Transcriptional profiling of pig embryogenesis by using a 15-K member unigene set specific for pig reproductive tissues and embryos

Biology of Reproduction

Volumn 72, Issue 6, 2005, Pages 1437-1451

  Whitworth, K M ^a   Agca, C ^a   Kim, J G ^a   Patel, R V ^a   Springer, G K ^b   Bivens, N J ^a   Forrester, L J ^a   Mathialagan, N ^c   Green, J A ^a   Prather, R S ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b University of Missouri   (United States)

^c MONSANTO COMPANY   (United States)

Author keywords

Early development; Embryo; Gene expression; Gene regulation; In vitro fertilization; Pig

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BLASTOCYST; CONTROLLED STUDY; DNA MICROARRAY; EMBRYO DEVELOPMENT; FERTILIZATION IN VITRO; GENE CONTROL; GENE EXPRESSION; GERMINAL VESICLE; HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OOCYTE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SWINE;

ANIMALS; BLASTOCYST; DNA, COMPLEMENTARY; EMBRYONIC DEVELOPMENT; FEMALE; FERTILIZATION IN VITRO; GENE EXPRESSION REGULATION, DEVELOPMENTAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OOCYTES; PREGNANCY; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; SWINE; TRANSCRIPTION, GENETIC;

SUS SCROFA;

EID: 21044444140     PISSN: 00063363     EISSN: None     Source Type: Journal    
DOI: 10.1095/biolreprod.104.037952     Document Type: Article

References (65)

1. Kanka J. Gene expression and chromatin structure in the pre-implantation embryo. Theriogenology 2003; 59:3-19.
2. Ko MSH. Embryogenomics of pre-implantation mammalian development: current status. Reprod Fertil Dev 2004; 16:79-85.
3. Schoenbeck RA, Peters MS, Rickords LF, Stumpf TT, Prather RS. Characterization of DNA synthesis and the transition from maternal to embryonic control in the 4-cell porcine embryo. Biol Reprod 1992; 47:1118-1125.
4. Prather RS, Hawley RJ, Carter DB, Lai L, Greenstein JL. Transgenic swine for biomedicine and agriculture. Theriogenology 2003; 59:115-123.
5. Greve T, Callesen H. Integrating new technologies with embryology and animal production. Reprod Fertil Dev 2004; 16:113-122.
6. Machaty Z, Day BN, Prather RS. Development of early porcine embryos in vitro and in vivo. Biol Reprod 1998; 59:451-455.
7. Wheeler MB, Clark SG, Beebe DJ. Developments in in vitro technologies for swine embryo production. Reprod Fertil Dev 2004; 16:15-25.
8. Jiang H, Bivens NJ, Ries JE, Whitworth KM, Green JA, Forrester LJ, Springer GK, Didion BA, Mathialagan N, Prather RS, Lucy MC. Constructing cDNA libraries with fewer clones that contain long poly(dA) tails. Biotechniques 2001; 31:38-40.
9. Jiang H, Bivens N, Ries J, Woods R, Whitworth KM, Green JA, Forrester LJ, Springer GK, Mathialagan N, Agca C, Prather RS, Lucy MC. Large-scale generation and analysis of expression sequence tags from porcine ovary. Biol Reprod 2004; 71:1991-2002.
10. Whitworth K, Springer GK, Forrester LJ, Spollen WG, Ries J, Lamberson WL, Bivens N, Murphy CN, Mathialigan N, Green JA, Prather RS. Developmental expression of 2,489 genes during pig embryogenesis: an EST project. Biol Reprod 2004; 71:1230-1243.
11. Evsikov AV, de Vries WN, Peaston AE, Radford EE, Fancher KS, Chen FH, Blake JA, Bult CJ, Latham KE, Solter D, Knowles BB. Systems biology of the 2-cell mouse embryo. Cytogenet Genome Res 2004; 105:240-250.
12. Rast JP, Amore G, Calestani C, Livi CB, Ransick A, Davidson EH. Recovery of developmentally defined gene sets from high-density cDNA macroarrays. Dev Biol 2000; 228:270-286.
13. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJC, Rust AG, Pan ZJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol 2002; 246:162-190.
14. Ko MSH, Kitchen JR, Wang XH, Threat TA, Wang XQ, Hasegawa A, Sun T, Grahovac MJ, Kargul GJ, Lim MK, Cui YS, Sano Y, Tanaka T, Liang YL, Mason S, Paonessa PD, Sauls AD, DePalma GE, Sharara R, Rowe LB, Eppig J, Morrell C, Doi H. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development 2000; 127:1737-1749.
15. Hamatani T, Carter MG, Sharov AA, Ko MSH. Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell 2004; 6:117-131.
16. Zeng FY, Baldwin DA, Schultz RM. Transcript profiling during preimplantation mouse development. Dev Biol 2004; 272:483-496.
17. Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, Wang S, Kurn N. Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques 2004; 37:854-857.
18. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques 2000; 29:548-556.
19. Tuggle CK, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares MB, Kucaba T, Crouch K, Smith C, Tack D, Robinson N, O'Leary B, Scheetz T, Casavant T, Pomp D, Edeal JB, Zhang YD, Rothschild MF, Garwood K, Beavis W. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mammalian Genome 2003; 14:565-579.
20. Eisen MB, Brown PO. DNA arrays for analysis of gene expression. In: Weissman SM (ed.), cDNA Preparation and Characterization. San Diego, CA: Academic Press; 1999;179-205.
21. Hosack DA, Dennis JG, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol 2003; 4:R70.
22. Jarrell VL, Day BN, Prather RS. The transition from maternal to zygotic control of development occurs during the 4-cell stage in the domestic pig, sus scrofa; quantitative and qualitative aspects of protein synthesis. Biol Reprod 1991; 44:62-68.
23. Prather RS. Nuclear control of early embryonic development in domestic pigs. J Reprod Fertil 1993; 48:17-29.
24. Wang QT, Piotrowska K, Ciemerych MA, Milenkovic L, Scott MP, Davis RW, Zernicka-Goetz M. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev Cell 2004; 6:133-144.
25. Rinaudo P, Schultz RM. Effects of embryo culture on global pattern of gene expression in preimplantation mouse embryos. Reproduction 2004; 128:301-311.
26. Fu H, Xia K, Pallas DC, Cui C, Conroy K, Narsimhan RP, Mamon H, Collier RJ, Roberts TM. Interaction of the protein kinase Raf-1 with 14-3-3 Proteins. Science 1994; 266:126-129.
27. Autieri MV, Carbone CJ. 14-3-3 Gamma interacts with and is phosphorylated by multiple protein kinase C isoforms in PDGF-stimulated human vascular smooth muscle cells. DNA Cell Biol 1999; 18:555-564.
28. Hoodbhoy T, Dean J. Insights into the molecular basis of sperm-egg recognition in mammals. Reproduction 2004; 127:417-422(review).
29. Biniszkiewicz D, Gribnau J, Ramsahoye B, Gaudet F, Eggan K, Humpherys D, Mastrangelo MA, Jun Z, Walter J, Jaenisch R. Dnmt1 overexpression causes genomic hypermethylation, loss of imprinting, and embryonic lethality. Mol Cell Biol 2002; 22:2124-2135.
30. Gaudet F, Rideout WM, Meissner A, Dausman J, Leonhardt H, Jaenisch R. Dnmt1 expression in pre- and postimplantation embryogenesis and the maintenance of IAP silencing. Mol Cell Biol 2004; 24:1640-1648.
31. Doherty AS, Bartolomei MS, Schultz RM. Regulation of stage-specific nuclear translocation of Dnmt1o during preimplantation mouse development. Dev Biol 2002; 242:255-266.
32. Cardoso MC, Leonhardt H. DNA methyltransferase is actively retained in the cytoplasm during early development. J Cell Biol 1999; 147:25-32.
33. Ratnam S, Mertineit C, Ding F, Howell CY, Clarke HJ, Bestor TH, Chaillet JR, Trasler JM. Dynamics of Dnmt1 methyltransferase expression and intracellular localization during oogenesis and preimplantation development. Dev Biol 2002; 245:304-314.
34. Evstafieva AG, Belov GA, Rubtsov YP, Kalkum M, Joseph B, Chichkova NV, Sukhacheva EA, Bogdanov AA, Pettersson RF, Agol VI, Vartapetian AB. Apoptosis-related fragmentation, translocation, and properties of human prothymosin alpha. Exp Cell Res 2003; 284:211-223.
35. Jiang XJ, Kim HE, Shu HJ, Zhao YM, Zhang HC, Kofron J, Donnelly J, Burns D, Ng SC, Rosenberg S, Wang XD. Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway. Science 2003; 299:223-226.
36. Knight JS, Lan K, Subramanian C, Robertson ES. Epstein-Barr virus nuclear antigen 3C recruits histone deacetylase activity and associates with the corepressors mSin3A and NCoR in human B-cell lines. J Virol 2003; 77:4261-4272.
37. Ciana P, Ghisletti S, Mussi P, Eberini I, Vegeto E, Maggi A. Estrogen receptor alpha, a molecular switch converting transforming growth factor-alpha-mediated proliferation into differentiation in neuroblastoma cells. J Biol Chem 2003; 278:31737-31744.
38. Markova OV, Evstafieva AG, Mansurova SE, Moussine SS, Palamarchuk LA, Pereverzev MO, Vartapetian AB, Skulachev VP. Cytochrome C is transformed from anti- to pro-oxidant when interacting with truncated oncoprotein prothymosin alpha. Biochim Biophys Acta Bioenergetics 2003; 1557:109-117.
39. Klivenyi P, Starkov AA, Calingasan NY, Gardian G, Browne SE, Yang LC, Bubber P, Gibson GE, Patel MS, Beal MF. Mice deficient in dihydrolipoamide dehydrogenase show increased vulnerability to MPTP, malonate and 3-nitropropionic acid neurotoxicity. J Neurochem 2004; 88:1352-1360.
40. Liu TC, Kim H, Arizmendi C, Kitano A, Patel MS. Identification of 2 missense mutations in a dihydrolipoamide dehydrogenase-deficient patient. Proc Natl Acad Sci U S A 1993; 90:5186-5190.
41. Xia L, Bjornstedt M, Nordman T, Eriksson LC, Olsson JM. Reduction of ubiquinone by lipoamide dehydrogenase - an antioxidant regenerating pathway. Eur J Biochem 2001; 268:1486-1490.
42. Xia L, Nordman T, Olsson JM, Damdimopoulos A, Bjorkhem-Bergman L, Nalvarte I, Eriksson LC, Arner ESJ, Spyrou G, Bjornstedt M. The mammalian cytosolic selenoenzyme thioredoxin reductase reduces ubiquinone - a novel mechanism for defense against oxidative stress. J Biol Chem 2003; 278:2141-2146.
43. Machaty Z, Thompson JG, Abeydeera LR, Day BN, Prather RS. Inhibitors of mitochondrial ATP production at the time of compaction improve development of in vitro produced porcine embryos. Mol Reprod Dev 2001; 58:39-44.
44. Ohman A, Rak A, Dontsova M, Garber MB, Hard T. NMR structure of the ribosomal protein L23 from Thermus thermophilus. J Biomolecular NMR 2003; 26:131-137.
45. Lee PD, Sladek R, Greenwood CMT, Hudson TJ. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Gen Res 2002; 12:292-297.
46. Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng ZP, Mutter GL, Frosch MP, MacDonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Gullans SR. A compendium of gene expression in normal human tissues. Physiol Genom 2001; 7:97-104.
47. Aizawa H, Sutoh K, Tsubuki S, Kawashima S, Ishii A, Yahara I. Identification, characterization, and intracellular distribution of cofilin in Dictyostelium discoideum. J Biol Chem 1995; 270:10923-10932.
48. Roy G, De Crescenzo G, Khaleghpour K, Kahvejian A, O'Connor-McCourt M, Sonenberg N. Paip1 interacts with poly(A) binding protein through two independent binding motifs. Mol Cell Biol 2002; 22:3769-3782.
49. Koegl M, Hoppe T, Schlenker S, Ulrich HD, Mayer TU, Jentsch S. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 1999; 96:635-644.
50. Lee YH, Orand MG. Ultrastructural localization of a nuclear autoantigenic sperm protein in spermatogenic cells and spermatozoa. Anat Rec 1993; 236:442-448.
51. Minami N, Sasaki K, Aizawa A, Miyamoto M, Imai H. Analysis of gene expression in mouse 2-cell embryos using fluorescein differential display: comparison of culture environments. Biol Reprod 2001; 64:30-35.
52. Bianchi ME, Manfredi A. Chromatin and cell death. Biochim Biophys Acta Gene Struct Express 2004; 1677:181-186(review).
53. Vinogradov AD. Mitochondrial ATP synthase: fifteen years later. Biochemistry (Moscow) 1999; 64:1219-1229(review).
54. Pedersen PL. Atp synthase - the machine that makes Atp. Curr Biol 1994; 4:1138-1141.
55. Lehmeier T, Raker V, Hermann H. Luhrmann R. cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins - evidence for a direct D1-D2 interaction. Proc Natl Acad Sci U S A 1994; 91:12317-12321.
56. Prather RS, Rickords LF. Developmental regulation of a snRNP core protein epitope during pig embryogenesis and after nuclear transfer for cloning. Mol Reprod Dev 1992; 33:119-123.
57. Macario AJL, Malz M, de Macario EC. Evolution of assisted protein folding: the distribution of the main chaperoning systems within the phylogenetic domain archaea. Front Biosci 2004; 9:1318-1332.
58. Gross M, Hessefort S, Olin A. Purification of a 38-kDa protein from rabbit reticulocyte lysate which promotes protein renaturation by heat shock protein 70 and its identification as delta-aminolevulinic acid dehydratase and as a putative DnaJ protein. J Biol Chem 1999; 274:3125-3134.
59. Zimmerman AW, Nelissen J, Van Emst-De Vries SE, Willems P, de Lange F, Collard JG, van Leeuwen FN, Figdor CG. Cytoskeletal restraints regulate homotypic ALCAM-mediated adhesion through PKC alpha independently of rho-like GTPases. J Sci 2004; 117:2841-2852.
60. Swart GWM. Activated leukocyte cell adhesion molecule (CD166/ALCAM): developmental and mechanistic aspects of cell clustering and cell migration. Eur J Cell Biol 2002; 81:313-321.
61. Tanaka KJ, Matsuomoto K, Tsujimoto M, Nishikata T. CiYB1 is a major component of storage mRNPs in ascidian oocytes: implications in translational regulation of localized mRNAs. Dev Biol 2004; 272:217-230.
62. Do HJ, Kim JH, Abeydeera LR, Han YM, Matteri RL, Green JA, Roberts RM, Day BN, Prather RS. Expression of pregnancy-associated glycoprotein 1 and 2 genes in in vivo, in vitro and parthenogenetically derived preimplantation pig embryos. Zygote 2001; 9:245-250.
63. Pennetier S, Uzbekova S, Rerreau C, Papillier P, Mermillod P, Dalbies-Tran R. Spatio-temporal expression of the germ cell marker genes MATER, ZAR1, GDF9, BMP15, and VASA in adult bovine tissues, oocytes, and preimplantation embryos. Biol Reprod 2004; 71:1359-1366.
64. Leyens G, Knoops B, Donnay I. Expression of peroxiredoxins in bovine oocytes and embryos produced in vitro. Mol Reprod Dev 2004; 69:243-251.
65. Wei Z. Effect of epidermal growth factor on preimplantation development and its receptor expression in porcine embryos. Mol Reprod Dev 2001; 60:457-462.