Eckert JJ, Fleming TP: Tight junction biogenesis during early development. Biochim Biophys Acta. 2008, 1778: 717-728. 10.1016/j.bbamem.2007.09.031.
Article
CAS
Google Scholar
Marikawa Y, Alarcón VB: Establishment of trophectoderm and inner cell mass lineages in the mouse embryo. Mol Reprod Dev. 2009, 76: 1019-1032. 10.1002/mrd.21057.
Article
PubMed Central
CAS
Google Scholar
Zernicka-Goetz M, Morris SA, Bruce AW: Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo. Nature Rev. 2009, 10: 467-477.
Article
CAS
Google Scholar
Rossant J, Tam PPL: Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Development. 2009, 136: 701-713. 10.1242/dev.017178.
Article
CAS
Google Scholar
Plachta N, Bollenbach T, Pease S, Fraser SE, Pantazis P: Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nat Cell Biol. 2011, 13: 117-123. 10.1038/ncb2154.
Article
CAS
Google Scholar
Berg DK, Smith CS, Pearton DJ, Wells DN, Broadhurst R, Donnison M, Pfeffer PL: Trophectoderm lineage determination in cattle. Dev Cell. 2011, 20: 244-255. 10.1016/j.devcel.2011.01.003.
Article
CAS
Google Scholar
Chen L, Wang D, Wu Z, Ma L, Daley GQ: Molecular basis of the first cell fate determination in mouse embryogenesis. Cell Res. 2010, 20: 982-993. 10.1038/cr.2010.106.
Article
CAS
Google Scholar
Gasperowicz M, Natale DR: Establishing three blastocyst lineages–then what?. Biol Reprod. 2011, 84: 621-630. 10.1095/biolreprod.110.085209.
Article
CAS
Google Scholar
Ozawa M, Hansen PJ: A novel method for purification of inner cell mass and trophectoderm cells from blastocysts using magnetic activated cell sorting. Fertil Steril. 2011, 95: 799-802. 10.1016/j.fertnstert.2010.10.006.
Article
Google Scholar
Loureiro B, Bonilla L, Block J, Fear JM, Bonilla AQS, Hansen PJ: Colony-stimulating factor 2 (CSF-2) improves development and posttransfer survival of bovine embryos produced in vitro. Endocrinology. 2009, 150: 5046-5054. 10.1210/en.2009-0481.
Article
PubMed Central
CAS
Google Scholar
Fields SD, Hansen PJ, Ealy AD: Fibroblast growth factor requirement for in vitro development of bovine embryos. Theriogenology. 2011, 75: 1466-1475. 10.1016/j.theriogenology.2010.12.007.
Article
CAS
Google Scholar
Zhang J, Chiodini R, Badr A, Zhang G: The impact of next-generation sequencing on genomics. J Genet Genom. 2011, 38: 95-109. 10.1016/j.jgg.2011.02.003.
Article
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25: 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10: R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
Google Scholar
Homer N, Merriman B, Nelson S: BFAST: An alignment tool for large scale genome resequencing. PLoS One. 2009, 4: e7767-10.1371/journal.pone.0007767.
Article
PubMed Central
Google Scholar
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11: R106-10.1186/gb-2010-11-10-r106.
Article
PubMed Central
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37: 1-13. 10.1093/nar/gkn923.
Article
PubMed Central
Google Scholar
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P: iPath2.0: interactive pathway explorer. Nucl Acids Res. 2011, 39: W412-W415. 10.1093/nar/gkr313.
Article
PubMed Central
CAS
Google Scholar
Liang J, Zhang L, Xiang Z, He N: Expression profile of cuticular genes of silkworm Bombyx mori. BMC Genom. 2010, 11: 173-10.1186/1471-2164-11-173.
Article
Google Scholar
Dash R, Mishra D, Rath AK, Acharya M: A hybridized K-means clustering approach for high dimensional dataset. Int J Eng Sci Tech. 2011, 2: 59-66.
Google Scholar
Wasserman WW, Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004, 5: 276-287. 10.1038/nrg1315.
Article
CAS
Google Scholar
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucl Acids Res. 2010, 38: D105-D110. 10.1093/nar/gkp950.
Article
PubMed Central
CAS
Google Scholar
Wingender E: The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform. 2008, 9: 326-332. 10.1093/bib/bbn016.
Article
CAS
Google Scholar
Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol. 1987, 196: 261-282. 10.1016/0022-2836(87)90689-9.
Article
CAS
Google Scholar
Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, Denise S, Wiggans GR, Sonstegard TS, Van Tassell CP, Liu GE: Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics. 2012, 13: 376-10.1186/1471-2164-13-376.
Article
PubMed Central
CAS
Google Scholar
Smith CS, Berg DK, Berg M, Pfeffer PL: Nuclear transfer-specific defects are not apparent during the second week of embryogenesis in cattle. Cell Reprogram. 2010, 12: 699-707. 10.1089/cell.2010.0040.
Article
CAS
Google Scholar
Ozawa M, Sakatani M, Hankowski KE, Terada N, Dobbs KB, Hansen PJ: Importance of culture conditions during the morula-to-blastocyst period on capacity of inner cell-mass cells of bovine blastocysts for establishment of self-renewing pluripotent cells. Theriogenology. 2012, 78: 1243-1251. 10.1016/j.theriogenology.2012.05.020.
Article
CAS
Google Scholar
Goossens K, Van Poucke M, Van Soom A, Vandesompele J, Van Zeveren A, Peelman LJ: Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos. BMC Dev Biol. 2005, 5: 27-10.1186/1471-213X-5-27.
Article
PubMed Central
Google Scholar
Hamatani T, Daikoku T, Wang H, Matsumoto H, Carter MG, Ko MS, Dey SK: Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc Natl Acad Sci USA. 2004, 101: 10326-10331. 10.1073/pnas.0402597101.
Article
PubMed Central
CAS
Google Scholar
Saitou M, Yabuta Y, Kurimoto K: Single-cell cDNA high-density oligonucleotide microarray analysis: detection of individual cell types and properties in complex biological processes. Reprod Biomed Online. 2008, 16: 26-40. 10.1016/S1472-6483(10)60554-8.
Article
CAS
Google Scholar
Tesar PJ, Chenoweth JG, Brook FA, Davies TJ, Evans EP, et al: New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature. 2007, 448: 196-199. 10.1038/nature05972.
Article
CAS
Google Scholar
Chou Y-F, Chen H-H, Eijpe M, Yabuuchi A, Chenoweth JG, et al: The growth factor environment defines distinct pluripotent ground states in novel blastocyst-derived stem cells. Cell. 2008, 135: 449-461. 10.1016/j.cell.2008.08.035.
Article
PubMed Central
CAS
Google Scholar
Adjaye J, Huntriss J, Herwig R, BenKahla A, Brink TC, et al: Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells. 2005, 23: 1514-1525. 10.1634/stemcells.2005-0113.
Article
CAS
Google Scholar
Edwards RG, Hansis C: Initial differentiation of blastomeres in 4-cell human embryos and its significance for early embryogenesis and implantation. Reprod Biomed Online. 2005, 11: 206-218. 10.1016/S1472-6483(10)60960-1.
Article
Google Scholar
Kimber SJ, Sneddon S, Bloor DJ, El-Bareg AM, Hawkhead JA, et al: Expression of genes involved in early cell fate decisions in human embryos and their regulation by growth factors. Reproduction. 2008, 135: 635-647. 10.1530/REP-07-0359.
Article
CAS
Google Scholar
Cauffman G, De Rycke M, Sermon K, Liebaers I, Van de Velde H: Markers that define stemness in ESC are unable to identify the totipotent cells in human preimplantation embryos. Hum Reprod. 2009, 24: 63-70.
Article
CAS
Google Scholar
Reijo Pera RA, DeJonge C, Bossert N, Yao M, Hwa Yang JY, Asadi NB, Wong W, Wong C, Firpo MT: Gene expression profiles of human inner cell mass cells and embryonic stem cells. Differentiation. 2009, 78: 18-23. 10.1016/j.diff.2009.03.004.
Article
Google Scholar
Galan A, Simon C: Monitoring stemness in long-term hESC cultures by real-time PCR. Methods Mol Biol. 2010, 584: 135-150.
Article
CAS
Google Scholar
Roberts RM, Chen Y, Ezashi T, Walker AM: Interferons and the maternal-conceptus dialog in mammals. Semin Cell Dev Biol. 2008, 19: 170-177. 10.1016/j.semcdb.2007.10.007.
Article
PubMed Central
CAS
Google Scholar
Telugu BP, Walker AM, Green JA: Characterization of the bovine pregnancy-associated glycoprotein gene family–analysis of gene sequences, regulatory regions within the promoter and expression of selected genes. BMC Genom. 2009, 10: 185-10.1186/1471-2164-10-185.
Article
Google Scholar
Chakrabarty A, 2nd MacLean JA, Hughes AL, Roberts RM, Green JA: Rapid evolution of the trophoblast kunitz domain proteins (TKDPs)-a multigene family in ruminant ungulates. J Mol Evol. 2006, 63: 274-282. 10.1007/s00239-005-0264-3.
Article
CAS
Google Scholar
Fujii T, Moriyasu S, Hirayama H, Hashizume T, Sawai K: Aberrant expression patterns of genes involved in segregation of inner cell mass and trophectoderm lineages in bovine embryos derived from somatic cell nuclear transfer. Cell Reprogram. 2010, 12: 617-625. 10.1089/cell.2010.0017.
Article
CAS
Google Scholar
Driver AM, Peñagaricano F, Huang W, Ahmad KR, Hackbart KS, Wiltbank MC, Khatib H: RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. BMC Genomics. 2012, 13: 118-10.1186/1471-2164-13-118.
Article
PubMed Central
CAS
Google Scholar
Giritharan G, Delle Piane L, Donjacour A, Esteban FJ, Horcajadas JA, Maltepe E, Rinaudo P: In vitro culture of mouse embryos reduces differential gene expression between inner cell mass and trophectoderm. Reprod Sci. 2012, 19: 243-252. 10.1177/1933719111428522.
Article
PubMed Central
CAS
Google Scholar
Smith AG, Nichols J, Robertson M, Pathjen PD: Differentiation inhibiting activity (DIA/LIF) and mouse development. Dev Biol. 1992, 151: 339-351. 10.1016/0012-1606(92)90174-F.
Article
CAS
Google Scholar
Cao S, Wang F, Chen Z, Liu Z, Mei C, et al: Isolation and culture of primary bovine embryonic stem cell colonies by a novel method. J Exp Zool A Ecol Genet Physiol. 2009, 311: 368-376.
Article
Google Scholar
Meilhac SM, Adams RJ, Morris SA, Danckaert A, Le Garrec JF, Zernicka-Goetz M: Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst. Dev Biol. 2009, 331: 210-221. 10.1016/j.ydbio.2009.04.036.
Article
PubMed Central
CAS
Google Scholar
Morris SA, Teo RT, Li H, Robson P, Glover DM, Zernicka-Goetz M: Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo. Proc Natl Acad Sci USA. 2010, 107: 6364-6369. 10.1073/pnas.0915063107.
Article
PubMed Central
CAS
Google Scholar
Yamanaka Y, Lanner F, Rossant J: FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst. Development. 2010, 137: 715-724. 10.1242/dev.043471.
Article
CAS
Google Scholar
Pearton DJ, Broadhurst R, Donnison M, Pfeffer PL: Elf5 regulation in the trophectoderm. Dev Biol. 2011, 360: 343-350. 10.1016/j.ydbio.2011.10.007.
Article
CAS
Google Scholar
Vasioukhin V, Bowers E, Bauer C, Degenstein L, Fuchs E: Desmoplakin is essential in epidermal sheet formation. Nat Cell Biol. 2011, 3: 1076-1085.
Article
Google Scholar
Morris SM, Tallquist MD, Rock CO, Cooper JA: Dual roles for the Dab2 adaptor protein in embryonic development and kidney transport. EMBO J. 2002, 21: 1555-1564. 10.1093/emboj/21.7.1555.
Article
PubMed Central
CAS
Google Scholar
Fleming TP, Warren PD, Chisholm JC, Johnson MH: Trophectodermal processes regulate the expression of totipotency within the inner cell mass of the mouse expanding blastocyst. J Embryol Exp Morphol. 1984, 84: 63-90.
CAS
Google Scholar
Abe H, Otoi T, Tachikawa S, Yamashita S, Satoh T, Hoshi H: Fine structure of bovine morulae and blastocysts in vivo and in vitro. Anat Embryol. 1999, 199: 519-527. 10.1007/s004290050249.
Article
CAS
Google Scholar
Abe H, Yamashita S, Itoh T, Satoh T, Hoshi H: 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. 1999, 53: 325-335. 10.1002/(SICI)1098-2795(199907)53:3<325::AID-MRD8>3.0.CO;2-T.
Article
CAS
Google Scholar
Bazer FW, Burghardt RC, Johnson GA, Spencer TE, Wu G: Interferons and progesterone for establishment and maintenance of pregnancy: interactions among novel cell signaling pathways. Reprod Biol. 2008, 8: 179-211.
Article
Google Scholar
de Moraes AA, Davidson JA, Fleming JG, Bazer FW, Edwards JL, et al: Lack of effect of granulocyte-macrophage colony-stimulating factor on secretion of interferon-τ, other proteins, and prostaglandin E2 by the bovine and ovine conceptus. Domest Anim Endocrinol. 1997, 14: 193-197. 10.1016/S0739-7240(97)00002-7.
Article
CAS
Google Scholar
Green JA, Xie S, Roberts RM: Pepsin-related molecules secreted by trophoblast. Rev Reprod. 1998, 3: 62-69. 10.1530/ror.0.0030062.
Article
CAS
Google Scholar
Seshagiri PB, Sen Roy S, Sireesha G, Rao RP: Cellular and molecular regulation of mammalian blastocyst hatching. J Reprod Immunol. 2009, 83: 79-84. 10.1016/j.jri.2009.06.264.
Article
CAS
Google Scholar
Blomberg L, Hashizume K, Viebahn C: Blastocyst elongation, trophoblastic differentiation, and embryonic pattern formation. Reproduction. 2008, 135: 181-195. 10.1530/REP-07-0355.
Article
CAS
Google Scholar
Gadsby JE, Heap RB, Burton RD: Oestrogen production by blastocyst and early embryonic tissue of various species. J Reprod Fertil. 1980, 60: 409-417. 10.1530/jrf.0.0600409.
Article
CAS
Google Scholar
Betteridge KJ, Flechon J-E: The anatomy and physiology of pre-attachment bovine embryos. Theriogenology. 1988, 29: 155-187. 10.1016/0093-691X(88)90038-6.
Article
Google Scholar
King GJ, Atkinson BA, Robertson HA: Development of the intercaruncular areas during early gestation and establishment of the bovine placenta. J Reprod Fertil. 1981, 61: 469-474. 10.1530/jrf.0.0610469.
Article
CAS
Google Scholar
Balboula AZ, Yamanaka K, Sakatani M, Hegab AO, Zaabel SM, Takahashi M: Intracellular cathepsin B activity is inversely correlated with the quality and developmental competence of bovine preimplantation embryos. Mol Reprod Dev. 2010, 77: 1031-1039. 10.1002/mrd.21250.
Article
CAS
Google Scholar
Marchand M, Horcajadas JA, Esteban FJ, McElroy SL, Fisher SJ, Giudice LC: Transcriptomic signature of trophoblast differentiation in a human embryonic stem cell model. Biol Reprod. 2011, 84: 1258-1271. 10.1095/biolreprod.110.086413.
Article
CAS
Google Scholar
Muggia A, Teesalu T, Neri A, Blasi F, Talarico D: Trophoblast giant cells express NF-κB2 during early mouse development. Dev Genet. 1999, 25: 23-30. 10.1002/(SICI)1520-6408(1999)25:1<23::AID-DVG3>3.0.CO;2-K.
Article
CAS
Google Scholar
Wilson A, Laurenti E, Trumpp A: Balancing dormant and self-renewing hematopoietic stem cells. Curr Opin Genet Dev. 2009, 19: 461-368. 10.1016/j.gde.2009.08.005.
Article
CAS
Google Scholar
Yu S, Cui K, Jothi R, Zhao DM, Jing X, et al: GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells. Blood. 2011, 117: 2166-2178. 10.1182/blood-2010-09-306563.
Article
PubMed Central
CAS
Google Scholar
Hromas R, Davis B, Rauscher FJ, Klemsz M, Tenen D, et al: Hematopoietic transcriptional regulation by the myeloid zinc finger gene, MZF-1. Curr Top Microbiol Immunol. 1996, 211: 159-164. 10.1007/978-3-642-85232-9_16.
CAS
Google Scholar
Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, et al: Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell. 2007, 129: 345-357. 10.1016/j.cell.2007.03.014.
Article
PubMed Central
CAS
Google Scholar
Kinoshita K, Ura H, Akagi T, Usuda M, Koide H, Yokota T: GABPα regulates Oct-3/4 expression in mouse embryonic stem cells. Biochem Biophys Res Commun. 2007, 353: 686-691. 10.1016/j.bbrc.2006.12.071.
Article
CAS
Google Scholar
Papp B, Plath K: Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. Cell Res. 2011, 21: 486-501. 10.1038/cr.2011.28.
Article
PubMed Central
CAS
Google Scholar
Li M, Kellems RE: Sp1 and Sp3 Are important regulators of AP-2γ gene transcription. Biol Reprod. 2003, 69: 1220-1230. 10.1095/biolreprod.103.015545.
Article
CAS
Google Scholar
Takeda T, Sakata M, Isobe A, Yamamoto T, Nishimoto F, et al: Involvement of Sp-1 in the regulation of the Id-1 gene during trophoblast cell differentiation. Placenta. 2007, 28: 192-198. 10.1016/j.placenta.2006.03.002.
Article
CAS
Google Scholar
Degrelle SA, Murthi P, Evain-Brion D, Fournier T, Hue I: Expression and localization of DLX3, PPARG and SP1 in bovine trophoblast during binucleated cell differentiation. Placenta. 2011, 32: 917-920. 10.1016/j.placenta.2011.08.014.
Article
CAS
Google Scholar
Niemann H, Carnwath JW, Herrmann D, Wieczorek G, Lemme E, et al: DNA methylation patterns reflect epigenetic reprogramming in bovine embryos. Cell Reprogram. 2010, 12: 33-42. 10.1089/cell.2009.0063.
Article
CAS
Google Scholar
Jurkowska RZ, Jurkowski TP, Jeltsch A: Structure and function of mammalian DNA methyltransferases. ChemBioChem. 2011, 12: 206-222. 10.1002/cbic.201000195.
Article
CAS
Google Scholar
Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, et al: Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc Natl Acad Sci USA. 2011, 98: 13734-13738.
Article
Google Scholar
Hou J, Liu L, Lei T, Cui X, An X, Chen Y: Genomic DNA methylation patterns in bovine preimplantation embryos derived from in vitro fertilization. Sci China C Life Sci. 2007, 50: 56-61. 10.1007/s11427-007-0003-7.
Article
CAS
Google Scholar
Kang YK, Park JS, Koo DB, Choi YH, Kim SU, et al: Limited demethylation leaves mosaic-type methylation states in cloned bovine pre-implantation embryos. EMBO J. 2002, 21: 1092-1100. 10.1093/emboj/21.5.1092.
Article
PubMed Central
CAS
Google Scholar
Ross PJ, Ragina NP, Rodriguez RM, Iager AE, Siripattarapravat K, et al: Polycomb gene expression and histone H3 lysine 27 trimethylation changes during bovine preimplantation development. Reproduction. 2008, 136: 777-785. 10.1530/REP-08-0045.
Article
CAS
Google Scholar
Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, et al: Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006, 439: 811-816. 10.1038/nature04433.
Article
CAS
Google Scholar
Frescas D, Guardavaccaro D, Bassermann F, Koyama-Nasu R, Pagano M: JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature. 2007, 450: 309-313. 10.1038/nature06255.
Article
CAS
Google Scholar