Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst

BMC Developmental Biology

Volumn 12, Issue , 2012, Pages

  Ozawa, Manabu ^a,d   Sakatani, Miki ^c   Yao, Jiqiang ^b   Shanker, Savita ^b   Yu, Fahong ^b   Yamashita, Rui ^d   Wakabayashi, Shunichi ^d   Nakai, Kenta ^d   Dobbs, Kyle B ^a   Sudano, Mateus José ^e   Farmerie, William G ^b   Hansen, Peter J ^a  

^a DH Barron Reproductive and Perinatal Biology Research Program   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c NATIONAL AGRICULTURAL RESEARCH CENTER FOR KYUSHU OKINAWA REGION   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

Blastocyst; Development; Inner cell mass; Trophectoderm

Indexed keywords

BOVINAE; MAMMALIA;

TRANSCRIPTOME;

ANIMAL; ARTICLE; CATTLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; CPG ISLAND; CYTOLOGY; ECTODERM; EMBRYO CULTURE; GENE EXPRESSION REGULATION; HUMAN; INNER CELL MASS; METABOLISM; MOLECULAR GENETICS; MOUSE; PROMOTER REGION; TROPHOBLAST; UPREGULATION;

ANIMALS; BLASTOCYST INNER CELL MASS; CATTLE; CLUSTER ANALYSIS; CPG ISLANDS; ECTODERM; EMBRYO CULTURE TECHNIQUES; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MICE; MOLECULAR SEQUENCE ANNOTATION; PROMOTER REGIONS, GENETIC; TRANSCRIPTOME; TROPHOBLASTS; UP-REGULATION;

EID: 84868274013     PISSN: None     EISSN: 1471213X     Source Type: Journal    
DOI: 10.1186/1471-213X-12-33     Document Type: Article

References (83)

1. Tight junction biogenesis during early development. Eckert JJ, Fleming TP, Biochim Biophys Acta 2008 1778 717 728 10.1016/j.bbamem.2007.09.031 18339299 (Pubitemid 351324816)
2. Establishment of trophectoderm and inner cell mass lineages in the mouse embryo. Marikawa Y, Alarcán VB, Mol Reprod Dev 2009 76 1019 1032 10.1002/mrd.21057 19479991
3. Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo. Zernicka-Goetz M, Morris SA, Bruce AW, Nature Rev 2009 10 467 477
4. Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Rossant J, Tam PPL, Development 2009 136 701 713 10.1242/dev.017178 19201946
5. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Plachta N, Bollenbach T, Pease S, Fraser SE, Pantazis P, Nat Cell Biol 2011 13 117 123 10.1038/ncb2154 21258368
6. Trophectoderm lineage determination in cattle. Berg DK, Smith CS, Pearton DJ, Wells DN, Broadhurst R, Donnison M, Pfeffer PL, Dev Cell 2011 20 244 255 10.1016/j.devcel.2011.01.003 21316591
7. Molecular basis of the first cell fate determination in mouse embryogenesis. Chen L, Wang D, Wu Z, Ma L, Daley GQ, Cell Res 2010 20 982 993 10.1038/cr.2010.106 20628366
8. Establishing three blastocyst lineages-then what? Gasperowicz M, Natale DR, Biol Reprod 2011 84 621 630 10.1095/biolreprod.110.085209 21123814
9. A novel method for purification of inner cell mass and trophectoderm cells from blastocysts using magnetic activated cell sorting. Ozawa M, Hansen PJ, Fertil Steril 2011 95 799 802 10.1016/j.fertnstert.2010.10.006 21055741
10. Colony-stimulating factor 2 (CSF-2) improves development and posttransfer survival of bovine embryos produced in vitro. Loureiro B, Bonilla L, Block J, Fear JM, Bonilla AQS, Hansen PJ, Endocrinology 2009 150 5046 5054 10.1210/en.2009-0481 19797121
11. Fibroblast growth factor requirement for in vitro development of bovine embryos. Fields SD, Hansen PJ, Ealy AD, Theriogenology 2011 75 1466 1475 10.1016/j.theriogenology.2010.12.007 21295834
12. The impact of next-generation sequencing on genomics. Zhang J, Chiodini R, Badr A, Zhang G, J Genet Genom 2011 38 95 109 10.1016/j.jgg.2011.02.003
13. TopHat: Discovering splice junctions with RNA-Seq. Trapnell C, Pachter L, Salzberg SL, Bioinformatics 2009 25 1105 1111 10.1093/bioinformatics/btp120 19289445
14. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead B, Trapnell C, Pop M, Salzberg SL, Genome Biol 2009 10 25 10.1186/gb-2009-10-3-r25 19261174
15. BFAST: An alignment tool for large scale genome resequencing. Homer N, Merriman B, Nelson S, PLoS One 2009 4 7767 10.1371/journal.pone.0007767 19907642
16. Differential expression analysis for sequence count data. Anders S, Huber W, Genome Biol 2010 11 106 10.1186/gb-2010-11-10-r106 20979621
17. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Huang DW, Sherman BT, Lempicki RA, Nucleic Acids Res 2009 37 1 13 10.1093/nar/gkn923 19033363
18. iPath2.0: interactive pathway explorer. Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P, Nucl Acids Res 2011 39 412 W415 10.1093/nar/gkr313 21546551
19. Expression profile of cuticular genes of silkworm Bombyx mori. Liang J, Zhang L, Xiang Z, He N, BMC Genom 2010 11 173 10.1186/1471-2164-11-173
20. A hybridized K-means clustering approach for high dimensional dataset. Dash R, Mishra D, Rath AK, Acharya M, Int J Eng Sci Tech 2011 2 59 66
21. Applied bioinformatics for the identification of regulatory elements. Wasserman WW, Sandelin A, Nat Rev Genet 2004 5 276 287 10.1038/nrg1315 15131651 (Pubitemid 38435623)
22. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al. Nucl Acids Res 2010 38 105 D110 10.1093/nar/gkp950 19906716
23. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Wingender E, Brief Bioinform 2008 9 326 332 10.1093/bib/bbn016 18436575 (Pubitemid 351894493)
24. CpG islands in vertebrate genomes. Gardiner-Garden M, Frommer M, J Mol Biol 1987 196 261 282 10.1016/0022-2836(87)90689-9 3656447 (Pubitemid 17122132)
25. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. 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, BMC Genomics 2012 13 376 10.1186/1471-2164-13-376 22866901
26. Nuclear transfer-specific defects are not apparent during the second week of embryogenesis in cattle. Smith CS, Berg DK, Berg M, Pfeffer PL, Cell Reprogram 2010 12 699 707 10.1089/cell.2010.0040 20973678
27. 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. Ozawa M, Sakatani M, Hankowski KE, Terada N, Dobbs KB, Hansen PJ, Theriogenology 2012 78 1243 1251 10.1016/j.theriogenology. 2012.05.020 22898023
28. Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos. Goossens K, Van Poucke M, Van Soom A, Vandesompele J, Van Zeveren A, Peelman LJ, BMC Dev Biol 2005 5 27 10.1186/1471-213X-5-27 16324220 (Pubitemid 41803274)
29. Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Hamatani T, Daikoku T, Wang H, Matsumoto H, Carter MG, Ko MS, Dey SK, Proc Natl Acad Sci USA 2004 101 10326 10331 10.1073/pnas.0402597101 15232000 (Pubitemid 38924924)
30. Single-cell cDNA high-density oligonucleotide microarray analysis: detection of individual cell types and properties in complex biological processes. Saitou M, Yabuta Y, Kurimoto K, Reprod Biomed Online 2008 16 26 40 10.1016/S1472-6483(10)60554-8 18252045 (Pubitemid 351187371)
31. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Tesar PJ, Chenoweth JG, Brook FA, Davies TJ, Evans EP, et al. Nature 2007 448 196 199 10.1038/nature05972 17597760 (Pubitemid 47067378)
32. The growth factor environment defines distinct pluripotent ground states in novel blastocyst-derived stem cells. Chou Y-F, Chen H-H, Eijpe M, Yabuuchi A, Chenoweth JG, et al. Cell 2008 135 449 461 10.1016/j.cell.2008.08.035 18984157
33. Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Adjaye J, Huntriss J, Herwig R, BenKahla A, Brink TC, et al. Stem Cells 2005 23 1514 1525 10.1634/stemcells.2005-0113 16081659 (Pubitemid 41741000)
34. Initial differentiation of blastomeres in 4-cell human embryos and its significance for early embryogenesis and implantation. Edwards RG, Hansis C, Reprod Biomed Online 2005 11 206 218 10.1016/S1472-6483(10)60960-1 16168219 (Pubitemid 41086947)
35. Expression of genes involved in early cell fate decisions in human embryos and their regulation by growth factors. Kimber SJ, Sneddon S, Bloor DJ, El-Bareg AM, Hawkhead JA, et al. Reproduction 2008 135 635 647 10.1530/REP-07-0359 18411410 (Pubitemid 351676448)
36. Markers that define stemness in ESC are unable to identify the totipotent cells in human preimplantation embryos. Cauffman G, De Rycke M, Sermon K, Liebaers I, Van de Velde H, Hum Reprod 2009 24 63 70 18824471
37. Gene expression profiles of human inner cell mass cells and embryonic stem cells. Reijo Pera RA, DeJonge C, Bossert N, Yao M, Hwa Yang JY, Asadi NB, Wong W, Wong C, Firpo MT, Differentiation 2009 78 18 23 10.1016/j.diff.2009.03. 004 19398262
38. Monitoring stemness in long-term hESC cultures by real-time PCR. Galan A, Simon C, Methods Mol Biol 2010 584 135 150 19907976
39. Interferons and the maternal-conceptus dialog in mammals. Roberts RM, Chen Y, Ezashi T, Walker AM, Semin Cell Dev Biol 2008 19 170 177 10.1016/j.semcdb.2007.10.007 18032074 (Pubitemid 351258373)
40. Characterization of the bovine pregnancy-associated glycoprotein gene family-analysis of gene sequences, regulatory regions within the promoter and expression of selected genes. Telugu BP, Walker AM, Green JA, BMC Genom 2009 10 185 10.1186/1471-2164-10-185
41. Rapid evolution of the trophoblast kunitz domain proteins (TKDPs)-a multigene family in ruminant ungulates. Chakrabarty A, 2nd MacLean JA, Hughes AL, Roberts RM, Green JA, J Mol Evol 2006 63 274 282 10.1007/s00239-005-0264-3 16830095 (Pubitemid 44126982)
42. Aberrant expression patterns of genes involved in segregation of inner cell mass and trophectoderm lineages in bovine embryos derived from somatic cell nuclear transfer. Fujii T, Moriyasu S, Hirayama H, Hashizume T, Sawai K, Cell Reprogram 2010 12 617 625 10.1089/cell.2010.0017 20726774
43. RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. Driver AM, Pẽagaricano F, Huang W, Ahmad KR, Hackbart KS, Wiltbank MC, Khatib H, BMC Genomics 2012 13 118 10.1186/1471-2164-13-118 22452724
44. In vitro culture of mouse embryos reduces differential gene expression between inner cell mass and trophectoderm. Giritharan G, Delle Piane L, Donjacour A, Esteban FJ, Horcajadas JA, Maltepe E, Rinaudo P, Reprod Sci 2012 19 243 252 10.1177/1933719111428522 22383776
45. Differentiation inhibiting activity (DIA/LIF) and mouse development. Smith AG, Nichols J, Robertson M, Pathjen PD, Dev Biol 1992 151 339 351 10.1016/0012-1606(92)90174-F 1601171
46. Isolation and culture of primary bovine embryonic stem cell colonies by a novel method. Cao S, Wang F, Chen Z, Liu Z, Mei C, et al. J Exp Zool A Ecol Genet Physiol 2009 311 368 376 19340839
47. Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst. Meilhac SM, Adams RJ, Morris SA, Danckaert A, Le Garrec JF, Zernicka-Goetz M, Dev Biol 2009 331 210 221 10.1016/j.ydbio.2009.04.036 19422818
48. Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo. Morris SA, Teo RT, Li H, Robson P, Glover DM, Zernicka-Goetz M, Proc Natl Acad Sci USA 2010 107 6364 6369 10.1073/pnas. 0915063107 20308546
49. FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst. Yamanaka Y, Lanner F, Rossant J, Development 2010 137 715 724 10.1242/dev.043471 20147376
50. Elf5 regulation in the trophectoderm. Pearton DJ, Broadhurst R, Donnison M, Pfeffer PL, Dev Biol 2011 360 343 350 10.1016/j.ydbio.2011.10.007 22020251
51. Desmoplakin is essential in epidermal sheet formation. Vasioukhin V, Bowers E, Bauer C, Degenstein L, Fuchs E, Nat Cell Biol 2011 3 1076 1085
52. Dual roles for the Dab2 adaptor protein in embryonic development and kidney transport. Morris SM, Tallquist MD, Rock CO, Cooper JA, EMBO J 2002 21 1555 1564 10.1093/emboj/21.7.1555 11927540 (Pubitemid 34614612)
53. Trophectodermal processes regulate the expression of totipotency within the inner cell mass of the mouse expanding blastocyst. Fleming TP, Warren PD, Chisholm JC, Johnson MH, J Embryol Exp Morphol 1984 84 63 90 6533258 (Pubitemid 15162501)
54. Fine structure of bovine morulae and blastocysts in vivo and in vitro. Abe H, Otoi T, Tachikawa S, Yamashita S, Satoh T, Hoshi H, Anat Embryol 1999 199 519 527 10.1007/s004290050249 10350132 (Pubitemid 29204425)
55. 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. Abe H, Yamashita S, Itoh T, Satoh T, Hoshi H, Mol Reprod Dev 1999 53 325 335 10.1002/(SICI)1098- 2795(199907)53:3<325::AID-MRD8>3.0.CO;2-T 10369393 (Pubitemid 29247332)
56. Interferons and progesterone for establishment and maintenance of pregnancy: interactions among novel cell signaling pathways. Bazer FW, Burghardt RC, Johnson GA, Spencer TE, Wu G, Reprod Biol 2008 8 179 211 19092983
57. Lack of effect of granulocyte-macrophage colony-stimulating factor on secretion of interferon-, other proteins, and prostaglandin E2 by the bovine and ovine conceptus. de Moraes AA, Davidson JA, Fleming JG, Bazer FW, Edwards JL, et al. Domest Anim Endocrinol 1997 14 193 197 10.1016/S0739-7240(97)00002-7 9171977 (Pubitemid 29314746)
58. Pepsin-related molecules secreted by trophoblast. Green JA, Xie S, Roberts RM, Rev Reprod 1998 3 62 69 10.1530/ror.0.0030062 9509990 (Pubitemid 28062310)
59. Cellular and molecular regulation of mammalian blastocyst hatching. Seshagiri PB, Sen Roy S, Sireesha G, Rao RP, J Reprod Immunol 2009 83 79 84 10.1016/j.jri.2009.06.264 19879652
60. Blastocyst elongation, trophoblastic differentiation, and embryonic pattern formation. Blomberg L, Hashizume K, Viebahn C, Reproduction 2008 135 181 195 10.1530/REP-07-0355 18239048 (Pubitemid 351267388)
61. Oestrogen production by blastocyst and early embryonic tissue of various species. Gadsby JE, Heap RB, Burton RD, J Reprod Fertil 1980 60 409 417 10.1530/jrf.0.0600409 6448924 (Pubitemid 11211613)
62. The anatomy and physiology of pre-attachment bovine embryos. Betteridge KJ, Flechon J-E, Theriogenology 1988 29 155 187 10.1016/0093-691X(88)90038-6
63. Development of the intercaruncular areas during early gestation and establishment of the bovine placenta. King GJ, Atkinson BA, Robertson HA, J Reprod Fertil 1981 61 469 474 10.1530/jrf.0.0610469 7205793 (Pubitemid 11141218)
64. Intracellular cathepsin B activity is inversely correlated with the quality and developmental competence of bovine preimplantation embryos. Balboula AZ, Yamanaka K, Sakatani M, Hegab AO, Zaabel SM, Takahashi M, Mol Reprod Dev 2010 77 1031 1039 10.1002/mrd.21250 21104746
65. Transcriptomic signature of trophoblast differentiation in a human embryonic stem cell model. Marchand M, Horcajadas JA, Esteban FJ, McElroy SL, Fisher SJ, Giudice LC, Biol Reprod 2011 84 1258 1271 10.1095/biolreprod.110. 086413 21368299
66. Trophoblast giant cells express NF-B2 during early mouse development. Muggia A, Teesalu T, Neri A, Blasi F, Talarico D, Dev Genet 1999 25 23 30 10.1002/(SICI)1520-6408(1999)25:1<23::AID-DVG3>3.0.CO;2-K 10402669 (Pubitemid 29305104)
67. Balancing dormant and self-renewing hematopoietic stem cells. Wilson A, Laurenti E, Trumpp A, Curr Opin Genet Dev 2009 19 461 368 10.1016/j.gde.2009.08. 005 19811902
68. GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells. Yu S, Cui K, Jothi R, Zhao DM, Jing X, et al. Blood 2011 117 2166 2178 10.1182/blood-2010-09-306563 21139080
69. Hematopoietic transcriptional regulation by the myeloid zinc finger gene, MZF-1. Hromas R, Davis B, Rauscher FJ 3rd, Klemsz M, Tenen D, et al. Curr Top Microbiol Immunol 1996 211 159 164 10.1007/978-3-642-85232-9-16 8585946 (Pubitemid 26019276)
70. Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK, et al. Cell 2007 129 345 357 10.1016/j.cell.2007.03.014 17448993 (Pubitemid 46574969)
71. GABP regulates Oct-3/4 expression in mouse embryonic stem cells. Kinoshita K, Ura H, Akagi T, Usuda M, Koide H, Yokota T, Biochem Biophys Res Commun 2007 353 686 691 10.1016/j.bbrc.2006.12.071 17194449 (Pubitemid 46048724)
72. Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. Papp B, Plath K, Cell Res 2011 21 486 501 10.1038/cr.2011.28 21321600
73. Sp1 and Sp3 Are important regulators of AP-2 gene transcription. Li M, Kellems RE, Biol Reprod 2003 69 1220 1230 10.1095/biolreprod.103.015545 12801994 (Pubitemid 37173855)
74. Involvement of Sp-1 in the regulation of the Id-1 gene during trophoblast cell differentiation. Takeda T, Sakata M, Isobe A, Yamamoto T, Nishimoto F, et al. Placenta 2007 28 192 198 10.1016/j.placenta.2006.03.002 16638616 (Pubitemid 44914528)
75. Expression and localization of DLX3, PPARG and SP1 in bovine trophoblast during binucleated cell differentiation. Degrelle SA, Murthi P, Evain-Brion D, Fournier T, Hue I, Placenta 2011 32 917 920 10.1016/j.placenta.2011.08.014 21937107
76. DNA methylation patterns reflect epigenetic reprogramming in bovine embryos. Niemann H, Carnwath JW, Herrmann D, Wieczorek G, Lemme E, et al. Cell Reprogram 2010 12 33 42 10.1089/cell.2009.0063 20132011
77. Structure and function of mammalian DNA methyltransferases. Jurkowska RZ, Jurkowski TP, Jeltsch A, ChemBioChem 2011 12 206 222 10.1002/cbic.201000195 21243710
78. Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, et al. Proc Natl Acad Sci USA 2011 98 13734 13738
79. Genomic DNA methylation patterns in bovine preimplantation embryos derived from in vitro fertilization. Hou J, Liu L, Lei T, Cui X, An X, Chen Y, Sci China C Life Sci 2007 50 56 61 10.1007/s11427-007-0003-7 17393083
80. Limited demethylation leaves mosaic-type methylation states in cloned bovine pre-implantation embryos. Kang YK, Park JS, Koo DB, Choi YH, Kim SU, et al. EMBO J 2002 21 1092 1100 10.1093/emboj/21.5.1092 11867537 (Pubitemid 34206182)
81. Polycomb gene expression and histone H3 lysine 27 trimethylation changes during bovine preimplantation development. Ross PJ, Ragina NP, Rodriguez RM, Iager AE, Siripattarapravat K, et al. Reproduction 2008 136 777 785 10.1530/REP-08-0045 18784248
82. Histone demethylation by a family of JmjC domain-containing proteins. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, et al. Nature 2006 439 811 816 10.1038/nature04433 16362057 (Pubitemid 43255695)
83. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Frescas D, Guardavaccaro D, Bassermann F, Koyama-Nasu R, Pagano M, Nature 2007 450 309 313 10.1038/nature06255 17994099 (Pubitemid 350100537)