Consequences of assisted reproductive techniques on the embryonic epigenome in cattle

References

Abe, H., Yamashita, S., Itoh, T., Satoh, T., and Hoshi, H. (1999). Ultrastructure of bovine embryos developed from in vitro-matured and -fertilized oocytes: comparative morphological evaluation of embryos cultured either in serum-free medium or in serum-supplemented medium. Mol. Reprod. Dev. 53, 325–335.
| Ultrastructure of bovine embryos developed from in vitro-matured and -fertilized oocytes: comparative morphological evaluation of embryos cultured either in serum-free medium or in serum-supplemented medium.Crossref | GoogleScholarGoogle Scholar | 10369393PubMed |

Adenot, P. G., Szollosi, M. S., Geze, M., Renard, J. P., and Debey, P. (1991). Dynamics of paternal chromatin changes in live one-cell mouse embryo after natural fertilization. Mol. Reprod. Dev. 28, 23–34.
| Dynamics of paternal chromatin changes in live one-cell mouse embryo after natural fertilization.Crossref | GoogleScholarGoogle Scholar | 1994977PubMed |

Allen, B. L., and Taatjes, D. J. (2015). The Mediator complex: a central integrator of transcription. Nat. Rev. Mol. Cell Biol. 16, 155–166.
| The Mediator complex: a central integrator of transcription.Crossref | GoogleScholarGoogle Scholar | 25693131PubMed |

Almamun, M. (2011). Size-dependent acquisition of global DNA methylation in oocytes is altered by hormonal stimulation. M.S. Thesis, University of Missouri. Available at https://mospace.umsystem.edu/xmlui/handle/10355/14952 [verified 10 October 2019].

Almamun, M., Levinson, B. T., Gater, S. T., Schnabel, R. D., Arthur, G. L., Davis, J. W., and Taylor, K. H. (2014). Genome-wide DNA methylation analysis in precursor B-cells. Epigenetics 9, 1588–1595.
| Genome-wide DNA methylation analysis in precursor B-cells.Crossref | GoogleScholarGoogle Scholar | 25484143PubMed |

Bakhtari, A., and Ross, P. J. (2014). DPPA3 prevents cytosine hydroxymethylation of the maternal pronucleus and is required for normal development in bovine embryos. Epigenetics 9, 1271–1279.
| DPPA3 prevents cytosine hydroxymethylation of the maternal pronucleus and is required for normal development in bovine embryos.Crossref | GoogleScholarGoogle Scholar | 25147917PubMed |

Balhorn, R., Corzett, M., and Mazrimas, J. A. (1992). Formation of intraprotamine disulfides in vitro. Arch. Biochem. Biophys. 296, 384–393.
| Formation of intraprotamine disulfides in vitro.Crossref | GoogleScholarGoogle Scholar | 1632631PubMed |

Bantignies, F., and Cavalli, G. (2011). Polycomb group proteins: repression in 3D. Trends Genet. 27, 454–464.
| Polycomb group proteins: repression in 3D.Crossref | GoogleScholarGoogle Scholar | 21794944PubMed |

Barlow, D. P., Stoger, R., Herrmann, B. G., Saito, K., and Schweifer, N. (1991). The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 349, 84–87.
| The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus.Crossref | GoogleScholarGoogle Scholar | 1845916PubMed |

Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233.
| MicroRNAs: target recognition and regulatory functions.Crossref | GoogleScholarGoogle Scholar | 19167326PubMed |

Bartolomei, M. S., and Ferguson-Smith, A. C. (2011). Mammalian genomic imprinting. Cold Spring Harb. Perspect. Biol. 3, a002592.
| Mammalian genomic imprinting.Crossref | GoogleScholarGoogle Scholar | 21576252PubMed |

Bartolomei, M. S., Zemel, S., and Tilghman, S. M. (1991). Parental imprinting of the mouse H19 gene. Nature 351, 153–155.
| Parental imprinting of the mouse H19 gene.Crossref | GoogleScholarGoogle Scholar | 1709450PubMed |

Beatty, L., Weksberg, R., and Sadowski, P. D. (2006). Detailed analysis of the methylation patterns of the KvDMR1 imprinting control region of human chromosome 11. Genomics 87, 46–56.
| Detailed analysis of the methylation patterns of the KvDMR1 imprinting control region of human chromosome 11.Crossref | GoogleScholarGoogle Scholar | 16321503PubMed |

Beaumont, H. M., and Smith, A. F. (1975). Embryonic mortality during the pre- and post-implantation periods of pregnancy in mature mice after superovulation. J. Reprod. Fertil. 45, 437–448.
| Embryonic mortality during the pre- and post-implantation periods of pregnancy in mature mice after superovulation.Crossref | GoogleScholarGoogle Scholar | 1206643PubMed |

Bedford, D. C., and Brindle, P. K. (2012). Is histone acetylation the most important physiological function for CBP and p300? Aging (Albany NY) 4, 247–255.
| Is histone acetylation the most important physiological function for CBP and p300?Crossref | GoogleScholarGoogle Scholar | 22511639PubMed |

Behboodi, E., Anderson, G. B., BonDurant, R. H., Cargill, S. L., Kreuscher, B. R., Medrano, J. F., and Murray, J. D. (1995). Birth of large calves that developed from in vitro-derived bovine embryos. Theriogenology 44, 227–232.
| Birth of large calves that developed from in vitro-derived bovine embryos.Crossref | GoogleScholarGoogle Scholar | 16727722PubMed |

Bermejo-Alvarez, P., Rizos, D., Lonergan, P., and Gutierrez-Adan, A. (2011). Transcriptional sexual dimorphism during preimplantation embryo development and its consequences for developmental competence and adult health and disease. Reproduction 141, 563–570.
| Transcriptional sexual dimorphism during preimplantation embryo development and its consequences for developmental competence and adult health and disease.Crossref | GoogleScholarGoogle Scholar | 21339284PubMed |

Bernal-Ulloa, S. M., Heinzmann, J., Herrmann, D., Hadeler, K. G., Aldag, P., Winkler, S., Pache, D., Baulain, U., Lucas-Hahn, A., and Niemann, H. (2016). Cyclic AMP affects oocyte maturation and embryo development in prepubertal and adult cattle. PLoS One 11, e0150264.
| Cyclic AMP affects oocyte maturation and embryo development in prepubertal and adult cattle.Crossref | GoogleScholarGoogle Scholar | 26926596PubMed |

Blondin, P., and Sirard, M. A. (1995). Oocyte and follicular morphology as determining characteristics for developmental competence in bovine oocytes. Mol. Reprod. Dev. 41, 54–62.
| Oocyte and follicular morphology as determining characteristics for developmental competence in bovine oocytes.Crossref | GoogleScholarGoogle Scholar | 7619506PubMed |

Blondin, P., Farin, P. W., Crosier, A. E., Alexander, J. E., and Farin, C. E. (2000). In vitro production of embryos alters levels of insulin-like growth factor-II messenger ribonucleic acid in bovine fetuses 63 days after transfer. Biol. Reprod. 62, 384–389.
| In vitro production of embryos alters levels of insulin-like growth factor-II messenger ribonucleic acid in bovine fetuses 63 days after transfer.Crossref | GoogleScholarGoogle Scholar | 10642577PubMed |

Blower, M. D., Sullivan, B. A., and Karpen, G. H. (2002). Conserved organization of centromeric chromatin in flies and humans. Dev. Cell 2, 319–330.
| Conserved organization of centromeric chromatin in flies and humans.Crossref | GoogleScholarGoogle Scholar | 11879637PubMed |

Boerke, A., Dieleman, S. J., and Gadella, B. M. (2007). A possible role for sperm RNA in early embryo development. Theriogenology 68, S147–S155.
| A possible role for sperm RNA in early embryo development.Crossref | GoogleScholarGoogle Scholar | 17583784PubMed |

Borchert, G. M., Lanier, W., and Davidson, B. L. (2006). RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13, 1097–1101.
| RNA polymerase III transcribes human microRNAs.Crossref | GoogleScholarGoogle Scholar | 17099701PubMed |

Bošković, A., Bender, A., Gall, L., Ziegler-Birling, C., Beaujean, N., and Torres-Padilla, M. E. (2012). Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation. Epigenetics 7, 747–757.
| Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation.Crossref | GoogleScholarGoogle Scholar | 22647320PubMed |

Bostick, M., Kim, J. K., Esteve, P. O., Clark, A., Pradhan, S., and Jacobsen, S. E. (2007). UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764.
| UHRF1 plays a role in maintaining DNA methylation in mammalian cells.Crossref | GoogleScholarGoogle Scholar | 17673620PubMed |

Brackett, B. G., Bousquet, D., Boice, M. L., Donawick, W. J., Evans, J. F., and Dressel, M. A. (1982). Normal development following in vitro fertilization in the cow. Biol. Reprod. 27, 147–158.
| Normal development following in vitro fertilization in the cow.Crossref | GoogleScholarGoogle Scholar | 6896830PubMed |

Brewer, L. R., Corzett, M., and Balhorn, R. (1999). Protamine-induced condensation and decondensation of the same DNA molecule. Science 286, 120–123.
| Protamine-induced condensation and decondensation of the same DNA molecule.Crossref | GoogleScholarGoogle Scholar | 10506559PubMed |

Buschbeck, M., and Hake, S. B. (2017). Variants of core histones and their roles in cell fate decisions, development and cancer. Nat. Rev. Mol. Cell Biol. 18, 299–314.
| Variants of core histones and their roles in cell fate decisions, development and cancer.Crossref | GoogleScholarGoogle Scholar | 28144029PubMed |

Campos, E. I., and Reinberg, D. (2009). Histones: annotating chromatin. Annu. Rev. Genet. 43, 559–599.
| Histones: annotating chromatin.Crossref | GoogleScholarGoogle Scholar | 19886812PubMed |

Canovas, S., Cibelli, J. B., and Ross, P. J. (2012). Jumonji domain-containing protein 3 regulates histone 3 lysine 27 methylation during bovine preimplantation development. Proc. Natl Acad. Sci. USA 109, 2400–2405.
| Jumonji domain-containing protein 3 regulates histone 3 lysine 27 methylation during bovine preimplantation development.Crossref | GoogleScholarGoogle Scholar | 22308433PubMed |

Carolan, C., Lonergan, P., Van Langendonckt, A., and Mermillod, P. (1995). Factors affecting bovine embryo development in synthetic oviduct fluid following oocyte maturation and fertilization in vitro. Theriogenology 43, 1115–1128.
| Factors affecting bovine embryo development in synthetic oviduct fluid following oocyte maturation and fertilization in vitro.Crossref | GoogleScholarGoogle Scholar | 16727698PubMed |

Carrell, D. T., and Hammoud, S. S. (2010). The human sperm epigenome and its potential role in embryonic development. Mol. Hum. Reprod. 16, 37–47.
| The human sperm epigenome and its potential role in embryonic development.Crossref | GoogleScholarGoogle Scholar | 19906823PubMed |

Chen, Z., Robbins, K. M., Wells, K. D., and Rivera, R. M. (2013). Large offspring syndrome: a bovine model for the human loss-of-imprinting overgrowth syndrome Beckwith–Wiedemann. Epigenetics 8, 591–601.
| Large offspring syndrome: a bovine model for the human loss-of-imprinting overgrowth syndrome Beckwith–Wiedemann.Crossref | GoogleScholarGoogle Scholar | 23751783PubMed |

Chen, Z., Hagen, D. E., Elsik, C. G., Ji, T., Morris, C. J., Moon, L. E., and Rivera, R. M. (2015). Characterization of global loss of imprinting in fetal overgrowth syndrome induced by assisted reproduction. Proc. Natl Acad. Sci. USA 112, 4618–4623.
| Characterization of global loss of imprinting in fetal overgrowth syndrome induced by assisted reproduction.Crossref | GoogleScholarGoogle Scholar | 25825726PubMed |

Chen, Z., Hagen, D. E., Wang, J., Elsik, C. G., Ji, T., Siqueira, L. G., Hansen, P. J., and Rivera, R. M. (2016). Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing. Epigenetics 11, 501–516.
| Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing.Crossref | GoogleScholarGoogle Scholar | 27245094PubMed |

Chen, Z., Hagen, D. E., Ji, T., Elsik, C. G., and Rivera, R. M. (2017). Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome. Sci. Rep. 7, 12667.
| Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome.Crossref | GoogleScholarGoogle Scholar | 28978943PubMed |

Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K., and Shiekhattar, R. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744.
| TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing.Crossref | GoogleScholarGoogle Scholar | 15973356PubMed |

Chuang, L. S., Ian, H. I., Koh, T. W., Ng, H. H., Xu, G., and Li, B. F. (1997). Human DNA-(cytosine-5) methyltransferase–PCNA complex as a target for p21WAF1. Science 277, 1996–2000.
| Human DNA-(cytosine-5) methyltransferase–PCNA complex as a target for p21WAF1.Crossref | GoogleScholarGoogle Scholar | 9302295PubMed |

Chung, N., Bogliotti, Y. S., Ding, W., Vilarino, M., Takahashi, K., Chitwood, J. L., Schultz, R. M., and Ross, P. J. (2017). Active H3K27me3 demethylation by KDM6B is required for normal development of bovine preimplantation embryos. Epigenetics 12, 1048–1056.
| Active H3K27me3 demethylation by KDM6B is required for normal development of bovine preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 29160132PubMed |

Clouaire, T., and Stancheva, I. (2008). Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell. Mol. Life Sci. 65, 1509–1522.
| Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin?Crossref | GoogleScholarGoogle Scholar | 18322651PubMed |

Coan, P. M., Burton, G. J., and Ferguson-Smith, A. C. (2005). Imprinted genes in the placenta – a review. Placenta 26, S10–S20.
| Imprinted genes in the placenta – a review.Crossref | GoogleScholarGoogle Scholar | 15837057PubMed |

Combelles, C. M., Gupta, S., and Agarwal, A. (2009). Could oxidative stress influence the in-vitro maturation of oocytes? Reprod. Biomed. Online 18, 864–880.
| Could oxidative stress influence the in-vitro maturation of oocytes?Crossref | GoogleScholarGoogle Scholar | 19490793PubMed |

Cooper, D. N., Mort, M., Stenson, P. D., Ball, E. V., and Chuzhanova, N. A. (2010). Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum. Genomics 4, 406–410.
| Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides.Crossref | GoogleScholarGoogle Scholar | 20846930PubMed |

Corcoran, D., Fair, T., Park, S., Rizos, D., Patel, O., Smith, G., Coussens, P., Ireland, J., Boland, M., and Evans, A. (2006). Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos. Reproduction 131, 651–660.
| Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos.Crossref | GoogleScholarGoogle Scholar | 16595716PubMed |

Cotton, A. M., Lam, L., Affleck, J. G., Wilson, I. M., Penaherrera, M. S., McFadden, D. E., Kobor, M. S., Lam, W. L., Robinson, W. P., and Brown, C. J. (2011). Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum. Genet. 130, 187–201.
| Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation.Crossref | GoogleScholarGoogle Scholar | 21597963PubMed |

Currin, L., Michalovic, L., Bellefleur, A. M., Gutierrez, K., Glanzner, W., Schuermann, Y., Bohrer, R. C., Dicks, N., da Rosa, P. R., De Cesaro, M. P., Lopez, R., Grand, F. X., Vigneault, C., Blondin, P., Gourdon, J., Baldassarre, H., and Bordignon, V. (2017). The effect of age and length of gonadotropin stimulation on the in vitro embryo development of Holstein calf oocytes. Theriogenology 104, 87–93.
| The effect of age and length of gonadotropin stimulation on the in vitro embryo development of Holstein calf oocytes.Crossref | GoogleScholarGoogle Scholar | 28822904PubMed |

Dada, R., Kumar, M., Jesudasan, R., Fernandez, J. L., Gosalvez, J., and Agarwal, A. (2012). Epigenetics and its role in male infertility. J. Assist. Reprod. Genet. 29, 213–223.
| Epigenetics and its role in male infertility.Crossref | GoogleScholarGoogle Scholar | 22290605PubMed |

DeBaun, M. R., Niemitz, E. L., and Feinberg, A. P. (2003). Association of in vitro fertilization with Beckwith–Wiedemann syndrome and epigenetic alterations of LIT1 and H19. Am. J. Hum. Genet. 72, 156–160.
| Association of in vitro fertilization with Beckwith–Wiedemann syndrome and epigenetic alterations of LIT1 and H19.Crossref | GoogleScholarGoogle Scholar | 12439823PubMed |

DeChiara, T. M., Robertson, E. J., and Efstratiadis, A. (1991). Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64, 849–859.
| Parental imprinting of the mouse insulin-like growth factor II gene.Crossref | GoogleScholarGoogle Scholar | 1997210PubMed |

Delaval, K., Govin, J., Cerqueira, F., Rousseaux, S., Khochbin, S., and Feil, R. (2007). Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J. 26, 720–729.
| Differential histone modifications mark mouse imprinting control regions during spermatogenesis.Crossref | GoogleScholarGoogle Scholar | 17255950PubMed |

Diederich, M., Hansmann, T., Heinzmann, J., Barg-Kues, B., Herrmann, D., Aldag, P., Baulain, U., Reinhard, R., Kues, W., Weissgerber, C., Haaf, T., and Niemann, H. (2012). DNA methylation and mRNA expression profiles in bovine oocytes derived from prepubertal and adult donors. Reproduction 144, 319–330.
| DNA methylation and mRNA expression profiles in bovine oocytes derived from prepubertal and adult donors.Crossref | GoogleScholarGoogle Scholar | 22733804PubMed |

Dobbs, K. B., Rodriguez, M., Sudano, M. J., Ortega, M. S., and Hansen, P. J. (2013). Dynamics of DNA methylation during early development of the preimplantation bovine embryo. PLoS One 8, e66230.
| Dynamics of DNA methylation during early development of the preimplantation bovine embryo.Crossref | GoogleScholarGoogle Scholar | 23799080PubMed |

Dobbs, K. B., Gagne, D., Fournier, E., Dufort, I., Robert, C., Block, J., Sirard, M. A., Bonilla, L., Ealy, A. D., Loureiro, B., and Hansen, P. J. (2014). Sexual dimorphism in developmental programming of the bovine preimplantation embryo caused by colony-stimulating factor 2. Biol. Reprod. 91, 80.
| Sexual dimorphism in developmental programming of the bovine preimplantation embryo caused by colony-stimulating factor 2.Crossref | GoogleScholarGoogle Scholar | 25078682PubMed |

Doench, J. G., and Sharp, P. A. (2004). Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504–511.
| Specificity of microRNA target selection in translational repression.Crossref | GoogleScholarGoogle Scholar | 15014042PubMed |

Doherty, A. S., Mann, M. R., Tremblay, K. D., Bartolomei, M. S., and Schultz, R. M. (2000). Differential effects of culture on imprinted H19 expression in the preimplantation mouse embryo. Biol. Reprod. 62, 1526–1535.
| Differential effects of culture on imprinted H19 expression in the preimplantation mouse embryo.Crossref | GoogleScholarGoogle Scholar | 10819752PubMed |

Driver, A. M., Peñagaricano, F., Huang, W., Ahmad, K. R., Hackbart, K. S., Wiltbank, M. C., and Khatib, H. (2012). RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo-and in vitro-derived bovine blastocysts. BMC Genomics 13, 118.
| RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo-and in vitro-derived bovine blastocysts.Crossref | GoogleScholarGoogle Scholar | 22452724PubMed |

Duan, J., Zhu, L., Dong, H., Zheng, X., Jiang, Z., Chen, J., and Tian, X. C. (2019). Analysis of mRNA abundance for histone variants, histone- and DNA-modifiers in bovine in vivo and in vitro oocytes and embryos. Sci. Rep. 9, 1217.
| Analysis of mRNA abundance for histone variants, histone- and DNA-modifiers in bovine in vivo and in vitro oocytes and embryos.Crossref | GoogleScholarGoogle Scholar | 30718778PubMed |

Edwards, R. G. (1965). Maturation in vitro of mouse, sheep, cow, pig, rhesus monkey and human ovarian oocytes. Nature 208, 349–351.
| Maturation in vitro of mouse, sheep, cow, pig, rhesus monkey and human ovarian oocytes.Crossref | GoogleScholarGoogle Scholar | 4957259PubMed |

Edwards, R. G., Steptoe, P. C., and Purdy, J. M. (1970). Fertilization and cleavage in vitro of preovulator human oocytes. Nature 227, 1307–1309.
| Fertilization and cleavage in vitro of preovulator human oocytes.Crossref | GoogleScholarGoogle Scholar | 4916973PubMed |

Edwards, J. R., Yarychkivska, O., Boulard, M., and Bestor, T. H. (2017). DNA methylation and DNA methyltransferases. Epigenetics Chromatin 10, 23.
| DNA methylation and DNA methyltransferases.Crossref | GoogleScholarGoogle Scholar | 28503201PubMed |

Engel, N., Thorvaldsen, J. L., and Bartolomei, M. S. (2006). CTCF binding sites promote transcription initiation and prevent DNA methylation on the maternal allele at the imprinted H19/Igf2 locus. Hum. Mol. Genet. 15, 2945–2954.
| CTCF binding sites promote transcription initiation and prevent DNA methylation on the maternal allele at the imprinted H19/Igf2 locus.Crossref | GoogleScholarGoogle Scholar | 16928784PubMed |

Erickson, B. H. (1966). Development and senescence of the postnatal bovine ovary. J. Anim. Sci. 25, 800–805.
| Development and senescence of the postnatal bovine ovary.Crossref | GoogleScholarGoogle Scholar | 6007918PubMed |

Ertzeid, G., and Storeng, R. (1992). Adverse effects of gonadotrophin treatment on pre- and postimplantation development in mice. J. Reprod. Fertil. 96, 649–655.
| Adverse effects of gonadotrophin treatment on pre- and postimplantation development in mice.Crossref | GoogleScholarGoogle Scholar | 1339844PubMed |

Ertzeid, G., and Storeng, R. (2001). The impact of ovarian stimulation on implantation and fetal development in mice. Hum. Reprod. 16, 221–225.
| The impact of ovarian stimulation on implantation and fetal development in mice.Crossref | GoogleScholarGoogle Scholar | 11157810PubMed |

Fagerlind, M., Stalhammar, H., Olsson, B., and Klinga-Levan, K. (2015). Expression of miRNAs in bull spermatozoa correlates with fertility rates. Reprod. Domest. Anim. 50, 587–594.
| Expression of miRNAs in bull spermatozoa correlates with fertility rates.Crossref | GoogleScholarGoogle Scholar | 25998690PubMed |

Fair, T., Hyttel, P., and Greve, T. (1995). Bovine oocyte diameter in relation to maturational competence and transcriptional activity. Mol. Reprod. Dev. 42, 437–442.
| Bovine oocyte diameter in relation to maturational competence and transcriptional activity.Crossref | GoogleScholarGoogle Scholar | 8607973PubMed |

Fair, T., Hulshof, S. C., Hyttel, P., Greve, T., and Boland, M. (1997). Oocyte ultrastructure in bovine primordial to early tertiary follicles. Anat. Embryol. (Berl.) 195, 327–336.
| Oocyte ultrastructure in bovine primordial to early tertiary follicles.Crossref | GoogleScholarGoogle Scholar | 9108198PubMed |

Fair, T., Carter, F., Park, S., Evans, A., and Lonergan, P. (2007). Global gene expression analysis during bovine oocyte in vitro maturation. Theriogenology 68, S91–S97.
| Global gene expression analysis during bovine oocyte in vitro maturation.Crossref | GoogleScholarGoogle Scholar | 17512044PubMed |

Farin, P. W., and Farin, C. E. (1995). Transfer of bovine embryos produced in vivo or in vitro: survival and fetal development. Biol. Reprod. 52, 676–682.
| Transfer of bovine embryos produced in vivo or in vitro: survival and fetal development.Crossref | GoogleScholarGoogle Scholar | 7756461PubMed |

Farin, P. W., Piedrahita, J. A., and Farin, C. E. (2006). Errors in development of fetuses and placentas from in vitro-produced bovine embryos. Theriogenology 65, 178–191.
| Errors in development of fetuses and placentas from in vitro-produced bovine embryos.Crossref | GoogleScholarGoogle Scholar | 16266745PubMed |

Farin, C. E., Farmer, W. T., and Farin, P. W. (2010). Pregnancy recognition and abnormal offspring syndrome in cattle. Reprod. Fertil. Dev. 22, 75–87.
| Pregnancy recognition and abnormal offspring syndrome in cattle.Crossref | GoogleScholarGoogle Scholar | 20003848PubMed |

Fatemi, M., Hermann, A., Pradhan, S., and Jeltsch, A. (2001). The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. J. Mol. Biol. 309, 1189–1199.
| The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA.Crossref | GoogleScholarGoogle Scholar | 11399088PubMed |

Fujita, N., Shimotake, N., Ohki, I., Chiba, T., Saya, H., Shirakawa, M., and Nakao, M. (2000). Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1. Mol. Cell. Biol. 20, 5107–5118.
| Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1.Crossref | GoogleScholarGoogle Scholar | 10866667PubMed |

Fukuda, Y., Ichikawa, M., Naito, K., and Toyoda, Y. (1990). Birth of normal calves resulting from bovine oocytes matured, fertilized, and cultured with cumulus cells in vitro up to the blastocyst stage. Biol. Reprod. 42, 114–119.
| Birth of normal calves resulting from bovine oocytes matured, fertilized, and cultured with cumulus cells in vitro up to the blastocyst stage.Crossref | GoogleScholarGoogle Scholar | 2310811PubMed |

Gamble, M. J., and Kraus, W. L. (2010). Multiple facets of the unique histone variant macroH2A: from genomics to cell biology. Cell Cycle 9, 2568–2574.
| Multiple facets of the unique histone variant macroH2A: from genomics to cell biology.Crossref | GoogleScholarGoogle Scholar | 20543561PubMed |

Gandolfi, F., and Moor, R. (1987). Stimulation of early embryonic development in the sheep by co-culture with oviduct epithelial cells. J. Reprod. Fertil. 81, 23–28.
| Stimulation of early embryonic development in the sheep by co-culture with oviduct epithelial cells.Crossref | GoogleScholarGoogle Scholar | 3668954PubMed |

Gao, X., Lin, S. H., Ren, F., Li, J. T., Chen, J. J., Yao, C. B., Yang, H. B., Jiang, S. X., Yan, G. Q., Wang, D., Wang, Y., Liu, Y., Cai, Z., Xu, Y. Y., Chen, J., Yu, W., Yang, P. Y., and Lei, Q. Y. (2016). Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia. Nat. Commun. 7, 11960.
| Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia.Crossref | GoogleScholarGoogle Scholar | 27357947PubMed |

Ginther, O. J., Knopf, L., and Kastelic, J. P. (1989). Temporal associations among ovarian events in cattle during oestrous cycles with two and three follicular waves. J. Reprod. Fertil. 87, 223–230.
| Temporal associations among ovarian events in cattle during oestrous cycles with two and three follicular waves.Crossref | GoogleScholarGoogle Scholar | 2621698PubMed |

Giraldez, A. J., Mishima, Y., Rihel, J., Grocock, R. J., Van Dongen, S., Inoue, K., Enright, A. J., and Schier, A. F. (2006). Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79.
| Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.Crossref | GoogleScholarGoogle Scholar | 16484454PubMed |

Giritharan, G., Talbi, S., Donjacour, A., Di Sebastiano, F., Dobson, A. T., and Rinaudo, P. F. (2007). Effect of in vitro fertilization on gene expression and development of mouse preimplantation embryos. Reproduction 134, 63–72.
| Effect of in vitro fertilization on gene expression and development of mouse preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 17641089PubMed |

Gòdia, M., Swanson, G., and Krawetz, S. A. (2018). A history of why fathers’ RNA matters. Biol. Reprod. 99, 147–159.
| A history of why fathers’ RNA matters.Crossref | GoogleScholarGoogle Scholar | 29514212PubMed |

Golderer, G., Loidl, P., and Grobner, P. (1987). Histone acetyltransferase activity during the cell cycle. FEBS Lett. 222, 322–326.
| Histone acetyltransferase activity during the cell cycle.Crossref | GoogleScholarGoogle Scholar | 3653410PubMed |

Görisch, S. M., Wachsmuth, M., Toth, K. F., Lichter, P., and Rippe, K. (2005). Histone acetylation increases chromatin accessibility. J. Cell Sci. 118, 5825–5834.
| Histone acetylation increases chromatin accessibility.Crossref | GoogleScholarGoogle Scholar | 16317046PubMed |

Gregory, R. I., Yan, K.-p., Amuthan, G., Chendrimada, T., Doratotaj, B., Cooch, N., and Shiekhattar, R. (2004). The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240.
| The Microprocessor complex mediates the genesis of microRNAs.Crossref | GoogleScholarGoogle Scholar | 15531877PubMed |

Guo, H., Zhu, P., Yan, L., Li, R., Hu, B., Lian, Y., Yan, J., Ren, X., Lin, S., Li, J., Jin, X., Shi, X., Liu, P., Wang, X., Wang, W., Wei, Y., Li, X., Guo, F., Wu, X., Fan, X., Yong, J., Wen, L., Xie, S. X., Tang, F., and Qiao, J. (2014). The DNA methylation landscape of human early embryos. Nature 511, 606–610.
| The DNA methylation landscape of human early embryos.Crossref | GoogleScholarGoogle Scholar | 25079557PubMed |

Gutiérrez-Adán, A., Rizos, D., Fair, T., Moreira, P., Pintado, B., Boland, M., and Lonergan, P. (2004). Effect of speed of development on mRNA expression pattern in early bovine embryos cultured in vivo or in vitro. Mol. Reprod. Dev. 68, 441–448.
| Effect of speed of development on mRNA expression pattern in early bovine embryos cultured in vivo or in vitro.Crossref | GoogleScholarGoogle Scholar | 15236328PubMed |

Hackett, J. A., Sengupta, R., Zylicz, J. J., Murakami, K., Lee, C., Down, T. A., and Surani, M. A. (2013). Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339, 448–452.
| Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine.Crossref | GoogleScholarGoogle Scholar | 23223451PubMed |

Hajkova, P., Jeffries, S. J., Lee, C., Miller, N., Jackson, S. P., and Surani, M. A. (2010). Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 329, 78–82.
| Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway.Crossref | GoogleScholarGoogle Scholar | 20595612PubMed |

Han, J., Lee, Y., Yeom, K. H., Kim, Y. K., Jin, H., and Kim, V. N. (2004). The Drosha–DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027.
| The Drosha–DGCR8 complex in primary microRNA processing.Crossref | GoogleScholarGoogle Scholar | 15574589PubMed |

Hansen, P. J., Dobbs, K. B., Denicol, A. C., and Siqueira, L. G. (2016). Sex and the preimplantation embryo: implications of sexual dimorphism in the preimplantation period for maternal programming of embryonic development. Cell Tissue Res. 363, 237–247.
| Sex and the preimplantation embryo: implications of sexual dimorphism in the preimplantation period for maternal programming of embryonic development.Crossref | GoogleScholarGoogle Scholar | 26391275PubMed |

Hasler, J. F. (2014). Forty years of embryo transfer in cattle: a review focusing on the journal Theriogenology, the growth of the industry in North America, and personal reminisces. Theriogenology 81, 152–169.
| Forty years of embryo transfer in cattle: a review focusing on the journal Theriogenology, the growth of the industry in North America, and personal reminisces.Crossref | GoogleScholarGoogle Scholar | 24274419PubMed |

Hasler, J. F., Henderson, W. B., Hurtgen, P. J., Jin, Z. Q., McCauley, A. D., Mower, S. A., Neely, B., Shuey, L. S., Stokes, J. E., and Trimmer, S. A. (1995). Production, freezing and transfer of bovine IVF embryos and subsequent calving results. Theriogenology 43, 141–152.
| Production, freezing and transfer of bovine IVF embryos and subsequent calving results.Crossref | GoogleScholarGoogle Scholar |

Hatanaka, Y., Tsusaka, T., Shimizu, N., Morita, K., Suzuki, T., Machida, S., Satoh, M., Honda, A., Hirose, M., Kamimura, S., Ogonuki, N., Nakamura, T., Inoue, K., Hosoi, Y., Dohmae, N., Nakano, T., Kurumizaka, H., Matsumoto, K., Shinkai, Y., and Ogura, A. (2017). Histone H3 methylated at arginine 17 is essential for reprogramming the paternal genome in zygotes. Cell Rep. 20, 2756–2765.
| Histone H3 methylated at arginine 17 is essential for reprogramming the paternal genome in zygotes.Crossref | GoogleScholarGoogle Scholar | 28930672PubMed |

Heinzmann, J., Hansmann, T., Herrmann, D., Wrenzycki, C., Zechner, U., Haaf, T., and Niemann, H. (2011). Epigenetic profile of developmentally important genes in bovine oocytes. Mol. Reprod. Dev. 78, 188–201.
| Epigenetic profile of developmentally important genes in bovine oocytes.Crossref | GoogleScholarGoogle Scholar | 21290475PubMed |

Hendrickson, D. G., Hogan, D. J., McCullough, H. L., Myers, J. W., Herschlag, D., Ferrell, J. E., and Brown, P. O. (2009). Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 7, e1000238.
| Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.Crossref | GoogleScholarGoogle Scholar | 19901979PubMed |

Hermann, A., Goyal, R., and Jeltsch, A. (2004). The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem. 279, 48350–48359.
| The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites.Crossref | GoogleScholarGoogle Scholar | 15339928PubMed |

Hirasawa, R., Chiba, H., Kaneda, M., Tajima, S., Li, E., Jaenisch, R., and Sasaki, H. (2008). Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 22, 1607–1616.
| Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development.Crossref | GoogleScholarGoogle Scholar | 18559477PubMed |

Holm, P., Walker, S. K., and Seamark, R. F. (1996). Embryo viability, duration of gestation and birth weight in sheep after transfer of in vitro matured and in vitro fertilized zygotes cultured in vitro or in vivo. J. Reprod. Fertil. 107, 175–181.
| Embryo viability, duration of gestation and birth weight in sheep after transfer of in vitro matured and in vitro fertilized zygotes cultured in vitro or in vivo.Crossref | GoogleScholarGoogle Scholar | 8882282PubMed |

Howell, C. Y., Bestor, T. H., Ding, F., Latham, K. E., Mertineit, C., Trasler, J. M., and Chaillet, J. R. (2001). Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene. Cell 104, 829–838.
| Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene.Crossref | GoogleScholarGoogle Scholar | 11290321PubMed |

Huffman, S. R., Pak, Y., and Rivera, R. M. (2015). Superovulation induces alterations in the epigenome of zygotes, and results in differences in gene expression at the blastocyst stage in mice. Mol. Reprod. Dev. 82, 207–217.
| Superovulation induces alterations in the epigenome of zygotes, and results in differences in gene expression at the blastocyst stage in mice.Crossref | GoogleScholarGoogle Scholar | 25737418PubMed |

Hutchison, J. M., Rau, D. C., and DeRouchey, J. E. (2017). Role of disulfide bonds on DNA packaging forces in bull sperm chromatin. Biophys. J. 113, 1925–1933.
| Role of disulfide bonds on DNA packaging forces in bull sperm chromatin.Crossref | GoogleScholarGoogle Scholar | 29117517PubMed |

Hutvágner, G., and Zamore, P. D. (2002). A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060.
| A microRNA in a multiple-turnover RNAi enzyme complex.Crossref | GoogleScholarGoogle Scholar | 12154197PubMed |

Hutvágner, G., McLachlan, J., Pasquinelli, A. E., Balint, E., Tuschl, T., and Zamore, P. D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838.
| A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA.Crossref | GoogleScholarGoogle Scholar | 11452083PubMed |

Ideraabdullah, F. Y., Vigneau, S., and Bartolomei, M. S. (2008). Genomic imprinting mechanisms in mammals. Mutat. Res. 647, 77–85.
| Genomic imprinting mechanisms in mammals.Crossref | GoogleScholarGoogle Scholar | 18778719PubMed |

Illingworth, R. S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R., James, K. D., Turner, D. J., Smith, C., Harrison, D. J., Andrews, R., and Bird, A. P. (2010). Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6, e1001134.
| Orphan CpG islands identify numerous conserved promoters in the mammalian genome.Crossref | GoogleScholarGoogle Scholar | 20885785PubMed |

Inoue, A., and Zhang, Y. (2011). Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334, 194.
| Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 21940858PubMed |

Inoue, A., Shen, L., Dai, Q., He, C., and Zhang, Y. (2011). Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. 21, 1670–1676.
| Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development.Crossref | GoogleScholarGoogle Scholar | 22124233PubMed |

Institute of Medicine, and National Research Council (2004). ‘Methods and Mechanisms for Genetic Manipulation of Plants, Animals, and Microorganisms. In ‘Safety of Genetically Engineered Foods: Approaches to Assessing Unintended Health Effects’. pp. 23–38. (National Acadamies Press: Washington, DC.)

Jiang, Z., Sun, J., Dong, H., Luo, O., Zheng, X., Obergfell, C., Tang, Y., Bi, J., O’Neill, R., Ruan, Y., Chen, J., and Tian, X. C. (2014). Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics 15, 756.
| Transcriptional profiles of bovine in vivo pre-implantation development.Crossref | GoogleScholarGoogle Scholar | 25185836PubMed |

Jiang, Z., Lin, J., Dong, H., Zheng, X., Marjani, S. L., Duan, J., Ouyang, Z., Chen, J., and Tian, X. C. (2018). DNA methylomes of bovine gametes and in vivo produced preimplantation embryos. Biol. Reprod. 99, 949–959.
| DNA methylomes of bovine gametes and in vivo produced preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 29912291PubMed |

Jodar, M., Selvaraju, S., Sendler, E., Diamond, M. P., and Krawetz, S. A. (2013). The presence, role and clinical use of spermatozoal RNAs. Hum. Reprod. Update 19, 604–624.
| The presence, role and clinical use of spermatozoal RNAs.Crossref | GoogleScholarGoogle Scholar | 23856356PubMed |

John, R. M., and Lefebvre, L. (2011). Developmental regulation of somatic imprints. Differentiation 81, 270–280.
| Developmental regulation of somatic imprints.Crossref | GoogleScholarGoogle Scholar | 21316143PubMed |

Jones, P. A. (2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492.
| Functions of DNA methylation: islands, start sites, gene bodies and beyond.Crossref | GoogleScholarGoogle Scholar | 22641018PubMed |

Jones, G. M., Cram, D. S., Song, B., Magli, M. C., Gianaroli, L., Lacham-Kaplan, O., Findlay, J. K., Jenkin, G., and Trounson, A. O. (2008). Gene expression profiling of human oocytes following in vivo or in vitro maturation. Hum. Reprod. 23, 1138–1144.
| Gene expression profiling of human oocytes following in vivo or in vitro maturation.Crossref | GoogleScholarGoogle Scholar | 18346995PubMed |

Jung, Y. H., Sauria, M. E. G., Lyu, X., Cheema, M. S., Ausio, J., Taylor, J., and Corces, V. G. (2017). Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes. Cell Rep. 18, 1366–1382.
| Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Crossref | GoogleScholarGoogle Scholar | 28178516PubMed |

Kahlon, N. (2016). The effects of oocyte exposure to bisphenol a on early bovine embryo development. M.S. Thesis, The University of Guelph. Available at https://atrium.lib.uoguelph.ca/xmlui/handle/10214/9640?show=full [verified 10 October 2019].

Kahn, C., and Line, S. (Eds) (2010). ‘The Merck Veterinary Manual.’ 10th edn. (Merck and Company: Whitehouse Station, NJ.)

Kalousek, F., and Morris, N. R. (1969). The purification and properties of deoxyribonucleic acid methylase from rat spleen. J. Biol. Chem. 244, 1157–1163.
| 4975067PubMed |

Katari, S., Turan, N., Bibikova, M., Erinle, O., Chalian, R., Foster, M., Gaughan, J. P., Coutifaris, C., and Sapienza, C. (2009). DNA methylation and gene expression differences in children conceived in vitro or in vivo. Hum. Mol. Genet. 18, 3769–3778.
| DNA methylation and gene expression differences in children conceived in vitro or in vivo.Crossref | GoogleScholarGoogle Scholar | 19605411PubMed |

Kiriakidou, M., Tan, G. S., Lamprinaki, S., De Planell-Saguer, M., Nelson, P. T., and Mourelatos, Z. (2007). An mRNA m7G cap binding-like motif within human Ago2 represses translation. Cell 129, 1141–1151.
| An mRNA m7G cap binding-like motif within human Ago2 represses translation.Crossref | GoogleScholarGoogle Scholar | 17524464PubMed |

Klemetti, R., Sevon, T., Gissler, M., and Hemminki, E. (2010). Health of children born after ovulation induction. Fertil. Steril. 93, 1157–1168.
| Health of children born after ovulation induction.Crossref | GoogleScholarGoogle Scholar | 19171331PubMed |

Kohli, R. M., and Zhang, Y. (2013). TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479.
| TET enzymes, TDG and the dynamics of DNA demethylation.Crossref | GoogleScholarGoogle Scholar | 24153300PubMed |

Kunowska, N. (2019). Studying DNA methylation in single-cell format with scBS-seq. Methods Mol. Biol. 1979, 235–250.
| Studying DNA methylation in single-cell format with scBS-seq.Crossref | GoogleScholarGoogle Scholar | 31028642PubMed |

Kutchy, N. A., Menezes, E. S. B., Chiappetta, A., Tan, W., Wills, R. W., Kaya, A., Topper, E., Moura, A. A., Perkins, A. D., and Memili, E. (2018). Acetylation and methylation of sperm histone 3 lysine 27 (H3K27ac and H3K27me3) are associated with bull fertility. Andrologia 50, e12915.
| Acetylation and methylation of sperm histone 3 lysine 27 (H3K27ac and H3K27me3) are associated with bull fertility.Crossref | GoogleScholarGoogle Scholar | 29057498PubMed |

Kuzan, F. B., and Wright, R. W. (1982). Blastocyst expansion, hatching, and attachment of porcine embryos cocultured with bovine fibroblasts in vitro. Anim. Reprod. Sci. 5, 57–63.
| Blastocyst expansion, hatching, and attachment of porcine embryos cocultured with bovine fibroblasts in vitro.Crossref | GoogleScholarGoogle Scholar |

La Spina, F. A., Romanato, M., Brugo-Olmedo, S., De Vincentiis, S., Julianelli, V., Rivera, R. M., and Buffone, M. G. (2014). Heterogeneous distribution of histone methylation in mature human sperm. J. Assist. Reprod. Genet. 31, 45–49.
| Heterogeneous distribution of histone methylation in mature human sperm.Crossref | GoogleScholarGoogle Scholar | 24221913PubMed |

Landry, D. A., Bellefleur, A. M., Labrecque, R., Grand, F. X., Vigneault, C., Blondin, P., and Sirard, M. A. (2016). Effect of cow age on the in vitro developmental competence of oocytes obtained after FSH stimulation and coasting treatments. Theriogenology 86, 1240–1246.
| Effect of cow age on the in vitro developmental competence of oocytes obtained after FSH stimulation and coasting treatments.Crossref | GoogleScholarGoogle Scholar | 27215669PubMed |

Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862.
| An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.Crossref | GoogleScholarGoogle Scholar | 11679671PubMed |

Lazzari, G., Wrenzycki, C., Herrmann, D., Duchi, R., Kruip, T., Niemann, H., and Galli, C. (2002). Cellular and molecular deviations in bovine in vitro-produced embryos are related to the large offspring syndrome. Biol. Reprod. 67, 767–775.
| Cellular and molecular deviations in bovine in vitro-produced embryos are related to the large offspring syndrome.Crossref | GoogleScholarGoogle Scholar | 12193383PubMed |

Lee, Y., Jeon, K., Lee, J. T., Kim, S., and Kim, V. N. (2002). MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670.
| MicroRNA maturation: stepwise processing and subcellular localization.Crossref | GoogleScholarGoogle Scholar | 12198168PubMed |

Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S., and Kim, V. N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419.
| The nuclear RNase III Drosha initiates microRNA processing.Crossref | GoogleScholarGoogle Scholar | 14508493PubMed |

Lee, Y., Kim, M., Han, J., Yeom, K. H., Lee, S., Baek, S. H., and Kim, V. N. (2004). MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060.
| MicroRNA genes are transcribed by RNA polymerase II.Crossref | GoogleScholarGoogle Scholar | 15372072PubMed |

Lepikhov, K., Zakhartchenko, V., Hao, R., Yang, F., Wrenzycki, C., Niemann, H., Wolf, E., and Walter, J. (2008). Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes. Epigenetics Chromatin 1, 8.
| Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes.Crossref | GoogleScholarGoogle Scholar | 19014417PubMed |

Li, Y., Donnelly, C. G., and Rivera, R. M. (2019a). Overgrowth syndrome. Vet. Clin. North Am. Food Anim. Pract. 35, 265–276.
| Overgrowth syndrome.Crossref | GoogleScholarGoogle Scholar | 31103180PubMed |

Li, Y., Hagen, D. E., Ji, T., Bakhtiarizadeh, M. R., Frederic, W. M., Traxler, E. M., Kalish, J. M., and Rivera, R. M. (2019b). Altered microRNA expression profiles in large offspring syndrome and Beckwith–Wiedemann syndrome. Epigenetics 14, 850–876.
| Altered microRNA expression profiles in large offspring syndrome and Beckwith–Wiedemann syndrome.Crossref | GoogleScholarGoogle Scholar | 31144574PubMed |

Lodde, V., Modina, S. C., Franciosi, F., Zuccari, E., Tessaro, I., and Luciano, A. M. (2009). Localization of DNA methyltransferase-1 during oocyte differentiation, in vitro maturation and early embryonic development in cow. Eur. J. Histochem. 53, e24.
| Localization of DNA methyltransferase-1 during oocyte differentiation, in vitro maturation and early embryonic development in cow.Crossref | GoogleScholarGoogle Scholar | 22073356PubMed |

Lucifero, D., Mann, M. R., Bartolomei, M. S., and Trasler, J. M. (2004). Gene-specific timing and epigenetic memory in oocyte imprinting. Hum. Mol. Genet. 13, 839–849.
| Gene-specific timing and epigenetic memory in oocyte imprinting.Crossref | GoogleScholarGoogle Scholar | 14998934PubMed |

Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260.
| Crystal structure of the nucleosome core particle at 2.8 A resolution.Crossref | GoogleScholarGoogle Scholar | 9305837PubMed |

Luo, C., Hajkova, P., and Ecker, J. R. (2018). Dynamic DNA methylation: in the right place at the right time. Science 361, 1336–1340.
| Dynamic DNA methylation: in the right place at the right time.Crossref | GoogleScholarGoogle Scholar | 30262495PubMed |

Luvoni, G. C., Keskintepe, L., and Brackett, B. G. (1996). Improvement in bovine embryo production in vitro by glutathione-containing culture media. Mol. Reprod. Dev. 43, 437–443.
| Improvement in bovine embryo production in vitro by glutathione-containing culture media.Crossref | GoogleScholarGoogle Scholar | 9052934PubMed |

Ma, X., Zhang, S., Zhang, M., Zhu, Y., Ma, P., Yang, S., Su, L., Li, Z., Lv, W., and Luan, W. (2018). TRIM28 down-regulation on methylation imprints in bovine preimplantation embryos. Zygote 26, 449–456.
| TRIM28 down-regulation on methylation imprints in bovine preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 30670109PubMed |

MacDonald, W. A., and Mann, M. R. (2014). Epigenetic regulation of genomic imprinting from germ line to preimplantation. Mol. Reprod. Dev. 81, 126–140.
| Epigenetic regulation of genomic imprinting from germ line to preimplantation.Crossref | GoogleScholarGoogle Scholar | 23893518PubMed |

Market-Velker, B. A., Zhang, L., Magri, L. S., Bonvissuto, A. C., and Mann, M. R. (2010). Dual effects of superovulation: loss of maternal and paternal imprinted methylation in a dose-dependent manner. Hum. Mol. Genet. 19, 36–51.
| Dual effects of superovulation: loss of maternal and paternal imprinted methylation in a dose-dependent manner.Crossref | GoogleScholarGoogle Scholar | 19805400PubMed |

Marsico, A., Huska, M. R., Lasserre, J., Hu, H., Vucicevic, D., Musahl, A., Orom, U. A., and Vingron, M. (2013). PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 14, R84.
| PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.Crossref | GoogleScholarGoogle Scholar | 23958307PubMed |

Marzluff, W. F., Wagner, E. J., and Duronio, R. J. (2008). Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat. Rev. Genet. 9, 843–854.
| Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.Crossref | GoogleScholarGoogle Scholar | 18927579PubMed |

Maxfield, E. K., Sinclair, K. D., Dolman, D. F., Staines, M. E., and Maltin, C. A. (1997). In vitro culture of sheep embryos increases weight, primary fiber size and secondary to primary fiber ratio in fetal muscle at Day 61 of gestation. Theriogenology 47, 376.
| In vitro culture of sheep embryos increases weight, primary fiber size and secondary to primary fiber ratio in fetal muscle at Day 61 of gestation.Crossref | GoogleScholarGoogle Scholar |

McGrath, J., and Solter, D. (1984). Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37, 179–183.
| Completion of mouse embryogenesis requires both the maternal and paternal genomes.Crossref | GoogleScholarGoogle Scholar | 6722870PubMed |

McLay, D. W., Carroll, J., and Clarke, H. J. (2002). The ability to develop an activity that transfers histones onto sperm chromatin is acquired with meiotic competence during oocyte growth. Dev. Biol. 241, 195–206.
| The ability to develop an activity that transfers histones onto sperm chromatin is acquired with meiotic competence during oocyte growth.Crossref | GoogleScholarGoogle Scholar | 11784105PubMed |

Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., and Tuschl, T. (2004). Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197.
| Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs.Crossref | GoogleScholarGoogle Scholar | 15260970PubMed |

Memili, E., and First, N. L. (1998). Developmental changes in RNA polymerase II in bovine oocytes, early embryos, and effect of alpha-amanitin on embryo development. Mol. Reprod. Dev. 51, 381–389.
| Developmental changes in RNA polymerase II in bovine oocytes, early embryos, and effect of alpha-amanitin on embryo development.Crossref | GoogleScholarGoogle Scholar | 9820196PubMed |

Mermillod, P., Oussaid, B., and Cognie, Y. (1999). Aspects of follicular and oocyte maturation that affect the developmental potential of embryos. J. Reprod. Fertil. Suppl. 54, 449–460.
| 10692875PubMed |

Messerschmidt, D. M., Knowles, B. B., and Solter, D. (2014). DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev. 28, 812–828.
| DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 24736841PubMed |

Miyoshi, N., Barton, S. C., Kaneda, M., Hajkova, P., and Surani, M. A. (2006). The continuing quest to comprehend genomic imprinting. Cytogenet. Genome Res. 113, 6–11.
| The continuing quest to comprehend genomic imprinting.Crossref | GoogleScholarGoogle Scholar | 16575156PubMed |

Monteys, A. M., Spengler, R. M., Wan, J., Tecedor, L., Lennox, K. A., Xing, Y., and Davidson, B. L. (2010). Structure and activity of putative intronic miRNA promoters. RNA 16, 495–505.
| Structure and activity of putative intronic miRNA promoters.Crossref | GoogleScholarGoogle Scholar | 20075166PubMed |

Moore, S. G., and Hasler, J. F. (2017). A 100-year review: reproductive technologies in dairy science. J. Dairy Sci. 100, 10314–10331.
| A 100-year review: reproductive technologies in dairy science.Crossref | GoogleScholarGoogle Scholar | 29153167PubMed |

Morin-Doré, L., Blondin, P., Vigneault, C., Grand, F. X., Labrecque, R., and Sirard, M. A. (2017). Transcriptomic evaluation of bovine blastocysts obtained from peri-pubertal oocyte donors. Theriogenology 93, 111–123.
| Transcriptomic evaluation of bovine blastocysts obtained from peri-pubertal oocyte donors.Crossref | GoogleScholarGoogle Scholar | 28257859PubMed |

Morotti, F., Sanches, B. V., Pontes, J. H., Basso, A. C., Siqueira, E. R., Lisboa, L. A., and Seneda, M. M. (2014). Pregnancy rate and birth rate of calves from a large-scale IVF program using reverse-sorted semen in Bos indicus, Bos indicus-taurus, and Bos taurus cattle. Theriogenology 81, 696–701.
| Pregnancy rate and birth rate of calves from a large-scale IVF program using reverse-sorted semen in Bos indicus, Bos indicus-taurus, and Bos taurus cattle.Crossref | GoogleScholarGoogle Scholar | 24412681PubMed |

Mundim, T. C., Ramos, A. F., Sartori, R., Dode, M. A., Melo, E. O., Gomes, L. F., Rumpf, R., and Franco, M. M. (2009). Changes in gene expression profiles of bovine embryos produced in vitro, by natural ovulation, or hormonal superstimulation. Genet. Mol. Res. 8, 1398–1407.
| Changes in gene expression profiles of bovine embryos produced in vitro, by natural ovulation, or hormonal superstimulation.Crossref | GoogleScholarGoogle Scholar | 19937584PubMed |

Munne, S., Magli, C., Adler, A., Wright, G., de Boer, K., Mortimer, D., Tucker, M., Cohen, J., and Gianaroli, L. (1997). Treatment-related chromosome abnormalities in human embryos. Hum. Reprod. 12, 780–784.
| Treatment-related chromosome abnormalities in human embryos.Crossref | GoogleScholarGoogle Scholar | 9159442PubMed |

Muth-Spurlock, A. M., Dix, J. A., Coleson, M. P., Hart, C. G., Lemley, C. O., Schulmeister, T. M., Lamb, G. C., and Larson, J. E. (2017). The effect of follicular wave on fertility characteristics in beef cattle. J. Anim. Sci. 95, 866–874.
| 28380577PubMed |

Nagae, G., Isagawa, T., Shiraki, N., Fujita, T., Yamamoto, S., Tsutsumi, S., Nonaka, A., Yoshiba, S., Matsusaka, K., Midorikawa, Y., Ishikawa, S., Soejima, H., Fukayama, M., Suemori, H., Nakatsuji, N., Kume, S., and Aburatani, H. (2011). Tissue-specific demethylation in CpG-poor promoters during cellular differentiation. Hum. Mol. Genet. 20, 2710–2721.
| Tissue-specific demethylation in CpG-poor promoters during cellular differentiation.Crossref | GoogleScholarGoogle Scholar | 21505077PubMed |

Nakamura, T., Arai, Y., Umehara, H., Masuhara, M., Kimura, T., Taniguchi, H., Sekimoto, T., Ikawa, M., Yoneda, Y., Okabe, M., Tanaka, S., Shiota, K., and Nakano, T. (2007). PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat. Cell Biol. 9, 64–71.
| PGC7/Stella protects against DNA demethylation in early embryogenesis.Crossref | GoogleScholarGoogle Scholar | 17143267PubMed |

Nakamura, T., Liu, Y.-J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., and Nakano, T. (2012a). PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature 486, 415–419.
| PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos.Crossref | GoogleScholarGoogle Scholar | 22722204PubMed |

Nakamura, T., Liu, Y. J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., and Nakano, T. (2012b). PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature 486, 415–419.
| PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos.Crossref | GoogleScholarGoogle Scholar | 22722204PubMed |

Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D., and Grewal, S. I. (2001). Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113.
| Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly.Crossref | GoogleScholarGoogle Scholar | 11283354PubMed |

Nakazawa, Y., Shimada, A., Noguchi, J., Domeki, I., Kaneko, H., and Kikuchi, K. (2002). Replacement of nuclear protein by histone in pig sperm nuclei during in vitro fertilization. Reproduction 124, 565–572.
| Replacement of nuclear protein by histone in pig sperm nuclei during in vitro fertilization.Crossref | GoogleScholarGoogle Scholar | 12361475PubMed |

Negrón-Perez, V. M., Zhang, Y., and Hansen, P. J. (2017). Single-cell gene expression of the bovine blastocyst. Reproduction 154, 627–644.
| Single-cell gene expression of the bovine blastocyst.Crossref | GoogleScholarGoogle Scholar | 28814615PubMed |

O’Doherty, A. M., O’Shea, L. C., and Fair, T. (2012). Bovine DNA methylation imprints are established in an oocyte size-specific manner, which are coordinated with the expression of the DNMT3 family proteins. Biol. Reprod. 86, 67.
| Bovine DNA methylation imprints are established in an oocyte size-specific manner, which are coordinated with the expression of the DNMT3 family proteins.Crossref | GoogleScholarGoogle Scholar | 22088914PubMed |

Ohki, I., Shimotake, N., Fujita, N., Jee, J., Ikegami, T., Nakao, M., and Shirakawa, M. (2001). Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 105, 487–497.
| Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.Crossref | GoogleScholarGoogle Scholar | 11371345PubMed |

Okano, M., Bell, D. W., Haber, D. A., and Li, E. (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257.
| DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.Crossref | GoogleScholarGoogle Scholar | 10555141PubMed |

Olson, C. K., Keppler-Noreuil, K. M., Romitti, P. A., Budelier, W. T., Ryan, G., Sparks, A. E., and Van Voorhis, B. J. (2005). In vitro fertilization is associated with an increase in major birth defects. Fertil. Steril. 84, 1308–1315.
| In vitro fertilization is associated with an increase in major birth defects.Crossref | GoogleScholarGoogle Scholar | 16275219PubMed |

Otoi, T., Yamamoto, K., Koyama, N., Tachikawa, S., and Suzuki, T. (1997). Bovine oocyte diameter in relation to developmental competence. Theriogenology 48, 769–774.
| Bovine oocyte diameter in relation to developmental competence.Crossref | GoogleScholarGoogle Scholar | 16728170PubMed |

Palma, G. A., Arganaraz, M. E., Barrera, A. D., Rodler, D., Mutto, A. A., and Sinowatz, F. (2012). Biology and biotechnology of follicle development. ScientificWorldJournal 2012, 938138.
| Biology and biotechnology of follicle development.Crossref | GoogleScholarGoogle Scholar | 22666170PubMed |

Pavani, K. C., Rocha, A., Baron, E., Lourenco, J., Faheem, M., and da Silva, F. M. (2017). The effect of kinetic heat shock on bovine oocyte maturation and subsequent gene expression of targeted genes. Zygote 25, 383–389.
| The effect of kinetic heat shock on bovine oocyte maturation and subsequent gene expression of targeted genes.Crossref | GoogleScholarGoogle Scholar | 28592345PubMed |

Pillai, R. S., Bhattacharyya, S. N., Artus, C. G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., and Filipowicz, W. (2005). Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309, 1573–1576.
| Inhibition of translational initiation by Let-7 MicroRNA in human cells.Crossref | GoogleScholarGoogle Scholar | 16081698PubMed |

Poleshko, A., Mansfield, K. M., Burlingame, C. C., Andrake, M. D., Shah, N. R., and Katz, R. A. (2013). The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. Cell Rep. 5, 292–301.
| The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit.Crossref | GoogleScholarGoogle Scholar | 24209742PubMed |

Pontes, J. H., Silva, K. C., Basso, A. C., Rigo, A. G., Ferreira, C. R., Santos, G. M., Sanches, B. V., Porcionato, J. P., Vieira, P. H., Faifer, F. S., Sterza, F. A., Schenk, J. L., and Seneda, M. M. (2010). Large-scale in vitro embryo production and pregnancy rates from Bos taurus, Bos indicus, and indicus-taurus dairy cows using sexed sperm. Theriogenology 74, 1349–1355.
| Large-scale in vitro embryo production and pregnancy rates from Bos taurus, Bos indicus, and indicus-taurus dairy cows using sexed sperm.Crossref | GoogleScholarGoogle Scholar | 20708245PubMed |

Popp, C., Dean, W., Feng, S., Cokus, S. J., Andrews, S., Pellegrini, M., Jacobsen, S. E., and Reik, W. (2010). Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105.
| Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.Crossref | GoogleScholarGoogle Scholar | 20098412PubMed |

Ptak, G., Matsukawa, K., Palmieri, C., Della Salda, L., Scapolo, P. A., and Loi P. (2006). Developmental and functional evidence of nuclear immaturity in prepubertal oocytes. Hum Reprod. 21, 2228–223710.1093/HUMREP/DEL184

Purdue Extension (2003). Estimating genetic merit. Available at: https://www.extension.purdue.edu/extmedia/nsif/nsif-8.pdf [verified 22 October 2019]

Qian, C., Li, S., Jakoncic, J., Zeng, L., Walsh, M. J., and Zhou, M. M. (2008). Structure and hemimethylated CpG binding of the SRA domain from human UHRF1. J. Biol. Chem. 283, 34490–34494.
| Structure and hemimethylated CpG binding of the SRA domain from human UHRF1.Crossref | GoogleScholarGoogle Scholar | 18945682PubMed |

Reese, K. J., Lin, S., Verona, R. I., Schultz, R. M., and Bartolomei, M. S. (2007). Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genet. 3, e137.
| Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3.Crossref | GoogleScholarGoogle Scholar | 17708683PubMed |

Riggs, A. D. (1975). X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14, 9–25.
| X inactivation, differentiation, and DNA methylation.Crossref | GoogleScholarGoogle Scholar | 1093816PubMed |

Rivera, R. M., Stein, P., Weaver, J. R., Mager, J., Schultz, R. M., and Bartolomei, M. S. (2008). Manipulations of mouse embryos prior to implantation result in aberrant expression of imprinted genes on Day 9.5 of development. Hum. Mol. Genet. 17, 1–14.
| Manipulations of mouse embryos prior to implantation result in aberrant expression of imprinted genes on Day 9.5 of development.Crossref | GoogleScholarGoogle Scholar | 17901045PubMed |

Rizos, D., Lonergan, P., Boland, M., Arroyo-Garcia, R., Pintado, B., Fuente, J. l., and Gutiérrez-Adán, A. (2002). Analysis of differential messenger RNA expression between bovine blastocysts produced in different culture systems: implications for blastocyst quality. Biol. Reprod. 66, 589–595.
| Analysis of differential messenger RNA expression between bovine blastocysts produced in different culture systems: implications for blastocyst quality.Crossref | GoogleScholarGoogle Scholar | 11870062PubMed |

Rizos, D., Gutiérrez-Adán, A., Perez-Garnelo, S., De La Fuente, J., Boland, M., and Lonergan, P. (2003). Bovine embryo culture in the presence or absence of serum: implications for blastocyst development, cryotolerance, and messenger RNA expression. Biol. Reprod. 68, 236–243.
| Bovine embryo culture in the presence or absence of serum: implications for blastocyst development, cryotolerance, and messenger RNA expression.Crossref | GoogleScholarGoogle Scholar | 12493719PubMed |

Robertson, K. D. (2005). DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610.
| DNA methylation and human disease.Crossref | GoogleScholarGoogle Scholar | 16136652PubMed |

Rodriguez-Osorio, N., Wang, H., Rupinski, J., Bridges, S. M., and Memili, E. (2010). Comparative functional genomics of mammalian DNA methyltransferases. Reprod. Biomed. Online 20, 243–255.
| Comparative functional genomics of mammalian DNA methyltransferases.Crossref | GoogleScholarGoogle Scholar | 20113962PubMed |

Russell, D. F., and Betts, D. H. (2008). Alternative splicing and expression analysis of bovine DNA methyltransferase 1. Dev. Dyn. 237, 1051–1059.
| Alternative splicing and expression analysis of bovine DNA methyltransferase 1.Crossref | GoogleScholarGoogle Scholar | 18297739PubMed |

Saksouk, N., Simboeck, E., and Dejardin, J. (2015). Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin 8, 3.
| Constitutive heterochromatin formation and transcription in mammals.Crossref | GoogleScholarGoogle Scholar | 25788984PubMed |

Scheer, S., and Zaph, C. (2017). The lysine methyltransferase G9a in immune cell differentiation and function. Front. Immunol. 8, 429.
| The lysine methyltransferase G9a in immune cell differentiation and function.Crossref | GoogleScholarGoogle Scholar | 28443098PubMed |

Schwartz, Y. B., Kahn, T. G., Nix, D. A., Li, X. Y., Bourgon, R., Biggin, M., and Pirrotta, V. (2006). Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38, 700–705.
| Genome-wide analysis of Polycomb targets in Drosophila melanogaster.Crossref | GoogleScholarGoogle Scholar | 16732288PubMed |

Seggerson, K., Tang, L., and Moss, E. G. (2002). Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243, 215–225.
| Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation.Crossref | GoogleScholarGoogle Scholar | 11884032PubMed |

Sharif, J., Muto, M., Takebayashi, S., Suetake, I., Iwamatsu, A., Endo, T. A., Shinga, J., Mizutani-Koseki, Y., Toyoda, T., Okamura, K., Tajima, S., Mitsuya, K., Okano, M., and Koseki, H. (2007). The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912.
| The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA.Crossref | GoogleScholarGoogle Scholar | 17994007PubMed |

Sillaste, G., Kaplinski, L., Meier, R., Jaakma, U., Eriste, E., and Salumets, A. (2017). A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa. Reproduction 153, 241–251.
| A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa.Crossref | GoogleScholarGoogle Scholar | 27899719PubMed |

Sinclair, K. D., McEvoy, T. G., Maxfield, E. K., Maltin, C. A., Young, L. E., Wilmut, I., Broadbent, P. J., and Robinson, J. J. (1999). Aberrant fetal growth and development after in vitro culture of sheep zygotes. J. Reprod. Fertil. 116, 177–186.
| Aberrant fetal growth and development after in vitro culture of sheep zygotes.Crossref | GoogleScholarGoogle Scholar | 10505068PubMed |

Sirard, M. A. (2018). 40 years of bovine IVF in the new genomic selection context. Reproduction 156, R1–R7.
| 40 years of bovine IVF in the new genomic selection context.Crossref | GoogleScholarGoogle Scholar | 29636405PubMed |

Smallwood, S. A., and Kelsey, G. (2012). De novo DNA methylation: a germ cell perspective. Trends Genet. 28, 33–42.
| De novo DNA methylation: a germ cell perspective.Crossref | GoogleScholarGoogle Scholar | 22019337PubMed |

Smallwood, S. A., Tomizawa, S., Krueger, F., Ruf, N., Carli, N., Segonds-Pichon, A., Sato, S., Hata, K., Andrews, S. R., and Kelsey, G. (2011). Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat. Genet. 43, 811–814.
| Dynamic CpG island methylation landscape in oocytes and preimplantation embryos.Crossref | GoogleScholarGoogle Scholar | 21706000PubMed |

Smith, S. L., Everts, R. E., Sung, L. Y., Du, F., Page, R. L., Henderson, B., Rodriguez‐Zas, S. L., Nedambale, T. L., Renard, J. P., and Lewin, H. A. (2009). Gene expression profiling of single bovine embryos uncovers significant effects of in vitro maturation, fertilization and culture. Mol. Reprod. Dev. 76, 38–47.
| Gene expression profiling of single bovine embryos uncovers significant effects of in vitro maturation, fertilization and culture.Crossref | GoogleScholarGoogle Scholar | 18449896PubMed |

Soares, L. M., He, P. C., Chun, Y., Suh, H., Kim, T., and Buratowski, S. (2017). Determinants of histone H3K4 methylation patterns. Mol. Cell 68, 773–785.e6.
| Determinants of histone H3K4 methylation patterns.Crossref | GoogleScholarGoogle Scholar | 29129639PubMed |

Song, J., Rechkoblit, O., Bestor, T. H., and Patel, D. J. (2011). Structure of DNMT1–DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 1036–1040.
| Structure of DNMT1–DNA complex reveals a role for autoinhibition in maintenance DNA methylation.Crossref | GoogleScholarGoogle Scholar | 21163962PubMed |

Stegle, O., Teichmann, S. A., and Marioni, J. C. (2015). Computational and analytical challenges in single-cell transcriptomics. Nat. Rev. Genet. 16, 133–145.
| Computational and analytical challenges in single-cell transcriptomics.Crossref | GoogleScholarGoogle Scholar | 25628217PubMed |

Strichman-Almashanu, L. Z., Lee, R. S., Onyango, P. O., Perlman, E., Flam, F., Frieman, M. B., and Feinberg, A. P. (2002). A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res. 12, 543–554.
| A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes.Crossref | GoogleScholarGoogle Scholar | 11932239PubMed |

Sugimura, S., Akai, T., and Imai, K. (2017). Selection of viable in vitro-fertilized bovine embryos using time-lapse monitoring in microwell culture dishes. J. Reprod. Dev. 63, 353–357.
| Selection of viable in vitro-fertilized bovine embryos using time-lapse monitoring in microwell culture dishes.Crossref | GoogleScholarGoogle Scholar | 28552887PubMed |

Surani, M. A., Barton, S. C., and Norris, M. L. (1984). Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308, 548–550.
| Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis.Crossref | GoogleScholarGoogle Scholar | 6709062PubMed |

Takahashi, M., Goto, T., Tsuchiya, H., Ueki, A., and Kawahata, K. (2005). Ultrasonographic monitoring of nuclear transferred fetal weight during the final stage of gestation in Holstein cows. J. Vet. Med. Sci. 67, 807–811.
| Ultrasonographic monitoring of nuclear transferred fetal weight during the final stage of gestation in Holstein cows.Crossref | GoogleScholarGoogle Scholar | 16141668PubMed |

Takai, D., and Jones, P. A. (2002). Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl Acad. Sci. USA 99, 3740–3745.
| Comprehensive analysis of CpG islands in human chromosomes 21 and 22.Crossref | GoogleScholarGoogle Scholar | 11891299PubMed |

Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A., and Tajima, S. (2011). Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). Proc. Natl Acad. Sci. USA 108, 9055–9059.
| Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).Crossref | GoogleScholarGoogle Scholar | 21518897PubMed |

Tamura, H., Takasaki, A., Miwa, I., Taniguchi, K., Maekawa, R., Asada, H., Taketani, T., Matsuoka, A., Yamagata, Y., Shimamura, K., Morioka, H., Ishikawa, H., Reiter, R. J., and Sugino, N. (2008). Oxidative stress impairs oocyte quality and melatonin protects oocytes from free radical damage and improves fertilization rate. J. Pineal Res. 44, 280–287.
| Oxidative stress impairs oocyte quality and melatonin protects oocytes from free radical damage and improves fertilization rate.Crossref | GoogleScholarGoogle Scholar | 18339123PubMed |

Terranova, R., Yokobayashi, S., Stadler, M. B., Otte, A. P., van Lohuizen, M., Orkin, S. H., and Peters, A. H. (2008). Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev. Cell 15, 668–679.
| Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos.Crossref | GoogleScholarGoogle Scholar | 18848501PubMed |

Thélie, A., Papillier, P., Pennetier, S., Perreau, C., Traverso, J. M., Uzbekova, S., Mermillod, P., Joly, C., Humblot, P., and Dalbies-Tran, R. (2007). Differential regulation of abundance and deadenylation of maternal transcripts during bovine oocyte maturation in vitro and in vivo. BMC Dev. Biol. 7, 125.
| Differential regulation of abundance and deadenylation of maternal transcripts during bovine oocyte maturation in vitro and in vivo.Crossref | GoogleScholarGoogle Scholar | 17988387PubMed |

Thompson, J. G., Allen, N. W., McGowan, L. T., Bell, A. C. S., Lambert, M. G., and Tervit, H. R. (1998). Effect of delayed supplementation of fetal calf serum to culture medium on bovine embryo development in vitro and following transfer. Theriogenology 49, 1239–1249.
| Effect of delayed supplementation of fetal calf serum to culture medium on bovine embryo development in vitro and following transfer.Crossref | GoogleScholarGoogle Scholar | 10732061PubMed |

Tian, X., Wang, F., He, C., Zhang, L., Tan, D., Reiter, R. J., Xu, J., Ji, P., and Liu, G. (2014). Beneficial effects of melatonin on bovine oocytes maturation: a mechanistic approach. J. Pineal Res. 57, 239–247.
| Beneficial effects of melatonin on bovine oocytes maturation: a mechanistic approach.Crossref | GoogleScholarGoogle Scholar | 25070516PubMed |

Trojer, P., and Reinberg, D. (2007). Facultative heterochromatin: is there a distinctive molecular signature? Mol. Cell 28, 1–13.
| Facultative heterochromatin: is there a distinctive molecular signature?Crossref | GoogleScholarGoogle Scholar | 17936700PubMed |

Turk, P. W., Laayoun, A., Smith, S. S., and Weitzman, S. A. (1995). DNA adduct 8-hydroxyl-2′-deoxyguanosine (8-hydroxyguanine) affects function of human DNA methyltransferase. Carcinogenesis 16, 1253–1255.
| DNA adduct 8-hydroxyl-2′-deoxyguanosine (8-hydroxyguanine) affects function of human DNA methyltransferase.Crossref | GoogleScholarGoogle Scholar | 7767994PubMed |

Ugur, M. R., Kutchy, N. A., de Menezes, E. B., Ul-Husna, A., Haynes, B. P., Uzun, A., Kaya, A., Topper, E., Moura, A., and Memili, E. (2019). Retained acetylated histone four in bull sperm associated with fertility. Front. Vet. Sci. 6, 223.
| Retained acetylated histone four in bull sperm associated with fertility.Crossref | GoogleScholarGoogle Scholar | 31417913PubMed |

Valavanidis, A., Vlachogianni, T., and Fiotakis, C. (2009). 8-Hydroxy-2′-deoxyguanosine (8-OHdG): a critical biomarker of oxidative stress and carcinogenesis. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 27, 120–139.
| 8-Hydroxy-2′-deoxyguanosine (8-OHdG): a critical biomarker of oxidative stress and carcinogenesis.Crossref | GoogleScholarGoogle Scholar | 19412858PubMed |

Valley, C. M., Pertz, L. M., Balakumaran, B. S., and Willard, H. F. (2006). Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome. Hum. Mol. Genet. 15, 2335–2347.
| Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome.Crossref | GoogleScholarGoogle Scholar | 16787966PubMed |

Van Blerkom, J., and Henry, G. (1992). Oocyte dysmorphism and aneuploidy in meiotically mature human oocytes after ovarian stimulation. Hum. Reprod. 7, 379–390.
| Oocyte dysmorphism and aneuploidy in meiotically mature human oocytes after ovarian stimulation.Crossref | GoogleScholarGoogle Scholar | 1587948PubMed |

Van der Auwera, I., and D’Hooghe, T. (2001). Superovulation of female mice delays embryonic and fetal development. Hum. Reprod. 16, 1237–1243.
| Superovulation of female mice delays embryonic and fetal development.Crossref | GoogleScholarGoogle Scholar | 11387298PubMed |

Van Hoeck, V., Sturmey, R. G., Bermejo-Alvarez, P., Rizos, D., Gutierrez-Adan, A., Leese, H. J., Bols, P. E., and Leroy, J. L. (2011). Elevated non-esterified fatty acid concentrations during bovine oocyte maturation compromise early embryo physiology. PLoS One 6, e23183.
| Elevated non-esterified fatty acid concentrations during bovine oocyte maturation compromise early embryo physiology.Crossref | GoogleScholarGoogle Scholar | 21858021PubMed |

van Wagtendonk-de Leeuw, A. M., Aerts, B. J., and den Daas, J. H. (1998). Abnormal offspring following in vitro production of bovine preimplantation embryos: a field study. Theriogenology 49, 883–894.
| Abnormal offspring following in vitro production of bovine preimplantation embryos: a field study.Crossref | GoogleScholarGoogle Scholar | 10732097PubMed |

van Wagtendonk-de Leeuw, A. M., Mullaart, E., de Roos, A. P., Merton, J. S., den Daas, J. H., Kemp, B., and de Ruigh, L. (2000). Effects of different reproduction techniques: AI MOET or IVP, on health and welfare of bovine offspring. Theriogenology 53, 575–597.
| Effects of different reproduction techniques: AI MOET or IVP, on health and welfare of bovine offspring.Crossref | GoogleScholarGoogle Scholar | 10735051PubMed |

Verona, R. I., Mann, M. R., and Bartolomei, M. S. (2003). Genomic imprinting: intricacies of epigenetic regulation in clusters. Annu. Rev. Cell Dev. Biol. 19, 237–259.
| Genomic imprinting: intricacies of epigenetic regulation in clusters.Crossref | GoogleScholarGoogle Scholar | 14570570PubMed |

Viana, J. H. M., Silva Figueiredo, A. C., and Siqueira, L. G. B. (2017). Brazilian embryo industry in context: pitfalls, lessons, and expectations for the future. Anim. Reprod. 14, 476–481.
| Brazilian embryo industry in context: pitfalls, lessons, and expectations for the future.Crossref | GoogleScholarGoogle Scholar |

Vojtech, L., Woo, S., Hughes, S., Levy, C., Ballweber, L., Sauteraud, R. P., Strobl, J., Westerberg, K., Gottardo, R., Tewari, M., and Hladik, F. (2014). Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. Nucleic Acids Res. 42, 7290–7304.
| Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.Crossref | GoogleScholarGoogle Scholar | 24838567PubMed |

Voon, H. P., and Wong, L. H. (2016). New players in heterochromatin silencing: histone variant H3.3 and the ATRX/DAXX chaperone. Nucleic Acids Res. 44, 1496–1501.
| New players in heterochromatin silencing: histone variant H3.3 and the ATRX/DAXX chaperone.Crossref | GoogleScholarGoogle Scholar | 26773061PubMed |

Wakefield, R. I., Smith, B. O., Nan, X., Free, A., Soteriou, A., Uhrin, D., Bird, A. P., and Barlow, P. N. (1999). The solution structure of the domain from MeCP2 that binds to methylated DNA. J. Mol. Biol. 291, 1055–1065.
| The solution structure of the domain from MeCP2 that binds to methylated DNA.Crossref | GoogleScholarGoogle Scholar | 10518942PubMed |

Walker, S. K., Hartwich, K. M., and Seamark, R. F. (1996). The production of unusually large offspring following embryo manipulation: concepts and challenges. Theriogenology 45, 111–120.
| The production of unusually large offspring following embryo manipulation: concepts and challenges.Crossref | GoogleScholarGoogle Scholar |

Walsh, C. P., Chaillet, J. R., and Bestor, T. H. (1998). Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117.
| Transcription of IAP endogenous retroviruses is constrained by cytosine methylation.Crossref | GoogleScholarGoogle Scholar | 9771701PubMed |

Ward, W. S., and Coffey, D. S. (1991). DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells. Biol. Reprod. 44, 569–574.
| DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells.Crossref | GoogleScholarGoogle Scholar | 2043729PubMed |

Weitzman, S. A., Turk, P. W., Milkowski, D. H., and Kozlowski, K. (1994). Free radical adducts induce alterations in DNA cytosine methylation. Proc. Natl Acad. Sci. USA 91, 1261–1264.
| Free radical adducts induce alterations in DNA cytosine methylation.Crossref | GoogleScholarGoogle Scholar | 8108398PubMed |

Willett, E. L., Black, W. G., Casida, L. E., Stone, W. H., and Buckner, P. J. (1951). Successful transplantation of a fertilized bovine ovum. Science 113, 247.
| Successful transplantation of a fertilized bovine ovum.Crossref | GoogleScholarGoogle Scholar | 14809298PubMed |

Wrenzycki, C., Herrmann, D., Carnwath, J., and Niemann, H. (1999). Alterations in the relative abundance of gene transcripts in preimplantation bovine embryos cultured in medium supplemented with either serum or PVA. Mol. Reprod. Dev. 53, 8–18.
| Alterations in the relative abundance of gene transcripts in preimplantation bovine embryos cultured in medium supplemented with either serum or PVA.Crossref | GoogleScholarGoogle Scholar | 10230812PubMed |

Wrenzycki, C., Herrmann, D., Keskintepe, L., Martins, A., Sirisathien, S., Brackett, B., and Niemann, H. (2001). Effects of culture system and protein supplementation on mRNA expression in pre-implantation bovine embryos. Hum. Reprod. 16, 893–901.
| Effects of culture system and protein supplementation on mRNA expression in pre-implantation bovine embryos.Crossref | GoogleScholarGoogle Scholar | 11331635PubMed |

Wu, X., and Zhang, Y. (2017). TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534.
| TET-mediated active DNA demethylation: mechanism, function and beyond.Crossref | GoogleScholarGoogle Scholar | 28555658PubMed |

Wu, L., Fan, J., and Belasco, J. G. (2006). MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 103, 4034–4039.
| MicroRNAs direct rapid deadenylation of mRNA.Crossref | GoogleScholarGoogle Scholar | 16495412PubMed |

Wu, H., Min, J., Lunin, V. V., Antoshenko, T., Dombrovski, L., Zeng, H., Allali-Hassani, A., Campagna-Slater, V., Vedadi, M., Arrowsmith, C. H., Plotnikov, A. N., and Schapira, M. (2010). Structural biology of human H3K9 methyltransferases. PLoS One 5, e8570.
| Structural biology of human H3K9 methyltransferases.Crossref | GoogleScholarGoogle Scholar | 21209959PubMed |

Yamada, Y., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Sakaki, Y., and Ito, T. (2004). A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res. 14, 247–266.
| A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q.Crossref | GoogleScholarGoogle Scholar | 14762061PubMed |

Yang, X., Kubota, C., Suzuki, H., Taneja, M., Bols, P. E. J., and Presicce, G. A. (1998). Control of oocyte maturation in cows – Biological factors. Theriogenology 49, 471–48210.1016/S0093-691X(97)00419-6

Yi, R., Qin, Y., Macara, I. G., and Cullen, B. R. (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011–3016.
| Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs.Crossref | GoogleScholarGoogle Scholar | 14681208PubMed |

Young, L. E., Sinclair, K. D., and Wilmut, I. (1998). Large offspring syndrome in cattle and sheep. Rev. Reprod. 3, 155–163.
| Large offspring syndrome in cattle and sheep.Crossref | GoogleScholarGoogle Scholar | 9829550PubMed | 9829550PubMed |

Young, L. E., Fernandes, K., McEvoy, T. G., Butterwith, S. C., Gutierrez, C. G., Carolan, C., Broadbent, P. J., Robinson, J. J., Wilmut, I., and Sinclair, K. D. (2001). Epigenetic change in IGF2R is associated with fetal overgrowth after sheep embryo culture. Nat. Genet. 27, 153–154.
| Epigenetic change in IGF2R is associated with fetal overgrowth after sheep embryo culture.Crossref | GoogleScholarGoogle Scholar | 11175780PubMed | 11175780PubMed |

Zhao, Y., and Garcia, B. A. (2015). Comprehensive catalog of currently documented histone modifications. Cold Spring Harb. Perspect. Biol. 7, a025064.
| Comprehensive catalog of currently documented histone modifications.Crossref | GoogleScholarGoogle Scholar | 26330523PubMed | 26330523PubMed |

Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J., and Lee, J. T. (2008). Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750–756.
| Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome.Crossref | GoogleScholarGoogle Scholar | 18974356PubMed | 18974356PubMed |

Zhao, X. M., Wang, N., Hao, H. S., Li, C. Y., Zhao, Y. H., Yan, C. L., Wang, H. Y., Du, W. H., Wang, D., Liu, Y., Pang, Y. W., and Zhu, H. B. (2018). Melatonin improves the fertilization capacity and developmental ability of bovine oocytes by regulating cytoplasmic maturation events. J. Pineal Res. 64, e12445.
| Melatonin improves the fertilization capacity and developmental ability of bovine oocytes by regulating cytoplasmic maturation events.Crossref | GoogleScholarGoogle Scholar | 28833478PubMed | 28833478PubMed |

Ziller, M. J., Muller, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Boyle, P., Epstein, C. B., Bernstein, B. E., Lengauer, T., Gnirke, A., and Meissner, A. (2011). Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 7, e1002389.
| Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.Crossref | GoogleScholarGoogle Scholar | 22174693PubMed | 22174693PubMed |

Zou, X., Ma, W., Solov’yov, I. A., Chipot, C., and Schulten, K. (2012). Recognition of methylated DNA through methyl-CpG binding domain proteins. Nucleic Acids Res. 40, 2747–2758.
| Recognition of methylated DNA through methyl-CpG binding domain proteins.Crossref | GoogleScholarGoogle Scholar | 22110028PubMed | 22110028PubMed |