Gene function in early mouse embryonic stem cell differentiation

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Sene, Kagnew ^a   Porter, Christopher J ^a   Palidwor, Gareth ^a   Perez Iratxeta, Carolina ^a   Muro, Enrique M ^a   Campbell, Pearl A ^a   Rudnicki, Michael A ^a   Andrade Navarro, Miguel A ^a  

^a OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A DESATURASE; ACYL COENZYME A DESATURASE 2; BINDING PROTEIN; BRCA2 PROTEIN; CYSTEINE RICH PROTEIN 61; DNA; F BOX PROTEIN; F BOX PROTEIN 15; FILAMIN BINDING LIM PROTEIN 1; GLYCEROPHOSPHOINOSITOL INOSITOLPHOSPHODIESTERASE; GROWTH FACTOR; HELIX LOOP HELIX PROTEIN; INHIBIN; INHIBIN BETA B; KRUPPEL LIKE FACTOR 4; MEMBRANE RECEPTOR; MESSENGER RNA; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN BCL 3; PROTEIN KINASE; PROTEIN KINASE PIM 1; PROTEIN KINASE PIM 3; SCLEROPROTEIN; SUPPRESSOR OF CYTOKINE SIGNALING 1; SUPPRESSOR OF CYTOKINE SIGNALING 3; SURVIVAL MOTOR NEURON PROTEIN; TERATOCARCINOMA DERIVED GROWTH FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR OTX2; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; CYTOSKELETON; DNA MICROARRAY; DOWN REGULATION; EMBRYO; EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC DATABASE; HUMAN; MOLECULAR PHYLOGENY; MOUSE; NONHUMAN; RNA SPLICING; SIGNAL TRANSDUCTION; TIME SERIES ANALYSIS; TRANSCRIPTION REGULATION; UPREGULATION; ANIMAL; CELL LINE; CYTOLOGY; DEVELOPMENTAL BIOLOGY; GENETIC MARKER; METABOLISM; METHODOLOGY; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; TIME;

METAZOA;

ANIMALS; CELL DIFFERENTIATION; CELL LINE; DEVELOPMENTAL BIOLOGY; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENETIC MARKERS; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 34147197561     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-85     Document Type: Article

References (74)

1. StemBase http://www.stembase.ca/
2. Ralston A Rossant J Genetic regulation of stem cell origins in the mouse embryo. Clin Genet 2005 68 106-112 10.1111/j.1399-0004.2005.00478.x 15996204
3. Itskovitz-Eldor J Schuldiner M Karsenti D Eden A Yanuka O Amit M Soreq H Benvenisty N Differentiation of human embryonic stem cells into embryoid bodies compromising the three embryonic germ layers. Mol Med 2000 6 88-95 10859025
4. Leahy A Xiong JW Kuhnert F Stuhlmann H Use of developmental marker genes to define temporal and spatial patterns of differentiation during embryoid body formation J Exp Zool 1999 284 67-81 10.1002/ (SICI)1097-010X(19990615)284:1<67::AID-JEZ10>3.0.CO;2-O 10368935
5. Rodda SJ Kavanagh SJ Rathjen J Rathjen PD Embryonic stem cell differentiation and the analysis of mammalian development Int J Dev Biol 2002 46 449 458 12141431
6. Sekkai D Gruel G Herry M Moucadel V Constantinescu SN Albagli O Tronik-Le Roux D Vainchenker W Bennaceur-Griscelli A Microarray analysis of LIF/Stat3 transcriptional targets in embryonic stem cells. Stem Cells 2005 23 1634-1642 10.1634/stemcells.2005-0182 16099994
7. Palmqvist L Glover CH Hsu L Lu M Bossen B Piret JM Humphries RK Helgason CD Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells 2005 23 663-680 10.1634/stemcells.2004-0157 15849174
8. Loh YH Wu Q Chew JL Vega VB Zhang W Chen X Bourque G George J Leong B Liu J Wong KY Sung KW Lee CW Zhao XD Chiu KP Lipovich L Kuznetsov VA Robson P Stanton LW Wei CL Ruan Y Lim B Ng HH The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells Nat Genet 2006 38 431-440 10.1038/ng1760 16518401
9. Strizzi L Bianco C Normanno N Salomon D Cripto-1: A multifunctional modulator during embryogenesis and oncogenesis Oncogene 2005 24 5731-5741 10.1038/sj.onc.1208918 16123806
10. Thompson JR Gudas LJ Retinoic acid induces parietal endoderm but not primitive endoderm and visceral endoderm differentiation in F9 teratocarcinoma stem cells with a targeted deletion of the Rex-1 (Zfp-42) gene Mol Cell Endocrinol 2002 195 119-133 10.1016/ S0303-7207(02)00180-6 12354678
11. Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004 20 1464-1465 10.1093/bioinformatics/bth088 14962934
12. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000 25 25 29 10.1038/75556 10802651
13. Liu G Loraine AE Shigeta R Cline M Cheng J Valmeekam V Sun S Kulp D Siani-Rose MA NetAffx: Affymetrix probesets and annotations Nucl Acids Res 2003 31 82-86 165568 12519953 10.1093/nar/gkg121
14. Wu CH Apweiler R Bairoch A Natale DA Barker WC Boeckmann B Ferro S Gasteiger E Huang H Lopez R Magrane M Martin MJ Mazumder R O'Donovan C Redaschi N Suzek B The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res 2006 34
15. Van Hoffelen S Herman MA Stem cells: Specifying stem-cell niches in the worm. Curr Biol 2006 16
16. Lopez-Bigas N Ouzounis CA Genome-wide identification of genes likely to be involved in human genetic disease Nucleic Acids Res 2004 32 3108-3114 434425 15181176 10.1093/nar/gkh605
17. Park JM Kohn MJ Bruinsma MW Vech C Intine RV Fuhrmann S Grinberg A Mukherjee I Love PE Ko MS DePamphilis ML Maraia RJ The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells. Mol Cell Biol 2006 26 1445-1451 1367200 16449655 10.1128/MCB.26.4.1445-1451.2006
18. Ponting CP Schultz J Copley RR Andrade MA Bork P Evolution of domain families Adv Protein Chem 2000 54 185-244 10829229
19. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003 4 249-264 10.1093/biostatistics/4.2.249 12925520
20. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001 98 5116-5121 33173 11309499 10.1073/pnas.091062498
21. Ueki K Kondo T Kahn CR Suppressor of cytokine signaling 1 (SOCS-1) and SOCS-3 cause insulin resistance through inhibition of tyrosine phosphorylation of insulin receptor substrate proteins by discrete mechanisms Mol Cell Biol 2004 24 5434-5446 419873 15169905 10.1128/ MCB.24.12.5434-5446.2004
22. Hogan JC Stephens JM Effects of leukemia inhibitory factor on 3T3-L1 adipocytes J Endocrinol 2005 185 485-496 10.1677/joe.1.05980 15930175
23. Li Y McClintick J Zhong L Edenberg HJ Yoder MC Chan RJ Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4 Blood 2005 105 635 637 10.1182/ blood-2004-07-2681 15358627
24. Forrai A Boyle K Hart A Hartley L Rakar S Willson TA Simpson KM Roberts AW Alexander WS Voss AK Robb L Absence of SOCS3 reduces self-renewal and promotes differentiation in murine embryonic stem cells. Stem Cells 2005
25. Mikkers H Nawijn M Allen J Brouwers C Verhoeven E Jonkers J Berns A Mice deficient for all PIM kinases display reduced body size and impaired responses to hematopoietic growth factors. Mol Cell Biol 2004 24 6104-6115 480904 15199164 10.1128/MCB.24.13.6104-6115.2004
26. Shirogane T Fukada T Muller JM Shima DT Hibi M Hirano T Synergistic roles for Pim-1 and c-Myc in STAT3-mediated cell cycle progression and antiapoptosis. Immunity 1999 11 709 719 10.1016/S1074-7613(00)80145-4 10626893
27. Ehrhardt GR Leslie KB Lee F Wieler JS Schrader JW M-Ras, a widely expressed 29-kD homologue of p21 Ras: Expression of a constitutively active mutant results in factor-independent growth of an interleukin-3-dependent cell line. Blood 1999 94 2433-2444 10498616
28. Yang J Chatterjee-Kishore M Staugaitis SM Nguyen H Schlessinger K Levy DE Stark GR Novel roles of unphosphorylated STAT3 in oncogenesis and transcriptional regulation. Cancer Res 2005 65 939-947 15705894
29. Kimmelman AC Nuñez Rodriguez N Chan AM R-Ras3/M-Ras induces neuronal differentiation of PC12 cells through cell-type-specific activation of the mitogen-activated protein kinase cascade. Mol Cell Biol 2002 22 5946-5961 133986 12138204 10.1128/MCB.22.16.5946-5961.2002
30. Allam A Marshall AJ Role of the adaptor proteins Bam32, TAPP1 and TAPP2 in lymphocyte activation. Immunol Lett 2005 97 7-17 10.1016/ j.imlet.2004.09.019 15626471
31. Fujibuchi T Abe Y Takeuchi T Imai Y Kamei Y Murase R Ueda N Shigemoto K Yamamoto H Kito K AIP1/WDR1 supports mitotic cell rounding. Biochem Biophys Res Commun 2005 327 268-275 10.1016/j.bbrc.2004.11.156 15629458
32. Robinson RC Turbedsky K Kaiser DA Marchand JB Higgs HN Choe S Pollard TD Crystal structure of Arp2/3 complex. Science 2001 294 1679-1684 10.1126/ science.1066333 11721045
33. Kumar CC Mohan SR Zavodny PJ Narula SK Leibowitz PJ Characterization and differential expression of human vascular smooth muscle myosin light chain 2 isoform in nonmuscle cells. Biochemistry 1989 28 4027-4035 10.1021/bi00435a059 2526655
34. Wu C Migfilin and its binding partners: From cell biology to human diseases. J Cell Sci 2005 118 659-664 10.1242/jcs.01639 15701922
35. Feinberg MW Cao Z Wara AK Lebedeva MA Senbanerjee S Jain MK Kruppel-like factor 4 (KLF4) is a mediator of proinflammatory signaling in macrophages J Biol Chem 2005
36. Vernay B Koch M Vaccarino F Briscoe J Simeone A Kageyama R Ang SL Otx2 regulates subtype specification and neurogenesis in the midbrain J Neurosci 2005 25 4856-4867 10.1523/JNEUROSCI.5158-04.2005 15888661
37. Renvoise B Khoobarry K Gendron MC Cibert C Viollet L Lefebvre S Distinct domains of the spinal muscular atrophy protein SMN are required for targeting to Cajal bodies in mammalian cells. J Cell Sci 2006
38. Schrank B Gotz R Gunnersen JM Ure JM Toyka KV Smith AG Sendtner M Inactivation of the survival motor neuron gene, a candidate gene for human spinal muscular atrophy, leads to massive cell death in early mouse embryos Proc Natl Acad Sci U S A 1997 94 9920-9925 23295 9275227 10.1073/pnas.94.18.9920
39. Henderson BR Regulation of BRCA1, BRCA2 and BARD1 intracellular trafficking. Bioessays 2005 27 884-893 10.1002/bies.20277 16108063
40. Kannan S De Santis M Lohmeyer M Riese DJ Smith GH Hynes N Seno M Brandt R Bianco C Persico G Kenney N Normanno N Martinez-Lacaci I Ciardiello F Stern DF Gullick WJ Salomon DS Cripto enhances the tyrosine phosphorylation of Shc and activates mitogen-activated protein kinase (MAPK) in mammary epithelial cells. J Biol Chem 1997 272 3330-3335 10.1074/jbc.272.6.3330 9013573
41. Ding J Yang L Yan YT Chen A Desai N Wynshaw-Boris A Shen MM Cripto is required for correct orientation of the anterior-posterior axis in the mouse embryo. Nature 1998 395 702-707 10.1038/27215 9790191
42. Li X Chen Y Schacele S Arman E Haffner-Krausz R Ekblom P Lonai P Fibroblast growth factor signaling and basement membrane assembly are connected during epithelial morphogenesis of the embryoid body. J Cell Biol 2001 153 811-822 10.1083/jcb.153.4.811 11352941
43. Zhao Y Hague S Manek S Zhang L Bicknell R Rees MC PCR display identifies tamoxifen induction of the novel angiogenic factor adrenomedullin by a non estrogenic mechanism in the human endometrium. Oncogene 1998 16 409-415 10.1038/sj.onc.1201768 9467966
44. Mo FE Muntean AG Chen CC Stolz DB Watkins SC Lau LF CYR61 (CCN1) is essential for placental development and vascular integrity. Mol Cell Biol 2002 22 8709-8720 139880 12446788 10.1128/MCB.22.24.8709-8720.2002
45. Cabibbo A Pagani M Fabbri M Rocchi M Farmery MR Bulleid NJ Sitia R ERO1-L, a human protein that favors disulfide bond formation in the endoplasmic reticulum. J Biol Chem 2000 275 4827-4833 10.1074/ jbc.275.7.4827 10671517
46. Bard M Bruner DA Pierson CA Lees ND Biermann B Frye L Koegel C Barbuch R Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase. Proc Natl Acad Sci U S A 1996 93 186-190 40203 8552601 10.1073/pnas.93.1.186
47. Kaestner KH Ntambi JM Kelly TJ Lane MD Differentiation-induced gene expression in 3T3-L1 preadipocytes. A second differentially expressed gene encoding stearoyl-CoA desaturase. J Biol Chem 1989 264 14755-14761 2570068
48. Nguyen LH Erzberger JP Root J Wilson DM The human homolog of Escherichia coli Orn degrades small single-stranded RNA and DNA oligomers. J Biol Chem 2000 275 25900-25906 10.1074/jbc.M002672200 10851236
49. Tokuzawa Y Kaiho E Maruyama M Takahashi K Mitsui K Maeda M Niwa H Yamanaka S Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development. Mol Cell Biol 2003 23 2699-2708 152544 12665572 10.1128/MCB.23.8.2699-2708.2003
50. Brereton P Suzuki T Sasano H Li K Duarte C Obeyesekere V Haeseleer F Palczewski K Smith I Komesaroff P Krozowski Z Pan1b (17betaHSD11)-enzymatic activity and distribution in the lung. Mol Cell Endocrinol 2001 171 111-117 10.1016/S0303-7207(00)00417-2 11165019
51. Bhattacharya B Miura T Brandenberger R Mejido J Luo Y Yang AX Joshi BH Ginis I Thies RS Amit M Lyons I Condie BG Itskovitz-Eldor J Rao MS Puri RK Gene expression in human embryonic stem cell lines: Unique molecular signature. Blood 2004 103 2956-2964 10.1182/blood-2003-09-3314 15070671
52. Dvash T Mayshar Y Darr H McElhaney M Barker D Yanuka O Kotkow KJ Rubin LL Benvenisty N Eiges R Temporal gene expression during differentiation of human embryonic stem cells and embryoid bodies. Hum Reprod 2004 19 2875-2883 10.1093/humrep/deh529 15375076
53. Wade R Bohl J Vande Pol S Paxillin null embryonic stem cells are impaired in cell spreading and tyrosine phosphorylation of focal adhesion kinase Oncogene 2002 21 96 107 10.1038/sj.onc.1205013 11791180
54. Bloch W Fan Y Han J Xue S Schoneberg T Ji G Lu ZJ Walther M Fassler R Hescheler J Addicks K Fleischmann BK Disruption of cytoskeletal integrity impairs Gi-mediated signaling due to displacement of Gi proteins J Cell Biol 2001 154 753-761 10.1083/jcb.200103011 11514589
55. Nur-E-Kamal A Ahmed I Kamal J Schindler M Meiners S Three-dimensional nanofibrillar surfaces promote self-renewal in mouse embryonic stem cells. Stem Cells 2006 24 426-433 10.1634/stemcells.2005-0170 16150921
56. Meshorer E Yellajoshula D George E Scambler PJ Brown DT Misteli T Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells Dev Cell 2006 10 105-116 10.1016/j.devcel.2005.10.017 16399082
57. Daniel DC Highlight: BRCA1 and BRCA2 proteins in breast cancer Microsc Res Tech 2002 59 68-83 10.1002/jemt.10178 12242698
58. Schwarz EM Krimpenfort P Berns A Verma IM Immunological defects in mice with a targeted disruption in Bcl-3 Genes Dev 1997 11 187-197 9009202
59. Kawamura H Tomozoe Y Akagi T Kamei D Ochiai M Yamada M Identification of the nucleocytoplasmic shuttling sequence of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its interaction with mRNA. J Biol Chem 2002 277 2732-2739 10.1074/jbc.M108477200 11705999
60. Perez-Iratxeta C Palidwor G Porter CJ Sanche NA Huska MR Suomela BP Muro EM Krzyzanowski PM Hughes E Campbell PA Study of stem cell function using microarray experiments FEBS Letters 2005 579 1795-1801 10.1016/ j.febslet.2005.02.020 15763554
61. Wheeler DL Barrett T Benson DA Bryant SH Canese K Church DM DiCuccio M Edgar R Federhen S Helmberg W Kenton DL Khovayko O Lipman DJ Madden TL Maglott DR Ostell J Pontius JU Pruitt KD Schuler GD Schriml LM Sequeira E Sherry ST Sirotkin K Starchenko G Suzek TO Tatusov R Tatusova TA Wagner L Yaschenko E Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2005 33 Database Issue D39 45
62. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth G Tierney L Yang JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004 5 R80 545600 15461798 10.1186/gb-2004-5-10-r80
63. NetAffx http://www.affymetrix.com/analysis/index.affx
64. Muro EM Perez-Iratxeta C Andrade MA Amplification of the Gene Ontology annotation of Affymetrix probe sets BMC Bioinformatics 2006 7 159 1435773 16549014 10.1186/1471-2105-7-159
65. NCBI http://www.ncbi.nlm.nih.gov/
66. Letunic I Copley RR Schmidt S Ciccarelli FD Doerks T Schultz J Ponting CP Bork P SMART 4.0: Towards genomic data integration Nucleic Acids Res 2004 32 D142 4 308822 14681379 10.1093/nar/gkh088
67. Bateman A Coin L Durbin R Finn RD Hollich V Griffiths-Jones S Khanna A Marshall M Moxon S Sonnhammer EL Studholme DJ Yeats C Eddy SR The Pfam protein families database Nucleic Acids Res 2004 32 D138 41 308855 14681378 10.1093/nar/gkh121
68. Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bradley P Bork P Bucher P Cerutti L Copley R Courcelle E Das U Durbin R Fleischmann W Gough J Haft D Harte N Hulo N Kahn D Kanapin A Krestyaninova M Lonsdale D Lopez R Letunic I Madera M Maslen J McDowall J Mitchell A Nikolskaya AN Orchard S Pagni M Ponting CP Quevillon E Selengut J Sigrist CJ Silventoinen V Studholme DJ Vaughan R Wu CH InterPro, progress and status in 2005 Nucleic Acids Res 2005 33 Database Issue D201 5
69. GOstat http://gostat.wehi.edu.au/
70. MGI http://www.informatics.jax.org/
71. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997 25 3389-3402 146917 9254694 10.1093/nar/ 25.17.3389
72. Java TreeView http://jtreeview.sourceforge.net/
73. Kanehisa M Goto S Hattori M Aoki-Kinoshita KF Itoh M Kawashima S Katayama T Araki M Hirakawa M From genomics to chemical genomics: New developments in KEGG Nucleic Acids Res 2006 34 D354 7 1347464 16381885 10.1093/nar/gkj102
74. Additional files http://www.ogic.ca/projects/Hailesellasse07/