Identification of inappropriately reprogrammed genes by large-scale transcriptome analysis of individual cloned mouse blastocysts

PLoS ONE

Volumn 5, Issue 6, 2010, Pages

  Fukuda, Atsushi ^a   Cao, Feng ^a   Morita, Shinnosuke ^a   Yamada, Kaori ^a   Jincho, Yuko ^a   Tane, Shouji ^a   Sotomaru, Yusuke ^b   Kono, Tomohiro ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE   (Japan)

^b HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

3 HYDROXYACYL COENZYME A DEHYDROGENASE; AMYLOID PRECURSOR PROTEIN; CD47 ANTIGEN; CD81 ANTIGEN; FRAGILE X MENTAL RETARDATION PROTEIN; GLYCEROL KINASE; MELANOMA ANTIGEN; MEMBRANE PROTEIN; MEVALONATE DECARBOXYLASE; MEVALONIC ACID; MOESIN; N4 (BETA N ACETYLGLUCOSAMINYL)ASPARAGINASE; NUCLEOSOME BINDING PROTEIN 1; PHOSPHOGLYCERATE KINASE; PHOSPHOGLYCERATE KINASE 1; PROMININ 1; PROTEIN ASZ1; PROTEIN KINASE WNK1; SEH1 LIKE PROTEIN; STATHMIN; TRANSCRIPTOME; TRANSMEMBRANE PROTEIN 158; TUMOR REJECTION ANTIGEN; UNCLASSIFIED DRUG; X LINKED LYMPHOCYTE REGULATED 3A; X LINKED LYMPHOCYTE REGULATED 4B; X LINKED LYMPHOCYTE REGULATED 5C; ZINC FINGER PROTEIN; ZINC FINGER PROTEIN 820; ZINC FINGER PROTEIN 97;

ANIMAL CELL; ARTICLE; BLASTOCYST; CELL NUCLEUS TRANSPLANTATION; CONTROLLED STUDY; CUMULUS CELL; EMBRYO; EMBRYONIC STEM CELL; FEMALE; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; MICROARRAY ANALYSIS; MOLECULAR CLONING; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; PRINCIPAL COMPONENT ANALYSIS; RNA ANALYSIS; SERTOLI CELL; SOMATIC EMBRYONIC STEM CELL NUCLEAR TRANSFER;

ANIMALS; BLASTOCYST; CLONING, ORGANISM; DOWN-REGULATION; GENE EXPRESSION PROFILING; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; UP-REGULATION;

EID: 77956223470     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011274     Document Type: Article

References (63)

1. Hochedlinger K, Jaenisch R (2006) Nuclear reprogramming and pluripotency. Nature 441: 1061-1067.
2. Wilmut I, Schnieke AE, McWhir J, Kind AJ, Campbell KH (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385: 810-813.
3. Egli D, Rosains J, Birkhoff G, Eggan K (2007) Developmental reprogramming after chromosome transfer into mitotic mouse zygotes. Nature 447: 679-685.
4. Hanna J, Markoulaki S, Schorderet P, Carey BW, Beard C, et al. (2008) Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 133: 250-264.
5. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131: 861-872.
6. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-676.
7. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, et al. (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318: 1917-1920.
8. Inoue K, Wakao H, Ogonuki N, Miki H, Seino K, et al. (2005) Generation of cloned mice by direct nuclear transfer from natural killer T cells. Curr Biol 15: 1114-1118.
9. Hanna J, Wernig M, Markoulaki S, Sun CW, Meissner A, et al. (2007) Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science 318: 1920-1923.
10. Rideout WM 3rd, Hochedlinger K, Kyba M, Daley GQ, Jaenisch R (2002) Correction of a genetic defect by nuclear transplantation and combined cell and gene therapy. Cell 109: 17-27.
11. Dimos JT, Rodolfa KT, Niakan KK, Weisenthal LM, Mitsumoto H, et al. (2008) Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science 321: 1218-1221.
12. Gurdon J, Murdoch A (2008) Nuclear transfer and iPS may work best together. Cell Stem Cell 2: 135-138.
13. Chung YG, Ratnam S, Chaillet JR, Latham KE (2003) Abnormal regulation of DNA methyltransferase expression in cloned mouse embryos. Biol Reprod 69: 146-153.
14. Humpherys D, Eggan K, Akutsu H, Friedman A, Hochedlinger K, et al. (2002) Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei. Proc Natl Acad Sci U S A 99: 12889-12894.
15. Ogawa H, Ono Y, Shimozawa N, Sotomaru Y, Katsuzawa Y, et al. (2003) Disruption of imprinting in cloned mouse fetuses from embryonic stem cells. Reproduction 126: 549-557.
16. Rideout WM 3rd, Eggan K, Jaenisch R (2001) Nuclear cloning and epigenetic reprogramming of the genome. Science 293: 1093-1098.
17. Tong GQ, Heng BC, Tan LG, Ng SC (2006) Aberrant profile of gene expression in cloned mouse embryos derived from donor cumulus nuclei. Cell Tissue Res 325: 231-243.
18. Li X, Kato Y, Tsunoda Y (2005) Comparative analysis of development-related gene expression in mouse preimplantation embryos with different developmental potential. Mol Reprod Dev 72: 152-160.
19. Yang X, Smith SL, Tian XC, Lewin HA, Renard JP, et al. (2007) Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nat Genet 39: 295-302.
20. Jincho Y, Sotomaru Y, Kawahara M, Ono Y, Ogawa H, et al. (2008) Identification of genes aberrantly expressed in mouse embryonic stem cell-cloned blastocysts. Biol Reprod 78: 568-576.
21. Ono Y, Kono T (2006) Irreversible barrier to the reprogramming of donor cells in cloning with mouse embryos and embryonic stem cells. Biol Reprod 75: 210-216.
22. Ogonuki N, Inoue K, Yamamoto Y, Noguchi Y, Tanemura K, et al. (2002) Early death of mice cloned from somatic cells. Nat Genet 30: 253-254.
23. Oishi M, Gohma H, Hashizume K, Taniguchi Y, Yasue H, et al. (2006) Early embryonic death-associated changes in genome-wide gene expression profiles in the fetal placenta of the cow carrying somatic nuclear-derived cloned embryo. Mol Reprod Dev 73: 404-409.
24. Ono Y, Shimozawa N, Muguruma K, Kimoto S, Hioki K, et al. (2001) Production of cloned mice from embryonic stem cells arrested at metaphase. Reproduction 122: 731-736.
25. Renard JP, Chastant S, Chesne P, Richard C, Marchal J, et al. (1999) Lymphoid hypoplasia and somatic cloning. Lancet 353: 1489-1491.
26. Shimozawa N, Ono Y, Kimoto S, Hioki K, Araki Y, et al. (2002) Abnormalities in cloned mice are not transmitted to the progeny. Genesis 34: 203-207.
27. Tamashiro KL, Wakayama T, Akutsu H, Yamazaki Y, Lachey JL, et al. (2002) Cloned mice have an obese phenotype not transmitted to their offspring. Nat Med 8: 262-267.
28. Beyhan Z, Ross PJ, Iager AE, Kocabas AM, Cunniff K, et al. (2007) Transcriptional reprogramming of somatic cell nuclei during preimplantation development of cloned bovine embryos. Dev Biol 305: 637-649.
29. Gelineau-van Waes J, Maddox JR, Smith LM, van Waes M, Wilberding J, et al. (2008) Microarray analysis of E9.5 reduced folate carrier (RFC1; Slc19a1) knockout embryos reveals altered expression of genes in the cubilin-megalin multiligand endocytic receptor complex. BMC Genomics 9: 156.
30. Smith SL, Everts RE, Tian XC, Du F, Sung LY, et al. (2005) Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proc Natl Acad Sci U S A 102: 17582-17587.
31. Somers J, Smith C, Donnison M, Wells DN, Henderson H, et al. (2006) Gene expression profiling of individual bovine nuclear transfer blastocysts. Reproduction 131: 1073-1084.
32. Bortvin A, Eggan K, Skaletsky H, Akutsu H, Berry DL, et al. (2003) Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei. Development 130: 1673-1680.
33. Blelloch R, Wang Z, Meissner A, Pollard S, Smith A, et al. (2006) Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells 24: 2007-2013.
34. Wang F, Kou Z, Zhang Y, Gao S (2007) Dynamic reprogramming of histone acetylation and methylation in the first cell cycle of cloned mouse embryos. Biol Reprod 77: 1007-1016.
35. Wee G, Koo DB, Song BS, Kim JS, Kang MJ, et al. (2006) Inheritable histone H4 acetylation of somatic chromatins in cloned embryos. J Biol Chem 281: 6048-6057.
36. Wee G, Shim JJ, Koo DB, Chae JI, Lee KK, et al. (2007) Epigenetic alteration of the donor cells does not recapitulate the reprogramming of DNA methylation in cloned embryos. Reproduction 134: 781-787.
37. Avilion AA, Nicolis SK, Pevny LH, Perez L, Vivian N, et al. (2003) Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev 17: 126-140.
38. Feldman B, Poueymirou W, Papaioannou VE, DeChiara TM, Goldfarb M (1995) Requirement of FGF-4 for postimplantation mouse development. Science 267: 246-249.
39. Niwa H (2007) How is pluripotency determined and maintained? Development 134: 635-646.
40. Artus J, Cohen-Tannoudji M (2008) Cell cycle regulation during early mouse embryogenesis. Mol Cell Endocrinol 282: 78-86.
41. Zhang HS, Dean DC (2001) Rb-mediated chromatin structure regulation and transcriptional repression. Oncogene 20: 3134-3138.
42. Iwamori N, Naito K, Sugiura K, Tojo H (2002) Preimplantation-embryo-specific cell cycle regulation is attributed to the low expression level of retinoblastoma protein. FEBS Lett 526: 119-123.
43. Harper JW, Elledge SJ, Keyomarsi K, Dynlacht B, Tsai LH, et al. (1995) Inhibition of cyclin-dependent kinases by p21. Mol Biol Cell 6: 387-400.
44. Utikal J, Polo JM, Stadtfeld M, Maherali N, Kulalert W, et al. (2009) Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature 460: 1145-1148.
45. Pasini D, Bracken AP, Hansen JB, Capillo M, Helin K (2007) The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cell Biol 27: 3769-3779.
46. Zhang M, Wang F, Kou Z, Zhang Y, Gao S (2009) Defective chromatin structure in somatic cell cloned mouse embryos. J Biol Chem 284: 24981-24987.
47. Muller C, Calkhoven CF, Sha X, Leutz A (2004) The CCAAT enhancer-binding protein alpha (C/EBPalpha) requires a SWI/SNF complex for proliferation arrest. J Biol Chem 279: 7353-7358.
48. Kuo CT, Veselits ML, Barton KP, Lu MM, Clendenin C, et al. (1997) The LKLF transcription factor is required for normal tunica media formation and blood vessel stabilization during murine embryogenesis. Genes Dev 11: 2996-3006.
49. Pai SR, Bird RC (1994) Overexpression of c-fos induces expression of the retinoblastoma tumor suppressor gene Rb in transfected cells. Anticancer Res 14: 2501-2508.
50. Strumpf D, Mao CA, Yamanaka Y, Ralston A, Chawengsaksophak K, et al. (2005) Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132: 2093-2102.
51. Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP (2009) Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41: 246-250.
52. Yokochi T, Poduch K, Ryba T, Lu J, Hiratani I, et al. (2009) G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc Natl Acad Sci U S A 106: 19363-19368.
53. Shi Y, Do JT, Desponts C, Hahm HS, Scholer HR, et al. (2008) A combined chemical and genetic approach for the generation of induced pluripotent stem cells. Cell Stem Cell 2: 525-528.
54. Nolen LD, Gao S, Han Z, Mann MR, Gie Chung Y, et al. (2005) X chromosome reactivation and regulation in cloned embryos. Dev Biol 279: 525-540.
55. Nichols J, Zevnik B, Anastassiadis K, Niwa H, Klewe-Nebenius D, et al. (1998) Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95: 379-391.
56. Takeda K, Noguchi K, Shi W, Tanaka T, Matsumoto M, et al. (1997) Targeted disruption of the mouse Stat3 gene leads to early embryonic lethality. Proc Natl Acad Sci U S A 94: 3801-3804.
57. Bao S, Miyoshi N, Okamoto I, Jenuwein T, Heard E, et al. (2005) Initiation of epigenetic reprogramming of the X chromosome in somatic nuclei transplanted to a mouse oocyte. EMBO Rep 6: 748-754.
58. Ng K, Pullirsch D, Leeb M, Wutz A (2007) Xist and the order of silencing. EMBO Rep 8: 34-39.
59. Li X, Kato Y, Tsunoda Y (2006) Comparative studies on the mRNA expression of development-related genes in an individual mouse blastocyst with different developmental potential. Cloning Stem Cells 8: 214-224.
60. Boiani M, Eckardt S, Scholer HR, McLaughlin KJ (2002) Oct4 distribution and level in mouse clones: consequences for pluripotency. Genes Dev 16: 1209-1219.
61. Ogura A, Inoue K, Ogonuki N, Noguchi A, Takano K, et al. (2000) Production of male cloned mice from fresh, cultured, and cryopreserved immature Sertoli cells. Biol Reprod 62: 1579-1584.
62. Kishigami S, Wakayama S, Thuan NV, Ohta H, Mizutani E, et al. (2006) Production of cloned mice by somatic cell nuclear transfer. Nat Protoc 1: 125-138.
63. Kawahara M, Obata Y, Sotomaru Y, Shimozawa N, Bao S, et al. (2008) Protocol for the production of viable bimaternal mouse embryos. Nat Protoc 3: 197-209.