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Repeats as global DNA methylation marker in bovine preimplantation embryos

Author

Listed:
  • Wenwen Li

    (Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium)

  • Ann Van Soom

    (Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium)

  • Luc Peelman

    (Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium)

Abstract

DNA methylation undergoes dynamic changes and is a crucial part of the epigenetic regulation during mammalian early development. To determine the DNA methylation levels in bovine embryos, we applied a bisulfite sequencing based method aimed at repetitive sequences including three retrotransposons (L1_BT, BovB, and ERV1-1-I_BT) and Satellite I. A more accurate estimate of the global DNA methylation level compared to previous methods using only one repeat sequence, like Alu, could be made by calculation of the weighted arithmetic mean of multiple repetitive sequences, considering the copy number of each repetitive sequence. Satellite I and L1_BT showed significant methylation reduction at the blastocyst stage, while BovB and ERV1-1-I_BT showed no difference. The mean methylation level of the repetitive sequences during preimplantation development was the lowest at the blastocyst stage. No methylation difference was found between embryos cultured in 5% and 20% O2. Because mutations of CpGs negatively influence the calculation accuracy, we checked the mutation rate of the sequenced CpG sites. Satellite I and L1_BT showed a relatively low mutation rate (1.92 and 3.72% respectively) while that of ERV1-1-I_BT and BovB was higher (11.95 and 24% respectively). Therefore we suggest using a combination of repeats with low mutation rate, taking into account the proportion of each sequence, as a relatively quick marker for the global DNA methylation status of preimplantation stages and possibly also for other cell types.

Suggested Citation

  • Wenwen Li & Ann Van Soom & Luc Peelman, 2017. "Repeats as global DNA methylation marker in bovine preimplantation embryos," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 62(2), pages 43-50.
    • Handle: RePEc:caa:jnlcjs:v:62:y:2017:i:2:id:29-2016-cjas
    DOI: 10.17221/29/2016-CJAS
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    References listed on IDEAS

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    1. Hongshan Guo & Ping Zhu & Liying Yan & Rong Li & Boqiang Hu & Ying Lian & Jie Yan & Xiulian Ren & Shengli Lin & Junsheng Li & Xiaohu Jin & Xiaodan Shi & Ping Liu & Xiaoye Wang & Wei Wang & Yuan Wei & , 2014. "The DNA methylation landscape of human early embryos," Nature, Nature, vol. 511(7511), pages 606-610, July.
    2. Zachary D. Smith & Michelle M. Chan & Tarjei S. Mikkelsen & Hongcang Gu & Andreas Gnirke & Aviv Regev & Alexander Meissner, 2012. "A unique regulatory phase of DNA methylation in the early mammalian embryo," Nature, Nature, vol. 484(7394), pages 339-344, April.
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