Nakanishi S, Imura H (1993) The human endothelin-B receptor gene. Structural organization and chromosomal assignment. J Biol Chem 268:3463–3470PubMedGoogle Scholar
  3. Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3:370–379PubMedCrossRefGoogle Scholar
  4. Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E (1996) Standardized nomenclature for Alu repeats. J Mol Evol 42:3–6PubMedCrossRefGoogle Scholar
  5. Bellet D, Lavaissiere L, Mock P, Laurent A, Sabourin JC, Bedossa P, Le Bouteiller P, Frydman R, Troalen F, Bidart JM (1997) Identification of pro-EPIL and EPIL peptides translated from insulin-like 4 (INSL4) mRNA in human placenta. J Clin Endocrinol Metab 82:3169–3172PubMedCrossRefGoogle Scholar
  6. Benirschke K, Kaufmann P, Baergen RN (2006) Pathology of the human placenta, 5th edn. Springer, New YorkGoogle Scholar
  7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37:D26–D31PubMedCrossRefGoogle Scholar
  8. Bianchi DW, Wilkins-Haug LE, Enders AC, Hay ED (1993) Origin of extraembryonic mesoderm in experimental animals: relevance to chorionic mosaicism in humans. Am J Med Genet 46:542–550PubMedCrossRefGoogle Scholar
  9. Bieche I, Laurent A, Laurendeau I, Duret L, Giovangrandi Y, Frendo JL, Olivi M, Fausser JL, Evain-Brion D, Vidaud M (2003) Placenta-specific INSL4 expression is mediated by a human endogenous retrovirus element. Biol Reprod 68:1422–1429PubMedCrossRefGoogle Scholar
  10. Blond JL, Lavillette D, Cheynet V, Bouton O, Oriol G, Chapel-Fernandes S, Mandrand B, Mallet F, Cosset FL (2000) An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor. J Virol 74:3321–3329PubMedCrossRefGoogle Scholar
  11. Brandt B, Kemming D, Packeisen J, Simon R, Helms M, Feldmann U, Matuschek A, Kersting C, Hinrichs B, Bidart JM, Bellet D, Bartkowiak K, Dankbar N, Dittmar T, Sauter G, Boecker W, Buerger H (2005) Expression of early placenta insulin-like growth factor in breast cancer cells provides an autocrine loop that predominantly enhances invasiveness and motility. Endocr Relat Cancer 12:823–837PubMedCrossRefGoogle Scholar
  12. Castellucci M, Kaufmann P (1982) A three-dimensional study of the normal human placental villous core: II. Stromal architecture. Placenta 3:269–285PubMedCrossRefGoogle Scholar
  13. Chapman V, Forrester L, Sanford J, Hastie N, Rossant J (1984) Cell lineage-specific undermethylation of mouse repetitive DNA. Nature 307:284–286PubMedCrossRefGoogle Scholar
  14. Chassin D, Laurent A, Janneau JL, Berger R, Bellet D (1995) Cloning of a new member of the insulin gene superfamily (INSL4) expressed in human placenta. Genomics 29:465–470PubMedCrossRefGoogle Scholar
  15. Cheng YH, Richardson BD, Hubert MA, Handwerger S (2004) Isolation and characterization of the human syncytin gene promoter. Biol Reprod 70:694–701PubMedCrossRefGoogle Scholar
  16. Coan PM, Burton GJ, Ferguson-Smith AC (2005) Imprinted genes in the placenta—a review. Placenta 26:S10–S20PubMedCrossRefGoogle Scholar
  17. Cohen M, Bischof P (2007) Factors regulating trophoblast invasion. Gynecol Obstet Investig 64:126–130CrossRefGoogle Scholar
  18. Constancia M, Kelsey G, Reik W (2004) Resourceful imprinting. Nature 432:53–57PubMedCrossRefGoogle Scholar
  19. Cotton AM, Avila L, Penaherrera MS, Affleck JG, Robinson WP, Brown CJ (2009) Inactive X chromosome-specific reduction in placental DNA methylation. Hum Mol Genet 18:3544–3552PubMedCrossRefGoogle Scholar
  20. Cross JC (2005) How to make a placenta: mechanisms of trophoblast cell differentiation in mice—a review. Placenta 26(Suppl A):S3–S9PubMedCrossRefGoogle Scholar
  21. Cross JC, Werb Z, Fisher SJ (1994) Implantation and the placenta: key pieces of the development puzzle. Science 266:1508–1518PubMedCrossRefGoogle Scholar
  22. Dean W, Santos F, Reik W (2003) Epigenetic reprogramming in early mammalian development and following somatic nuclear transfer. Semin Cell Dev Biol 14:93–100PubMedCrossRefGoogle Scholar
  23. Deuel TF, Zhang N, Yeh HJ, Silos-Santiago I, Wang ZY (2002) Pleiotrophin: a cytokine with diverse functions and a novel signaling pathway. Arch Biochem Biophys 397:162–171PubMedCrossRefGoogle Scholar
  24. Downs KM (2009) The enigmatic primitive streak: prevailing notions and challenges concerning the body axis of mammals. Bioessays 31:892–902PubMedCrossRefGoogle Scholar
  25. Enders AC, King BF (1988) Formation and differentiation of extraembryonic mesoderm in the rhesus monkey. Am J Anat 181:327–340PubMedCrossRefGoogle Scholar
  26. Enders AC, Schlafke S (1981) Differentiation of the blastocyst of the rhesus monkey. Am J Anat 162:1–21PubMedCrossRefGoogle Scholar
  27. Enders AC, Schlafke S, Hendrickx AG (1986) Differentiation of the embryonic disc, amnion, and yolk sac in the rhesus monkey. Am J Anat 177:161–185PubMedCrossRefGoogle Scholar
  28. Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M, Reik W (2008) Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet 4:e1000116PubMedCrossRefGoogle Scholar
  29. Ferguson-Smith AC, Moore T, Detmar J, Lewis A, Hemberger M, Jammes H, Kelsey G, Roberts CT, Jones H, Constancia M (2006) Epigenetics and imprinting of the trophoblast—a workshop report. Placenta 27:S122–S126PubMedCrossRefGoogle Scholar
  30. Fleagle JG (1999) Primate adaptation and evolution, 2nd edn. Academic Press, San DiegoGoogle Scholar
  31. Frendo JL, Olivier D, Cheynet V, Blond JL, Bouton O, Vidaud M, Rabreau M, Evain-Brion D, Mallet F (2003) Direct involvement of HERV-W Env glycoprotein in human trophoblast cell fusion and differentiation. Mol Cell Biol 23:3566–3574PubMedCrossRefGoogle Scholar
  32. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514PubMedCrossRefGoogle Scholar
  33. Handwerger S (1995) Endothelins and the placenta. J Lab Clin Med 125:679–681PubMedGoogle Scholar
  34. Heiss C, Wong ML, Block VI, Lao D, Real WM, Yeghiazarians Y, Lee RJ, Springer ML (2008) Pleiotrophin induces nitric oxide dependent migration of endothelial progenitor cells. J Cell Physiol 215:366–373PubMedCrossRefGoogle Scholar
  35. Hemberger M (2007) Epigenetic landscape required for placental development. Cell Mol Life Sci 64:2422–2436PubMedCrossRefGoogle Scholar
  36. Jeng CJ, Chang CC, Tang CY (2005) Differential localization of rat Eag1 and Eag2K+ channels in hippocampal neurons. Neuroreport 16:229–233PubMedCrossRefGoogle Scholar
  37. Ju M, Wray D (2002) Molecular identification and characterisation of the human eag2 potassium channel. FEBS Lett 524:204–210PubMedCrossRefGoogle Scholar
  38. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002) The human genome browser at UCSC. Genome Res 12:996–1006PubMedGoogle Scholar
  39. King BF (1987) Ultrastructural differentiation of stromal and vascular components in early macaque placental villi. Am J Anat 178:30–44PubMedCrossRefGoogle Scholar
  40. Landry JR, Mager DL (2002) Widely spaced alternative promoters, conserved between human and rodent, control expression of the Opitz syndrome gene MID1. Genomics 80:499–508PubMedCrossRefGoogle Scholar
  41. Landry JR, Mager DL (2003) Functional analysis of the endogenous retroviral promoter of the human endothelin B receptor gene. J Virol 77:7459–7466PubMedCrossRefGoogle Scholar
  42. Luckett WP (1978) Origin and differentiation of the yolk sac and extraembryonic mesoderm in presomite human and rhesus monkey embryos. Am J Anat 152:59–97PubMedCrossRefGoogle Scholar
  43. Ludwig J, Weseloh R, Karschin C, Liu Q, Netzer R, Engeland B, Stansfeld C, Pongs O (2000) Cloning and functional expression of rat eag2, a new member of the ether-a-go-go family of potassium channels and comparison of its distribution with that of eag1. Mol Cell Neurosci 16:59–70PubMedCrossRefGoogle Scholar
  44. Magarinos MP, Sanchez-Margalet V, Kotler M, Calvo JC, Varone CL (2007) Leptin promotes cell proliferation and survival of trophoblastic cells. Biol Reprod 76:203–210PubMedCrossRefGoogle Scholar
  45. Mak W, Nesterova TB, de Napoles M, Appanah R, Yamanaka S, Otte AP, Brockdorff N (2004) Reactivation of the paternal X chromosome in early mouse embryos. Science 303:666–669PubMedCrossRefGoogle Scholar
  46. Matouskova M, Blazkova J, Pajer P, Pavlicek A, Hejnar J (2006) CpG methylation suppresses transcriptional activity of human syncytin-1 in non-placental tissues. Exp Cell Res 312:1011–1020PubMedCrossRefGoogle Scholar
  47. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T (2000) Demethylation of the zygotic paternal genome. Nature 403:501–502PubMedCrossRefGoogle Scholar
  48. Medstrand P, Landry JR, Mager DL (2001) Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J Biol Chem 276:1896–1903PubMedCrossRefGoogle Scholar
  49. Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, Mager DL (2005) Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 110:342–352PubMedCrossRefGoogle Scholar
  50. Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM (2000) Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403:785–789PubMedCrossRefGoogle Scholar
  51. Millar L, Streiner N, Webster L, Yamamoto S, Okabe R, Kawamata T, Shimoda J, Bullesbach E, Schwabe C, Bryant-Greenwood G (2005) Early placental insulin-like protein (INSL4 or EPIL) in placental and fetal membrane growth. Biol Reprod 73:695–702PubMedCrossRefGoogle Scholar
  52. Monk M, Harper MI (1979) Sequential X chromosome inactivation coupled with cellular differentiation in early mouse embryos. Nature 281:311–313PubMedCrossRefGoogle Scholar
  53. Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ (2011) Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6:34–44PubMedCrossRefGoogle Scholar
  54. Norwitz ER, Schust DJ, Fisher SJ (2001) Implantation and the survival of early pregnancy. N Engl J Med 345:1400–1408PubMedCrossRefGoogle Scholar
  55. Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E (2004) Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303:644–649PubMedCrossRefGoogle Scholar
  56. Pardo LA, del Camino D, Sanchez A, Alves F, Bruggemann A, Beckh S, Stuhmer W (1999) Oncogenic potential of EAG K(+) channels. EMBO J 18:5540–5547PubMedCrossRefGoogle Scholar
  57. Rahnama F, Shafiei F, Gluckman PD, Mitchell MD, Lobie PE (2006) Epigenetic regulation of human trophoblastic cell migration and invasion. Endocrinology 147:5275–5283PubMedCrossRefGoogle Scholar
  58. Rajendram R, Ferreira JC, Grafodatskaya D, Choufani S, Chiang T, Pu S, Butcher DT, Wodak SJ, Weksberg R (2011) Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms. Epigenetics 6:410–415PubMedCrossRefGoogle Scholar
  59. Rawn SM, Cross JC (2008) The evolution, regulation, and function of placenta-specific genes. Annu Rev Cell Dev Biol 24:159–181PubMedCrossRefGoogle Scholar
  60. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293:1089–1093PubMedCrossRefGoogle Scholar
  61. Reik W, Santos F, Mitsuya K, Morgan H, Dean W (2003) Epigenetic asymmetry in the mammalian zygote and early embryo: relationship to lineage commitment? Philos Trans R Soc Lond B Biol Sci 358:1403–1409PubMedCrossRefGoogle Scholar
  62. Reiss D, Zhang Y, Mager DL (2007) Widely variable endogenous retroviral methylation levels in human placenta. Nucleic Acids Res 35:4743–4754PubMedCrossRefGoogle Scholar
  63. Romanish MT, Nakamura H, Lai CB, Wang Y, Mager DL (2009) A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PLoS ONE 4:e5761PubMedCrossRefGoogle Scholar
  64. Rossant J (2007) Stem cells and lineage development in the mammalian blastocyst. Reprod Fertil Dev 19:111–118PubMedCrossRefGoogle Scholar
  65. Saganich MJ, Vega-Saenz de Miera E, Nadal MS, Baker H, Coetzee WA, Rudy B (1999) Cloning of components of a novel subthreshold-activating K(+) channel with a unique pattern of expression in the cerebral cortex. J Neurosci 19:10789–10802PubMedGoogle Scholar
  66. Santos F, Hendrich B, Reik W, Dean W (2002) Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol 241:172–182PubMedCrossRefGoogle Scholar
  67. Schulte AM, Lai S, Kurtz A, Czubayko F, Riegel AT, Wellstein A (1996) Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus. Proc Natl Acad Sci USA 93:14759–14764PubMedCrossRefGoogle Scholar
  68. Schweiger S, Foerster J, Lehmann T, Suckow V, Muller YA, Walter G, Davies T, Porter H, van Bokhoven H, Lunt PW, Traub P, Ropers HH (1999) The Opitz syndrome gene product, MID1, associates with microtubules. Proc Natl Acad Sci USA 96:2794–2799PubMedCrossRefGoogle Scholar
  69. Serman L, Vlahovic M, Sijan M, Bulic-Jakus F, Serman A, Sincic N, Matijevic R, Juric-Lekic G, Katusic A (2007) The impact of 5-azacytidine on placental weight, glycoprotein pattern and proliferating cell nuclear antigen expression in rat placenta. Placenta 28:803–811PubMedCrossRefGoogle Scholar
  70. Shearwin KE, Callen BP, Egan JB (2005) Transcriptional interference—a crash course. Trends Genet 21:339–345PubMedCrossRefGoogle Scholar
  71. Voisset C, Blancher A, Perron H, Mandrand B, Mallet F, Paranhos-Baccala G (1999) Phylogeny of a novel family of human endogenous retrovirus sequences, HERV-W, in humans and other primates. AIDS Res Hum Retroviruses 15:1529–1533PubMedCrossRefGoogle Scholar
  72. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335–340PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Erin C. Macaulay
    • 1
  • Robert J. Weeks
    • 2
  • Simon Andrews
    • 3
  • Ian M. Morison
    • 1
    Email author
  1. 1.Department of Pathology, Dunedin School of Medicine and National Research Centre for Growth and DevelopmentUniversity of OtagoDunedinNew Zealand
  2. 2.Department of Pathology, Dunedin School of MedicineUniversity of OtagoDunedinNew Zealand
  3. 3.Bioinformatics GroupThe Babraham InstituteCambridgeUK

Personalised recommendations