A gene expression signature shared by human mature oocytes and embryonic stem cells

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Assou, Said ^a,b,c,d   Cerecedo, Doris ^a,b   Tondeur, Sylvie ^a,b,c   Pantesco, Véronique ^a,b   Hovatta, Outi ^e   Klein, Bernard ^a,b,c   Hamamah, Samir ^a,b,c,f   De Vos, John ^a,b,c  

^a HÔPITAL SAINT ELOI   (France)

^b INSERM   (France)

^c UNIV MONTPELLIER   (France)

^d MacoPharma   (France)

^e KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^f HÔPITAL ARNAUD DE VILLENEUVE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; DNA METHYLTRANSFERASE 3B; PROTEASOME; PROTEIN CBX1; PROTEIN CBX5; PROTEIN JARID2; PROTEIN KLHL7; PROTEIN LIN28; PROTEIN MRS2; PROTEIN SMARCA5; PROTEIN TDGF1; PROTEIN TOP2A; SELENOPHOSPHATE SYNTHETASE I; SYNTHETASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; ZINC FINGER PROTEIN 84;

ARTICLE; CELL CYCLE; CELL DIFFERENTIATION; CELL FUSION; CELL NUCLEUS TRANSPLANTATION; CELL TYPE; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPARATIVE STUDY; CONTROLLED STUDY; EMBRYONIC STEM CELL; FEMALE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE OVEREXPRESSION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; OOCYTE MATURATION; PLURIPOTENT STEM CELL; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; UBIQUITINATION; CELL CULTURE; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; OOCYTE; PRINCIPAL COMPONENT ANALYSIS;

CELL CYCLE; CELLS, CULTURED; CHROMATIN ASSEMBLY AND DISASSEMBLY; EMBRYONIC STEM CELLS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OOCYTES; PRINCIPAL COMPONENT ANALYSIS; PROTEASOME ENDOPEPTIDASE COMPLEX; UBIQUITINATION; ZINC FINGERS;

EID: 58849123232     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-10     Document Type: Article

References (52)

1. Huang JC Lei ZL Shi LH Miao YL Yang JW Ouyang YC Sun QY Chen DY Comparison of histone modifications in in vivo and in vitro fertilization mouse embryos Biochem Biophys Res Commun 2007, 354(1):77-83. 10.1016/j.bbrc.2006.12.163 17210126
2. Santos F Hendrich B Reik W Dean W Dynamic reprogramming of DNA methylation in the early mouse embryo Dev Biol 2002, 241(1):172-182. 10.1006/dbio.2001.0501 11784103
3. Campbell KH McWhir J Ritchie WA Wilmut I Sheep cloned by nuclear transfer from a cultured cell line Nature 1996, 380(6569):64-66. 10.1038/ 380064a0 8598906
4. Gurdon JB Byrne JA The first half-century of nuclear transplantation Proceedings of the National Academy of Sciences of the United States of America 2003, 100(14):8048-8052. 166179 12821779 10.1073/pnas.1337135100
5. Sung LY Gao S Shen H Yu H Song Y Smith SL Chang CC Inoue K Kuo L Lian J et al Differentiated cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer Nature genetics 2006, 38(11):1323-1328. 10.1038/ng1895 17013394
6. French AJ Adams CA Anderson LS Kitchen JR Hughes MR Wood SH Development of human cloned blastocysts following somatic cell nuclear transfer with adult fibroblasts Stem cells (Dayton, Ohio) 2008, 26(2):485-493. 10.1634/ stemcells.2007-0252 18202077
7. Cowan CA Atienza J Melton DA Eggan K Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells Science 2005, 309(5739):1369-1373. 16123299 16123299 10.1126/science.1116447
8. Hochedlinger K Blelloch R Brennan C Yamada Y Kim M Chin L Jaenisch R Reprogramming of a melanoma genome by nuclear transplantation Genes & development 2004, 18(15):1875-1885. 517407 15289459 10.1101/ gad.1213504
9. Takahashi K Yamanaka S Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors Cell 2006, 126(4):663-676. 10.1016/j.cell.2006.07.024 16904174
10. Park IH Zhao R West JA Yabuuchi A Huo H Ince TA Lerou PH Lensch MW Daley GQ Reprogramming of human somatic cells to pluripotency with defined factors Nature 2008, 451(7175):141-146. 10.1038/nature06534 18157115
11. Takahashi K Tanabe K Ohnuki M Narita M Ichisaka T Tomoda K Yamanaka S Induction of pluripotent stem cells from adult human fibroblasts by defined factors Cell 2007, 131(5):861-872. 10.1016/j.cell.2007.11.019 18035408
12. Aoi T Yae K Nakagawa M Ichisaka T Okita K Takahashi K Chiba T Yamanaka S Generation of pluripotent stem cells from adult mouse liver and stomach cells Science 2008, 321(5889):699-702. 18276851 10.1126/science.1154884
13. Boyer LA Lee TI Cole MF Johnstone SE Levine SS Zucker JP Guenther MG Kumar RM Murray HL Jenner RG et al Core transcriptional regulatory circuitry in human embryonic stem cells Cell 2005, 122(6):947-956. 10.1016/j.cell.2005.08.020 16153702
14. Hansis C Barreto G Maltry N Niehrs C Nuclear reprogramming of human somatic cells by xenopus egg extract requires BRG1 Curr Biol 2004, 14(16):1475-1480. 10.1016/j.cub.2004.08.031 15324664
15. Kikyo N Wade PA Guschin D Ge H Wolffe AP Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI Science 2000, 289(5488):2360-2362. 11009424 11009424 10.1126/science.289.5488.2360
16. Adewumi O Aflatoonian B Ahrlund-Richter L Amit M Andrews PW Beighton G Bello PA Benvenisty N Berry LS Bevan S et al Characterization of human embryonic stem cell lines by the International Stem Cell Initiative Nature biotechnology 2007, 25(7):803-816. 10.1038/nbt1318 17572666
17. Irizarry RA Warren D Spencer F Kim IF Biswal S Frank BC Gabrielson E Garcia JG Geoghegan J Germino G et al Multiple-laboratory comparison of microarray platforms Nature methods 2005, 2(5):345-350. 10.1038/nmeth756 15846361
18. Assou S Anahory T Pantesco V Le Carrour T Pellestor F Klein B Reyftmann L Dechaud H De Vos J Hamamah S The human cumulus-oocyte complex gene-expression profile Human reproduction (Oxford, England) 2006, 21(7):1705-1719. 2377388 16571642 10.1093/humrep/del065
19. Kocabas AM Crosby J Ross PJ Otu HH Beyhan Z Can H Tam WL Rosa GJ Halgren RG Lim B et al The transcriptome of human oocytes Proceedings of the National Academy of Sciences of the United States of America 2006, 103(38):14027-14032. 1599906 16968779 10.1073/pnas.0603227103
20. Assou S Le Carrour T Tondeur S Strom S Gabelle A Marty S Nadal L Pantesco V Reme T Hugnot JP et al A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas Stem cells (Dayton, Ohio) 2007, 25(4):961-973. 1906587 17204602 10.1634/ stemcells.2006-0352
21. Fluckiger AC Marcy G Marchand M Negre D Cosset FL Mitalipov S Wolf D Savatier P Dehay C Cell cycle features of primate embryonic stem cells Stem cells (Dayton, Ohio) 2006, 24(3):547-556. 1934406 16239321 10.1634/ stemcells.2005-0194
22. Dong Y Hakimi MA Chen X Kumaraswamy E Cooch NS Godwin AK Shiekhattar R Regulation of BRCC, a holoenzyme complex containing BRCA1 and BRCA2, by a signalosome-like subunit and its role in DNA repair Molecular cell 2003, 12(5):1087-1099. 10.1016/S1097-2765(03)00424-6 14636569
23. Szutorisz H Georgiou A Tora L Dillon N The proteasome restricts permissive transcription at tissue-specific gene loci in embryonic stem cells Cell 2006, 127(7):1375-1388. 10.1016/j.cell.2006.10.045 17190601
24. Dobson AT Raja R Abeyta MJ Taylor T Shen S Haqq C Pera RA The unique transcriptome through day 3 of human preimplantation development Hum Mol Genet 2004, 13(14):1461-1470. 10.1093/hmg/ddh157 15150160
25. Adjaye J Herwig R Brink TC Herrmann D Greber B Sudheer S Groth D Carnwath JW Lehrach H Niemann H Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression Physiol Genomics 2007, 31(2):315-327. 10.1152/physiolgenomics.00041.2007 17595343
26. Lemaitre JM Danis E Pasero P Vassetzky Y Mechali M Mitotic remodeling of the replicon and chromosome structure Cell 2005, 123(5):787-801. 10.1016/ j.cell.2005.08.045 16325575
27. Meshorer E Misteli T Chromatin in pluripotent embryonic stem cells and differentiation Nature reviews 2006, 7(7):540-546. 10.1038/nrm1938 16723974
28. Chen T Ueda Y Xie S Li E A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation The Journal of biological chemistry 2002, 277(41):38746-38754. 10.1074/jbc.M205312200 12138111
29. Roberts CW Galusha SA McMenamin ME Fletcher CD Orkin SH Haploinsufficiency of Snf5 (integrase interactor 1) predisposes to malignant rhabdoid tumors in mice Proceedings of the National Academy of Sciences of the United States of America 2000, 97(25):13796-13800. 17655 11095756 10.1073/pnas.250492697
30. Ying QL Wray J Nichols J Batlle-Morera L Doble B Woodgett J Cohen P Smith A The ground state of embryonic stem cell self-renewal Nature 2008, 453(7194):519-523. 10.1038/nature06968 18497825
31. Thornton BR Toczyski DP Precise destruction: An emerging picture of the APC Genes Dev 2006, 20(22):3069-3078. 10.1101/gad.1478306 17114580
32. Collins GA Tansey WP The proteasome: A utility tool for transcription? Current opinion in genetics & development 2006, 16(2):197-202. 10.1016/j.gde.2006.02.009 16503126
33. Yu J Vodyanik MA Smuga-Otto K Antosiewicz-Bourget J Frane JL Tian S Nie J Jonsdottir GA Ruotti V Stewart R et al Induced pluripotent stem cell lines derived from human somatic cells Science 2007, 318(5858):1917-1920. 10.1126/science.1151526 18029452
34. Zhao Y Yin X Qin H Zhu F Liu H Yang W Zhang Q Xiang C Hou P Song Z et al Two supporting factors greatly improve the efficiency of human iPSC generation Cell Stem Cell 2008, 3(5):475-479. 10.1016/j.stem.2008.10.002 18983962
35. Huangfu D Osafune K Maehr R Guo W Eijkelenboom A Chen S Muhlestein W Melton DA Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2 Nat Biotechnol 2008, 26(11):1269-1275. 10.1038/nbt.1502 18849973
36. Okita K Nakagawa M Hyenjong H Ichisaka T Yamanaka S Generation of mouse induced pluripotent stem cells without viral vectors Science 2008, 322(5903):949-953. 10.1126/science.1164270 18845712
37. Stadtfeld M Nagaya M Utikal J Weir G Hochedlinger K Induced pluripotent stem cells generated without viral integration Science 2008, 322(5903):945-949. 10.1126/science.1162494 18818365
38. Sato N Sanjuan IM Heke M Uchida M Naef F Brivanlou AH Molecular signature of human embryonic stem cells and its comparison with the mouse Developmental biology 2003, 260(2):404-413. 10.1016/ S0012-1606(03)00256-2 12921741
39. Golan-Mashiach M Dazard JE Gerecht-Nir S Amariglio N Fisher T Jacob-Hirsch J Bielorai B Osenberg S Barad O Getz G et al Design principle of gene expression used by human stem cells: Implication for pluripotency Faseb J 2005, 19(1):147-149. 15498892
40. Skottman H Mikkola M Lundin K Olsson C Stromberg AM Tuuri T Otonkoski T Hovatta O Lahesmaa R Gene expression signatures of seven individual human embryonic stem cell lines Stem cells (Dayton, Ohio) 2005, 23(9):1343-1356. 10.1634/stemcells.2004-0341 16081666
41. Hirst CE Ng ES Azzola L Voss AK Thomas T Stanley EG Elefanty AG Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene Developmental biology 2006, 293(1):90-103. 10.1016/j.ydbio.2006.01.023 16546155
42. Perez-Iratxeta C Palidwor G Porter CJ Sanche NA Huska MR Suomela BP Muro EM Krzyzanowski PM Hughes E Campbell PA et al Study of stem cell function using microarray experiments FEBS letters 2005, 579(8):1795-1801. 10.1016/j.febslet.2005.02.020 15763554
43. Baker DE Harrison NJ Maltby E Smith K Moore HD Shaw PJ Heath PR Holden H Andrews PW Adaptation to culture of human embryonic stem cells and oncogenesis in vivo Nature biotechnology 2007, 25(2):207-215. 10.1038/ nbt1285 17287758
44. Gasca S Pellestor F Assou S Loup V Anahory T Dechaud H De Vos J Hamamah S Identifying new human oocyte marker genes: A microarray approach Reproductive biomedicine online 2007, 14(2):175-183. 2367427 17298719
45. Wood JR Dumesic DA Abbott DH Strauss JF 3rd Molecular abnormalities in oocytes from women with polycystic ovary syndrome revealed by microarray analysis The Journal of clinical endocrinology and metabolism 2007, 92(2):705-713. 10.1210/jc.2006-2123
46. Ge X Yamamoto S Tsutsumi S Midorikawa Y Ihara S Wang SM Aburatani H Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues Genomics 2005, 86(2):127-141. 10.1016/j.ygeno.2005.04.008 15950434
47. Su AI Wiltshire T Batalov S Lapp H Ching KA Block D Zhang J Soden R Hayakawa M Kreiman G et al A gene atlas of the mouse and human protein-encoding transcriptomes Proceedings of the National Academy of Sciences of the United States of America 2004, 101(16):6062-6067. 395923 15075390 10.1073/pnas.0400782101
48. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proceedings of the National Academy of Sciences of the United States of America 1998, 95(25):14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
49. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response Proceedings of the National Academy of Sciences of the United States of America 2001, 98(9):5116-5121. 33173 11309499 10.1073/pnas.091062498
50. Al-Shahrour F Minguez P Vaquerizas JM Conde L Dopazo J BABELOMICS: A suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments Nucleic acids research 2005, 33(Web Server):W460-464. 1160217 15980512 10.1093/nar/gki456
51. Strom S Inzunza J Grinnemo KH Holmberg K Matilainen E Stromberg AM Blennow E Hovatta O Mechanical isolation of the inner cell mass is effective in derivation of new human embryonic stem cell lines Human reproduction (Oxford, England) 2007, 22(12):3051-3058. 10.1093/humrep/ dem335 17959612
52. A guide to microarray experiments - an open letter to the scientific journals Lancet 2002, 360(9338):1019. author reply 1019.