Advertisement

Epigenetic Features of Animal Biotechnologies

  • Nathalie Beaujean
Chapter

Abstract

Epigenetic mechanisms play a crucial role in many biological processes, such as regulation of gene expression especially after fertilization and during early embryonic development. Indeed, the parental genomes that carry special epigenetic signatures undergo important chromatin remodelling through epigenetic modifications during the first embryonic cleavages, some of which are crucial for the production of healthy embryos.

It is therefore very important for breeders and embryologists to understand how parentally inherited genomes may be epigenetically altered by animal biotechnologies as it could affect embryo quality and further development. This chapter introduces some of the basic epigenetic parameters underpinning early embryonic development and how they could be affected during the processes of embryo in vitro production, somatic cell nuclear transfer or stem cells derivation.

Keywords

DNA methylation Histone posttranslational modifications Reprogramming In vitro culture In vitro maturation 

References

  1. Adenot P, Mercier Y, Renard J, Thompson E (1997) Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos. Development 124:4615–4625PubMedGoogle Scholar
  2. Ahmed K, Dehghani H, Rugg-Gunn P et al (2010) Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo. PLoS One 5:e10531.  https://doi.org/10.1371/journal.pone.0010531 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Albert M, Peters AHFM (2009) Genetic and epigenetic control of early mouse development. Curr Opin Genet Dev 19:113–121.  https://doi.org/10.1016/j.gde.2009.03.004 CrossRefPubMedGoogle Scholar
  4. Amouroux R, Nashun B, Shirane K et al (2016) De novo DNA methylation drives 5hmC accumulation in mouse zygotes. Nat Cell Biol 18:225–233.  https://doi.org/10.1038/ncb3296 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Ancelin K, Syx L, Borensztein M, Ranisavljevic N, Vassilev I, Briseño-Roa L, Liu T, Metzger E, Servant N, Barillot E, Chen CJ, Schüle R, Heard E (2016) Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation. Elife 5:pii: e08851.  https://doi.org/10.7554/eLife.08851 CrossRefGoogle Scholar
  6. Anckaert E, Fair T (2015) DNA methylation reprogramming during oogenesis and interference by reproductive technologies: studies in mouse and bovine models. Reprod Fertil Dev 27:739.  https://doi.org/10.1071/RD14333 CrossRefPubMedGoogle Scholar
  7. Anckaert E, De Rycke M, Smitz J (2012) Culture of oocytes and risk of imprinting defects. Hum Reprod Update 0:1–15.  https://doi.org/10.1093/humupd/dms042 CrossRefGoogle Scholar
  8. Ao X, Sa R, Wang J et al (2016) Activation-induced cytidine deaminase selectively catalyzed active DNA demethylation in pluripotency gene and improved cell reprogramming in bovine SCNT embryo. Cytotechnology 68:2637–2648.  https://doi.org/10.1007/s10616-016-9988-8 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Auclair G, Weber M (2012) Mechanisms of DNA methylation and demethylation in mammals. Biochimie 94:2202–2211.  https://doi.org/10.1016/j.biochi.2012.05.016 CrossRefPubMedGoogle Scholar
  10. Azuara V, Perry P, Sauer S et al (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8:532–538.  https://doi.org/10.1038/ncb1403 CrossRefPubMedGoogle Scholar
  11. Beaujean N (2014) Histone post-translational modifications in preimplantation mouse embryos and their role in nuclear architecture. Mol Reprod Dev 81:100–112.  https://doi.org/10.1002/mrd.22268 CrossRefPubMedGoogle Scholar
  12. Beaujean N (2015) Epigenetics, embryo quality and developmental potential. Reprod Fertil Dev 27:53–62.  https://doi.org/10.1071/RD14309 CrossRefGoogle Scholar
  13. Beaujean N, Taylor J, Gardner J et al (2004) Effect of limited DNA methylation reprogramming in the normal sheep embryo on somatic cell nuclear transfer. Biol Reprod 71:185–193.  https://doi.org/10.1095/biolreprod.103.026559 CrossRefPubMedGoogle Scholar
  14. Bernstein BE, Mikkelsen TS et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315–326.  https://doi.org/10.1016/j.cell.2006.02.041 CrossRefPubMedGoogle Scholar
  15. Bogliotti YS, Ross PJ (2012) Mechanisms of histone 3 lysine 27 trimethylation remodeling during early mammalian development. Epigenetics 7:976–981CrossRefPubMedPubMedCentralGoogle Scholar
  16. Boissonnas CC, Jouannet P, Jammes H (2013) Epigenetic disorders and male subfertility. Fertil Steril 99:624–631.  https://doi.org/10.1016/j.fertnstert.2013.01.124 CrossRefPubMedGoogle Scholar
  17. Bonnet-Garnier A, Feuerstein P, Chebrout M et al (2012) Genome organization and epigenetic marks in mouse germinal vesicle oocytes. Int J Dev Biol 887:877–887.  https://doi.org/10.1387/ijdb.120149ab CrossRefGoogle Scholar
  18. Canovas S, Ivanova E, Romar R et al (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 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Cao Z, Hong R, Ding B, Zuo X, Li H, Ding J, Li Y, Huang W, Zhang Y (2017) TSA and BIX-01294 induced normal DNA and histone methylation and increased protein expression in porcine somatic cell nuclear transfer embryos. PLoS One 12(1):e0169092.  https://doi.org/10.1371/journal.pone.0169092 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Chao S, Li J, Jin X et al (2012) Epigenetic reprogramming of embryos derived from sperm frozen at −20°C. Sci China Life Sci 55:349–357.  https://doi.org/10.1007/s11427-012-4309-8 CrossRefPubMedGoogle Scholar
  21. Chen JJ, Liu H, Liu J et al (2013) H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 45:34–42.  https://doi.org/10.1038/ng.2491 CrossRefPubMedGoogle Scholar
  22. Chen H, Zhang L, Deng T et al (2016) Effects of oocyte vitrification on epigenetic status in early bovine embryos. Theriogenology 86:868–878.  https://doi.org/10.1016/j.theriogenology.2016.03.008 CrossRefPubMedGoogle Scholar
  23. Chung YG, Matoba S, Liu Y et al (2015) Histone demethylase expression enhances human somatic cell nuclear transfer efficiency and promotes derivation of pluripotent stem cells. Cell Stem Cell 17:758–766.  https://doi.org/10.1016/j.stem.2015.10.001 CrossRefPubMedGoogle Scholar
  24. Chung N, Bogliotti YS, Ding W, Vilarino M, Takahashi K, Chitwood JL, Schultz RM, Ross PJ (2017) Active H3K27me3 demethylation by KDM6B is required for normal development of bovine preimplantation embryos. Epigenetics 12(12):1048–1056.  https://doi.org/10.1080/15592294.2017 CrossRefPubMedGoogle Scholar
  25. Cyr AR, Domann FE (2011) The redox basis of epigenetic modifications: from mechanisms to functional consequences. Antioxid Redox Signal 15:551–589.  https://doi.org/10.1089/ars.2010.3492 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Denomme MM, Mann MRW (2012) Genomic imprints as a model for the analysis of epigenetic stability during assisted reproductive technologies. Reproduction 144:393–409.  https://doi.org/10.1530/REP-12-0237 CrossRefPubMedGoogle Scholar
  27. Ding B, Cao Z, Hong R, Li H, Zuo X, Luo L, Li Y, Huang W, Li W, Zhang K, Zhang Y (2017) WDR5 in porcine preimplantation embryos: expression, regulation of epigenetic modifications and requirement for early development. Biol Reprod 96(4):758–771.  https://doi.org/10.1093/biolre/iox020 CrossRefPubMedGoogle Scholar
  28. Doherty R, Farrelly CO, Meade KG (2014) Comparative epigenetics: relevance to the regulation of production and health traits in cattle. Anim Genet 45:3–14.  https://doi.org/10.1111/age.12140 CrossRefPubMedGoogle Scholar
  29. Dupont C, Cordier AG, Junien C et al (2012) Maternal environment and the reproductive function of the offspring. Theriogenology 78:1405–1414.  https://doi.org/10.1016/j.theriogenology.2012.06.016 CrossRefPubMedGoogle Scholar
  30. e Silva ARR, Bruno C, Fleurot R et al (2012) Alteration of DNA demethylation dynamics by in vitro culture conditions in rabbit pre-implantation embryos. Epigenetics 7:440–446.  https://doi.org/10.4161/epi.19563 CrossRefGoogle Scholar
  31. El Hajj N, Haaf T (2013) Epigenetic disturbances in in vitro cultured gametes and embryos: implications for human assisted reproduction. Fertil Steril 99:632–641.  https://doi.org/10.1016/j.fertnstert.2012.12.044 CrossRefPubMedGoogle Scholar
  32. Eymery A, Liu Z, Ozonov EA, Stadler MB, Peters AH (2016) The methyltransferase Setdb1 is essential for meiosis and mitosis in mouse oocytes and early embryos. Development 143(15):2767–2779.  https://doi.org/10.1242/dev.132746 CrossRefPubMedGoogle Scholar
  33. Fang L, Zhang J, Zhang H et al (2016) H3K4 methyltransferase set1a is a key Oct4 coactivator essential for generation of Oct4 positive inner cell mass. Stem Cells 34:565–580.  https://doi.org/10.1002/stem.2250 CrossRefPubMedGoogle Scholar
  34. Feeney A, Nilsson E, Skinner M (2014) Epigenetics and transgenerational inheritance in domesticated farm animals. J Anim Sci Biotechnol 5:48.  https://doi.org/10.1186/2049-1891-5-48 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Feil R, Fraga MF (2011) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13:97–109.  https://doi.org/10.1038/nrg3142 CrossRefGoogle Scholar
  36. Feldman N, Gerson A, Fang J et al (2006) G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat Cell Biol 8:188–194.  https://doi.org/10.1038/ncb1353 CrossRefPubMedGoogle Scholar
  37. Ficz G (2015) New insights into mechanisms that regulate DNA methylation patterning. J Exp Biol 218:14–20.  https://doi.org/10.1242/jeb.107961 CrossRefPubMedGoogle Scholar
  38. Fu Y, Xu JJ, Sun XL, Jiang H, Han DX, Liu C, Gao Y, Yuan B, Zhang JB (2017) Function of JARID2 in bovines during early embryonic development. PeerJ 5:e4189  https://doi.org/10.7717/peerj.4189 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Goolam M, Scialdone A, Graham SJL et al (2016) Heterogeneity in Oct4 and Sox2 targets biases cell fate in 4-cell mouse embryos. Cell 165:61–74.  https://doi.org/10.1016/j.cell.2016.01.047 CrossRefPubMedPubMedCentralGoogle Scholar
  40. Graham SJL, Zernicka-Goetz M (2016) The acquisition of cell fate in mouse development: how do cells first become heterogeneous? Curr Top Dev Biol 117:671–695.  https://doi.org/10.1016/bs.ctdb.2015.11.021 CrossRefPubMedGoogle Scholar
  41. Greally JM (2018) A user’s guide to the ambiguous word epigenetics. Nat Rev Mol Cell Biol 19(4):207–208.  https://doi.org/10.1038/nrm.2017.135 CrossRefPubMedGoogle Scholar
  42. Grewal SIS, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8:35–46.  https://doi.org/10.1038/nrg2008 CrossRefPubMedGoogle Scholar
  43. Gu T, Guo F, Yang H et al (2011) The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477:606–610.  https://doi.org/10.1038/nature10443 CrossRefPubMedGoogle Scholar
  44. Guo F, Li L, Li J et al (2017) Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Res 27:967–988.  https://doi.org/10.1038/cr.2017.82 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Gurdon JB, Wilmut I (2011) Nuclear transfer to eggs and oocytes. Cold Spring Harb Perspect Biol 3:1–14.  https://doi.org/10.1101/cshperspect.a002659 CrossRefGoogle Scholar
  46. Hai T, Hao J, Wang L et al (2011) Pluripotency maintenance in mouse somatic cell nuclear transfer embryos and its improvement by treatment with the histone deacetylase inhibitor TSA. Cell Reprogram 13:47–56.  https://doi.org/10.1089/cell.2010.0042 CrossRefPubMedGoogle Scholar
  47. Haines TR, Rodenhiser DI, Ainsworth PJ (2001) Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev Biol 240:585–598.  https://doi.org/10.1006/dbio.2001.0504 CrossRefPubMedGoogle Scholar
  48. Hasan S, Hottiger MO (2002) Histone acetyl transferases: a role in DNA repair and DNA replication. J Mol Med (Berl) 80:463–474.  https://doi.org/10.1007/s00109-002-0341-7 CrossRefGoogle Scholar
  49. Hawkins RD, Hon GC, Lee LK et al (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6:479–491.  https://doi.org/10.1016/j.stem.2010.03.018 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Hou L, Ma F, Yang J et al (2014) Effects of histone deacetylase inhibitor oxamflatin on in vitro porcine somatic cell nuclear transfer embryos. Cell Reprogram 16:253–265.  https://doi.org/10.1089/cell.2013.0058 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Huan Y, Zhu J, Huang B et al (2015a) Trichostatin a rescues the disrupted imprinting induced by somatic cell nuclear transfer in pigs. PLoS One 10:e0126607.  https://doi.org/10.1371/journal.pone.0126607 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Huan Y, Wu Z, Zhang J, Zhu J, Liu Z, Song X (2015b) Epigenetic modification agents improve gene-specific methylation reprogramming in porcine cloned embryos. PLoS One 10(6):e0129803.  https://doi.org/10.1371/journal.pone.0129803 CrossRefPubMedPubMedCentralGoogle Scholar
  53. Ito S, Alessio ACD, Taranova OV et al (2010) Role of Tet proteins in 5mC to 5hmC conversion , ES-cell self-renewal and inner cell mass specification. Nature 466:1129–1133.  https://doi.org/10.1038/nature09303 CrossRefPubMedPubMedCentralGoogle Scholar
  54. Jackson M, Krassowska A, Gilbert N et al (2004) Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells. Mol Cell Biol 24:8862–8871.  https://doi.org/10.1128/MCB.24.20.8862-8871.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  55. Jammes H, Junien C, Chavatte-Palmer P (2011) Epigenetic control of development and expression of quantitative traits. Reprod Fertil Dev 23:64–74.  https://doi.org/10.1071/RD10259 CrossRefPubMedGoogle Scholar
  56. Jin L, Guo Q, Zhu H-Y et al (2017) Quisinostat treatment improves histone acetylation and developmental competence of porcine somatic cell nuclear transfer embryos. Mol Reprod Dev 84:340–346.  https://doi.org/10.1002/mrd.22787 CrossRefPubMedGoogle Scholar
  57. Jost KL, Bertulat B, Cardoso MC (2012) Heterochromatin and gene positioning: inside, outside, any side? Chromosoma 121(6):555–563.  https://doi.org/10.1007/s00412-012-0389-2 CrossRefPubMedPubMedCentralGoogle Scholar
  58. Jullien J, Vodnala M, Pasque V et al (2017) Gene resistance to transcriptional reprogramming following nuclear transfer is directly mediated by multiple chromatin-repressive pathways. Mol Cell 65:873–884.e8.  https://doi.org/10.1016/j.molcel.2017.01.030 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Kallingappa PK, Turner PM, Eichenlaub MP et al (2016) Quiescence loosens epigenetic constraints in bovine somatic cells and improves their reprogramming into totipotency. Biol Reprod 95:16–16.  https://doi.org/10.1095/biolreprod.115.137109 CrossRefPubMedGoogle Scholar
  60. Kang YK, Koo DB, Park JS et al (2001) Aberrant methylation of donor genome in cloned bovine embryos. Nat Genet 28:173–177.  https://doi.org/10.1038/88903 CrossRefPubMedGoogle Scholar
  61. Kim K, Doi A, Wen B et al (2010) Epigenetic memory in induced pluripotent stem cells. Nature 467:285–292.  https://doi.org/10.1038/nature09342 CrossRefPubMedPubMedCentralGoogle Scholar
  62. Kim J, Zhao H, Dan J, Kim S, Hardikar S, Hollowell D, Lin K, Lu Y, Takata Y, Shen J, Chen T (2016) Maternal Setdb1 is required for meiotic progression and preimplantation development in mouse. PLoS Genet 12(4):e1005970.  https://doi.org/10.1371/journal.pgen.1005970 CrossRefPubMedPubMedCentralGoogle Scholar
  63. Koike T, Wakai T, Jincho Y et al (2016) DNA methylation errors in cloned mouse sperm by germ line barrier evasion. Biol Reprod 94:128.  https://doi.org/10.1095/biolreprod.116.138677 CrossRefPubMedGoogle Scholar
  64. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705.  https://doi.org/10.1016/j.cell.2007.02.005 CrossRefPubMedPubMedCentralGoogle Scholar
  65. Krejcí J, Uhlírová R, Galiová G et al (2009) Genome-wide reduction in H3K9 acetylation during human embryonic stem cell differentiation. J Cell Physiol 219:677–687.  https://doi.org/10.1002/jcp.21714 CrossRefPubMedGoogle Scholar
  66. Kretsovali A, Hadjimichael C, Charmpilas N (2012) Histone deacetylase inhibitors in cell pluripotency, differentiation, and reprogramming. Stem Cells Int 2012:184154.  https://doi.org/10.1155/2012/184154 CrossRefPubMedPubMedCentralGoogle Scholar
  67. Kropp J, Carrillo JA, Namous H et al (2017) Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC Genomics 18:280.  https://doi.org/10.1186/s12864-017-3673-y CrossRefPubMedPubMedCentralGoogle Scholar
  68. Laurentino S, Borgmann J, Gromoll J (2016) On the origin of sperm epigenetic heterogeneity. Reproduction 151:R71–R78.  https://doi.org/10.1530/REP-15-0436 CrossRefPubMedGoogle Scholar
  69. Li CH, Gao Y, Wang S, Xu FF, Dai LS, Jiang H, Yu XF, Chen CZ, Yuan B, Zhang JB (2015) Expression pattern of JMJD1C in oocytes and its impact on early embryonic development. Genet Mol Res 14(4):18249–18258.  https://doi.org/10.4238/2015.December.23.12 CrossRefPubMedGoogle Scholar
  70. Liao H-F, Mo C-F, Wu S-C et al (2015) Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency. Reproduction 150:245–256.  https://doi.org/10.1530/REP-15-0031 CrossRefPubMedGoogle Scholar
  71. Liu H, Kim J-MM, Aoki F (2004) Regulation of histone H3 lysine 9 methylation in oocytes and early pre-implantation embryos. Development 131:2269–2280.  https://doi.org/10.1242/dev.01116 CrossRefPubMedGoogle Scholar
  72. Liu Z, Cai Y, Wang Y et al (2018) Cloning of macaque monkeys by somatic cell nuclear transfer. Cell 172:881–887.e7.  https://doi.org/10.1016/j.cell.2018.01.020 CrossRefPubMedGoogle Scholar
  73. Lucas ES, Watkins AJ (2017) The long-term effects of the periconceptional period on embryo epigenetic profile and phenotype; the paternal role and his contribution, and how males can affect offspring’s phenotype/epigenetic profile. In: Advances in experimental medicine and biology. Springer, Cham, pp 137–154Google Scholar
  74. Ma X, Kong L, Zhu S (2017) Reprogramming cell fates by small molecules. Protein Cell 8:328–348.  https://doi.org/10.1007/s13238-016-0362-6 CrossRefPubMedPubMedCentralGoogle Scholar
  75. Maalouf WE, Liu Z, Brochard V et al (2009) Trichostatin a treatment of cloned mouse embryos improves constitutive heterochromatin remodeling as well as developmental potential to term. BMC Dev Biol 9:11.  https://doi.org/10.1186/1471-213X-9-11 CrossRefPubMedPubMedCentralGoogle Scholar
  76. Mahapatra PS, Singh R, Kumar K et al (2015) Valproic acid assisted reprogramming of fibroblasts for generation of pluripotent stem cellsin buffalo (Bubalus bubalis). Int J Dev Biol 61(1-2):81–88.  https://doi.org/10.1387/ijdb.160006sb CrossRefGoogle Scholar
  77. Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11:285–296.  https://doi.org/10.1038/nrg2752 CrossRefPubMedPubMedCentralGoogle Scholar
  78. Matoba S, Liu Y, Lu F et al (2014) Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation. Cell 159(4):884–895.  https://doi.org/10.1016/j.cell.2014.09.055 CrossRefPubMedPubMedCentralGoogle Scholar
  79. Mattout A, Biran A, Meshorer E (2011) Global epigenetic changes during somatic cell reprogramming to iPS cells. J Mol Cell Biol 3:341–350.  https://doi.org/10.1093/jmcb/mjr028 CrossRefPubMedGoogle Scholar
  80. Mayer W, Niveleau A, Walter J et al (2000) Demethylation of the zygotic paternal genome. Nature 403:501–502.  https://doi.org/10.1038/35000654 CrossRefPubMedGoogle Scholar
  81. Meshorer E, Misteli T (2006) Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol 7:540–546.  https://doi.org/10.1038/nrm1938 CrossRefPubMedGoogle Scholar
  82. Mikkelsen TTS, Hanna J, Zhang X et al (2008) Dissecting direct reprogramming through integrative genomic analysis. Nature 454:49–55.  https://doi.org/10.1038/nature07056.Dissecting CrossRefPubMedPubMedCentralGoogle Scholar
  83. Narlikar GJ, Fan H-Y, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487CrossRefPubMedGoogle Scholar
  84. Niemann H (2016) Epigenetic reprogramming in mammalian species after somatic cell nuclear transfer based cloning. Theriogenology 86(1):80–90.  https://doi.org/10.1016/j.theriogenology.2016.04.021 CrossRefPubMedGoogle Scholar
  85. Nowak-Imialek M, Niemann H (2012) Pluripotent cells in farm animals: state of the art and future perspectives. Reprod Fertil Dev 25:103–128.  https://doi.org/10.1071/RD12265 CrossRefPubMedGoogle Scholar
  86. Ogorevc J, Orehek S, Dovč P (2016) Cellular reprogramming in farm animals: an overview of iPSC generation in the mammalian farm animal species. J Anim Sci Biotechnol 7:10.  https://doi.org/10.1186/s40104-016-0070-3 CrossRefPubMedPubMedCentralGoogle Scholar
  87. Ogura A, Inoue K, Wakayama T (2013) Recent advancements in cloning by somatic cell nuclear transfer. Philos Trans R Soc Lond Ser B Biol Sci 368:20110329.  https://doi.org/10.1098/rstb.2011.0329 CrossRefGoogle Scholar
  88. Okamoto Y, Yoshida N, Suzuki T et al (2016) DNA methylation dynamics in mouse preimplantation embryos revealed by mass spectrometry. Sci Rep 6:1–9.  https://doi.org/10.1038/srep19134 CrossRefGoogle Scholar
  89. Ono T, Li C, Mizutani E et al (2010) Inhibition of class IIb histone deacetylase significantly improves cloning efficiency in mice. Biol Reprod 83:929–937.  https://doi.org/10.1095/biolreprod.110.085282 CrossRefPubMedGoogle Scholar
  90. Opiela J, Samiec M, Romanek J (2017) In vitro development and cytological quality of inter-species (porcine→bovine) cloned embryos are affected by trichostatin A-dependent epigenomic modulation of adult mesenchymal stem cells. Theriogenology 97:27–33.  https://doi.org/10.1016/J.THERIOGENOLOGY.2017.04.022 CrossRefPubMedGoogle Scholar
  91. Pan G, Tian S, Nie J et al (2007) Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1:299–312.  https://doi.org/10.1016/j.stem.2007.08.003 CrossRefPubMedGoogle Scholar
  92. Parfitt D (2010) Epigenetic modification affecting expression of cell polarity and cell fate genes to regulate lineage specification in the early mouse embryo. Mol Biol Cell 21:2649–2660.  https://doi.org/10.1091/mbc.E10 CrossRefPubMedPubMedCentralGoogle Scholar
  93. Piedrahita J, Olby N (2010) Perspectives on transgenic livestock in agriculture and biomedicine: an update. Reprod Fertil Dev 23(1):56–63CrossRefGoogle Scholar
  94. Plath K, Fang J, Mlynarczyk-Evans SK et al (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135.  https://doi.org/10.1126/science.1084274 CrossRefPubMedGoogle Scholar
  95. Ramsahoye BH, Biniszkiewicz D, Lyko F et al (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci U S A 97:5237–5242.  https://doi.org/10.1073/PNAS.97.10.5237 CrossRefPubMedPubMedCentralGoogle Scholar
  96. Reik W, Walter J (2001) Genomic imprinting: parental influence on the genome. Nat Rev Genet 2:21–32.  https://doi.org/10.1038/35047554 CrossRefPubMedGoogle Scholar
  97. Rollo C, Li Y, Jin XL, O’Neill C (2017) Histone 3 lysine 9 acetylation is a biomarker of the effects of culture on zygotes. Reproduction 154:375–385.  https://doi.org/10.1530/REP-17-0112 CrossRefPubMedPubMedCentralGoogle Scholar
  98. Rossant J (2008) Stem cells and early lineage development. Cell 132:527–531.  https://doi.org/10.1016/j.cell.2008.01.039 CrossRefPubMedGoogle Scholar
  99. Ruzov A, Tsenkina Y, Serio A, Dudnakova T (2011) Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell Res 21:1332–1342.  https://doi.org/10.1038/cr.2011.113 CrossRefPubMedPubMedCentralGoogle Scholar
  100. Saha B, Home P, Ray S et al (2013) EED and KDM6B coordinate the first mammalian cell lineage commitment to ensure embryo implantation. Mol Cell Biol 33:2691–2705.  https://doi.org/10.1128/MCB.00069-13 CrossRefPubMedPubMedCentralGoogle Scholar
  101. Saksouk N, Simboeck E, Déjardin J (2015) Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin 8:3.  https://doi.org/10.1186/1756-8935-8-3 CrossRefPubMedPubMedCentralGoogle Scholar
  102. Salvaing J, Aguirre-Lavin T, Boulesteix C et al (2012) 5-Methylcytosine and 5-hydroxymethylcytosine spatiotemporal profiles in the mouse zygote. PLoS One 7:e38156.  https://doi.org/10.1371/journal.pone.0038156 CrossRefPubMedPubMedCentralGoogle Scholar
  103. Salvaing J, Peynot N, Bedhane MNN et al (2016) Assessment of “one-step” versus “sequential” embryo culture conditions through embryonic genome methylation and hydroxymethylation changes. Hum Reprod 31:2471–2483.  https://doi.org/10.1093/humrep/dew214 CrossRefPubMedPubMedCentralGoogle Scholar
  104. Sankar A, Kooistra SM, Gonzalez JM, Ohlsson C, Poutanen M, Helin K (2017) Maternal expression of the histone demethylase Kdm4a is crucial for pre-implantation development. Development 144(18):3264–3277.  https://doi.org/10.1242/dev.155473 CrossRefPubMedGoogle Scholar
  105. Savatier P, Osteil P, Tam PPL (2017) Pluripotency of embryo-derived stem cells from rodents, lagomorphs, and primates: slippery slope, terrace and cliff. Stem Cell Res 19:104–112.  https://doi.org/10.1016/j.scr.2017.01.008 CrossRefPubMedGoogle Scholar
  106. Schneider R, Grosschedl R (2007) Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21:3027–3043.  https://doi.org/10.1101/gad.1604607 CrossRefPubMedGoogle Scholar
  107. Sepulveda-Rincon LP, del Llano Solanas E, Serrano-revuelta E et al (2016) Early epigenetic reprogramming in fertilized, cloned, and parthenogenetic embryos. Theriogenology 86:91–98.  https://doi.org/10.1016/j.theriogenology.2016.04.022 CrossRefPubMedGoogle Scholar
  108. Shi W, Haaf T (2002) Aberrant methylation patterns at the two-cell stage as an indicator of early developmental failure. Mol Reprod Dev 63:329–334.  https://doi.org/10.1002/mrd.90016 CrossRefPubMedGoogle Scholar
  109. Shi Y, Desponts C, Do JT et al (2008) Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell 3:568–574.  https://doi.org/10.1016/j.stem.2008.10.004 CrossRefPubMedGoogle Scholar
  110. Shirazi A, Naderi MM, Hassanpour H et al (2016) The effect of ovine oocyte vitrification on expression of subset of genes involved in epigenetic modifications during oocyte maturation and early embryo development. Theriogenology 86:2136–2146.  https://doi.org/10.1016/j.theriogenology.2016.07.005 CrossRefPubMedGoogle Scholar
  111. Simonsson S, Gurdon J (2004) Dna demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat Cell Biol 6:984–990CrossRefPubMedGoogle Scholar
  112. Smallwood SA, Tomizawa S, Krueger F et al (2011) Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 43:811–814.  https://doi.org/10.1038/ng.864 CrossRefPubMedPubMedCentralGoogle Scholar
  113. Song X, Liu Z, He H et al (2017) Dnmt1s in donor cells is a barrier to SCNT-mediated DNA methylation reprogramming in pigs. Oncotarget 8:34980–34991.  https://doi.org/10.18632/oncotarget.16507 CrossRefPubMedPubMedCentralGoogle Scholar
  114. Sun JM, Cui KQ, Li ZP et al (2017) Suberoylanilide hydroxamic acid, a novel histone deacetylase inhibitor, improves the development and acetylation level of miniature porcine handmade cloning embryos. Reprod Domest Anim 52:763–774.  https://doi.org/10.1111/rda.12977 CrossRefPubMedGoogle Scholar
  115. Suo L, Meng Q, Pei Y et al (2010) Effect of cryopreservation on acetylation patterns of lysine 12 of histone H4 (acH4K12) in mouse oocytes and zygotes. J Assist Reprod Genet 27:735–741.  https://doi.org/10.1007/s10815-010-9469-5 CrossRefPubMedPubMedCentralGoogle Scholar
  116. Szablowska-Gadomska I, Sypecka J, Zayat V et al (2012) Treatment with small molecules is an important milestone towards the induction of pluripotency in neural stem cells derived from human cord blood. Acta Neurobiol Exp (Wars) 72:337–350Google Scholar
  117. Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935.  https://doi.org/10.1126/science.1170116 CrossRefPubMedPubMedCentralGoogle Scholar
  118. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676CrossRefGoogle Scholar
  119. Tan M, Luo H, Lee S et al (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028.  https://doi.org/10.1016/j.cell.2011.08.008 CrossRefPubMedPubMedCentralGoogle Scholar
  120. Tao J, Zhang Y, Zuo X et al (2017) DOT1L inhibitor improves early development of porcine somatic cell nuclear transfer embryos. PLoS One 12(6):e0179436.  https://doi.org/10.1371/journal.pone.0179436 CrossRefPubMedPubMedCentralGoogle Scholar
  121. Tapponnier Y, Afanassieff M, Aksoy I et al (2017) Reprogramming of rabbit induced pluripotent stem cells toward epiblast and chimeric competency using Krüppel-like factors. Stem Cell Res 24:106–117.  https://doi.org/10.1016/j.scr.2017.09.001 CrossRefPubMedGoogle Scholar
  122. Torres-padilla ME, Parfitt DE, Kouzarides T, Zernicka-goetz M (2007) Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature 445:214–218CrossRefPubMedPubMedCentralGoogle Scholar
  123. Turner BM, Group GE (2002) Cellular memory and the histone code. Cell 111:285–291CrossRefPubMedGoogle Scholar
  124. Urrego R, Rodriguez-Osorio N, Niemann H (2014) Epigenetic disorders and altered gene expression after use of assisted reproductive technologies in domestic cattle. Epigenetics 9:803–815CrossRefPubMedPubMedCentralGoogle Scholar
  125. Van Soom A, Peelman L, Holt W, Fazeli A (2014) An introduction to epigenetics as the link between genotype and environment: a personal view. Reprod Domest Anim 49:2–10CrossRefPubMedGoogle Scholar
  126. Wang N, Le F, Zhan Q et al (2010) Effects of in vitro maturation on histone acetylation in metaphase II oocytes and early cleavage embryos. Obstet Gynecol Int 2010:989278.  https://doi.org/10.1155/2010/989278 CrossRefPubMedPubMedCentralGoogle Scholar
  127. Wee G, Koo D-B, Song B-S et al (2006) Inheritable histone H4 acetylation of somatic chromatins in cloned embryos. J Biol Chem 281:6048–6057.  https://doi.org/10.1074/jbc.M511340200 CrossRefPubMedGoogle Scholar
  128. Wei J, Antony J, Meng F et al (2017) KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency. Sci Rep 7:1–14.  https://doi.org/10.1038/s41598-017-06569-2 CrossRefGoogle Scholar
  129. White MD, Angiolini JF, Alvarez YD et al (2016) Long-lived binding of Sox2 to DNA predicts cell fate in the four-cell mouse embryo. Cell 165:75–87.  https://doi.org/10.1016/j.cell.2016.02.032 CrossRefPubMedGoogle Scholar
  130. Wilmut I, Schnieke AE, McWhir J et al (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385:810–813.  https://doi.org/10.1038/385810a0 CrossRefPubMedGoogle Scholar
  131. Woodcock CL, Ghosh RP (2010) Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol 2:a000596CrossRefPubMedPubMedCentralGoogle Scholar
  132. Wu J, Belmonte JCI (2016) The molecular harbingers of early mammalian embryo patterning. Cell 165:13–15.  https://doi.org/10.1016/j.cell.2016.03.005 CrossRefPubMedGoogle Scholar
  133. Wu F-R, Liu Y, Shang M-B et al (2012) Differences in H3K4 trimethylation in in vivo and in vitro fertilization mouse preimplantation embryos. Genet Mol Res 11:1099–1108.  https://doi.org/10.4238/2012.April.27.9 CrossRefPubMedGoogle Scholar
  134. Xu W, Li Z, Yu B et al (2013) Effects of DNMT1 and HDAC inhibitors on gene-specific methylation reprogramming during porcine somatic cell nuclear transfer. PLoS One 8:e64705.  https://doi.org/10.1371/journal.pone.0064705 CrossRefPubMedPubMedCentralGoogle Scholar
  135. Young LE, Fernandes K, McEvoy TG et al (2001) Epigenetic change in IGF2R is associated with fetal overgrowth after sheep embryo culture. Nat Genet 27:153–154.  https://doi.org/10.1038/84769 CrossRefPubMedGoogle Scholar
  136. Zhang M, Wang F, Kou Z et al (2009) Defective chromatin structure in somatic cell cloned mouse embryos. J Biol Chem 284:24981–24987.  https://doi.org/10.1074/jbc.M109.011973 CrossRefPubMedPubMedCentralGoogle Scholar
  137. Zink D, Martin C, Brochard V et al (2006) Architectural reorganization of the nuclei upon transfer into oocytes accompanies genome reprogramming. Mol Reprod Dev 73:1102–1111.  https://doi.org/10.1002/mrd.20506 CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Univ. Lyon, Université Claude Bernard Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute U1208, USC1361BronFrance

Personalised recommendations