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Repeats as global DNA methylation marker in bovine preimplantation embryos

Wenwen Li (UGent) , Ann Van Soom (UGent) and Luc Peelman (UGent)
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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% O-2. 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.
Keywords
epigenetics, retrotransposon, bisulfite sequencing, CLONED EMBRYOS, LANDSCAPE, PATTERNS, ELEMENTS

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MLA
Li, Wenwen, Ann Van Soom, and Luc Peelman. “Repeats as Global DNA Methylation Marker in Bovine Preimplantation Embryos.” CZECH JOURNAL OF ANIMAL SCIENCE 62.2 (2017): 43–50. Print.
APA
Li, Wenwen, Van Soom, A., & Peelman, L. (2017). Repeats as global DNA methylation marker in bovine preimplantation embryos. CZECH JOURNAL OF ANIMAL SCIENCE, 62(2), 43–50.
Chicago author-date
Li, Wenwen, Ann Van Soom, and Luc Peelman. 2017. “Repeats as Global DNA Methylation Marker in Bovine Preimplantation Embryos.” Czech Journal of Animal Science 62 (2): 43–50.
Chicago author-date (all authors)
Li, Wenwen, Ann Van Soom, and Luc Peelman. 2017. “Repeats as Global DNA Methylation Marker in Bovine Preimplantation Embryos.” Czech Journal of Animal Science 62 (2): 43–50.
Vancouver
1.
Li W, Van Soom A, Peelman L. Repeats as global DNA methylation marker in bovine preimplantation embryos. CZECH JOURNAL OF ANIMAL SCIENCE. 2017;62(2):43–50.
IEEE
[1]
W. Li, A. Van Soom, and L. Peelman, “Repeats as global DNA methylation marker in bovine preimplantation embryos,” CZECH JOURNAL OF ANIMAL SCIENCE, vol. 62, no. 2, pp. 43–50, 2017.
@article{8517634,
  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% O-2. 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.},
  author       = {Li, Wenwen and Van Soom, Ann and Peelman, Luc},
  issn         = {1212-1819},
  journal      = {CZECH JOURNAL OF ANIMAL SCIENCE},
  keywords     = {epigenetics,retrotransposon,bisulfite sequencing,CLONED EMBRYOS,LANDSCAPE,PATTERNS,ELEMENTS},
  language     = {eng},
  number       = {2},
  pages        = {43--50},
  title        = {Repeats as global DNA methylation marker in bovine preimplantation embryos},
  url          = {http://dx.doi.org/10.17221/29/2016-cjas},
  volume       = {62},
  year         = {2017},
}

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