DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

Abstract

The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in terms of cell number and hatching ability to. RNA-Seq and DNA methylation analyses showed that Natur-IVF embryos have expression and methylation patterns closer to in vivo blastocysts. Genes involved in reprogramming, imprinting and development were affected by culture, with fewer aberrations in Natur-IVF embryos. Methylation analysis detected methylated changes in C-IVF, but not in Natur-IVF, at genes whose methylation could be critical, such as IGF2R and NNAT.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Sebastian Canovas

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Elena Ivanova

    Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Raquel Romar

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Soledad García-Martínez

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. Cristina Soriano-Úbeda

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    Competing interests
    The authors declare that no competing interests exist.
  6. Francisco Alberto A García-Vázquez

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. Heba Saadeh

    Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Simon Andrews

    Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Gavin Kelsey

    Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9762-5634
  10. Pilar Coy

    Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
    For correspondence
    pcoy@um.es
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3943-1890

Funding

Research Councils UK

  • Gavin Kelsey

Ministerio de Economía y Competitividad (AGL2012-40180-C03-01 and AGL2015-66341-R)

  • Pilar Coy

Ministerio de Educación, Cultura y Deporte (PRX14/00348)

  • Pilar Coy

Fundación Séneca. Región de Murcia. Spain (20040/GERM/16)

  • Pilar Coy

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was carried out in strict accordance with the recommendations in the Guiding Principles for the Care and Use of Animals (DHEW Publication, NIH, 80-23). The protocol was approved by the Ethical Committee for Experimentation with Animals of the University of Murcia, Spain (Project Code: 192/2015).

Reviewing Editor

  1. Jessica K Tyler, Weill Cornell Medicine, United States

Publication history

  1. Received: November 26, 2016
  2. Accepted: January 28, 2017
  3. Accepted Manuscript published: January 30, 2017 (version 1)
  4. Accepted Manuscript updated: February 1, 2017 (version 2)
  5. Version of Record published: March 7, 2017 (version 3)
  6. Version of Record updated: April 11, 2017 (version 4)

Copyright

© 2017, Canovas et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Sebastian Canovas
  2. Elena Ivanova
  3. Raquel Romar
  4. Soledad García-Martínez
  5. Cristina Soriano-Úbeda
  6. Francisco Alberto A García-Vázquez
  7. Heba Saadeh
  8. Simon Andrews
  9. Gavin Kelsey
  10. Pilar Coy
(2017)
DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids
eLife 6:e23670.
https://doi.org/10.7554/eLife.23670
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