Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

  1. David Monk1,16,17
  1. 1Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain;
  2. 2Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan;
  3. 3Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, 08950 Barcelona, Spain;
  4. 4Department of Systems Biomedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan;
  5. 5Fundación IVI-Instituto Universitario IVI-Universidad de Valencia, INCLIVA, 46980 Paterna, Valencia, Spain;
  6. 6Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, United Kingdom;
  7. 7Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
  8. 8Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain;
  9. 9Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan;
  10. 10Instituto de Genética Médica y Molecular, CIBERER, IDIPAZ-Hospital Universitario La Paz, Universidad Autónoma de Madrid, 28046 Madrid, Spain;
  11. 11Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan;
  12. 12Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain;
  13. 13Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain;
  14. 14Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan

    Abstract

    Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole-genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta. This extra-embryonic tissue often adopts a different methylation profile compared to somatic tissues. Further, we profiled all imprinted DMRs in sperm and embryonic stem cells derived from parthenogenetically activated oocytes, individual blastomeres, and blastocysts, in order to identify primary DMRs and reveal the extent of reprogramming during preimplantation development. Intriguingly, we find that in contrast to ubiquitous imprints, the majority of placenta-specific imprinted DMRs are unmethylated in sperm and all human embryonic stem cells. Therefore, placental-specific imprinting provides evidence for an inheritable epigenetic state that is independent of DNA methylation and the existence of a novel imprinting mechanism at these loci.

    Footnotes

    • 15 These authors contributed equally to this work.

    • 16 These authors jointly directed this work.

    • 17 Corresponding authors

      E-mail nakabaya-k{at}ncchd.go.jp

      E-mail dmonk{at}idibell.cat

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.164913.113.

    • Received August 9, 2013.
    • Accepted December 26, 2013.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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