Transcriptional regulation in embryonic stem cells

Advances in Experimental Medicine and Biology

Volumn 695, Issue , 2010, Pages 76-91

  Dominic Heng, Jian Chien ^b   Ng, Huck Hui ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR 2; ENHANCEOSOME; HIGH MOBILITY GROUP PROTEIN; HISTONE DEACETYLASE 2; HOST CELL FACTOR C1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 1; KRUPPEL LIKE FACTOR 2; KRUPPEL LIKE FACTOR 4; KRUPPEL LIKE FACTOR 5; LEUKEMIA INHIBITORY FACTOR; LIVER RECEPTOR HOMOLOG 1; MYC PROTEIN; NUCLEAR RECEPTOR DAX 1; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN C JUN; PROTEIN P300; RNA POLYMERASE II; SMAD1 PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR 7 LIKE 2; TRANSCRIPTION FACTOR CDX2; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

ARTICLE; BINDING SITE; CELL DIFFERENTIATION; CELL RENEWAL; CHROMATIN IMMUNOPRECIPITATION; DIMERIZATION; DNA MICROARRAY; ECTODERM; EMBRYONIC STEM CELL; EPIGENETICS; HUMAN; INNER CELL MASS; MESODERM; MOLECULAR INTERACTION; NONHUMAN; PHENOTYPE; PLURIPOTENT STEM CELL; PRIMORDIAL GERM CELL; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; RNA INTERFERENCE; RNA SEQUENCE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC EPIGENESIS; GENETICS; METABOLISM;

EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; OCTAMER TRANSCRIPTION FACTOR-3;

EID: 79959708527     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-7037-4_6     Document Type: Article

References (76)

1. Lander ES, Linton LM, Birren B et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. (Pubitemid 32165345)
2. Johnson KM, Mitsouras K, Carey M. Eukaryotic transcription: the core of eukaryotic gene activation. Curr Biol 2001; ll:R510-3. (Pubitemid 32632706)
3. Levine M, Tjian R. Transcription regulation and animal diversity. Nature 2003; 424:147-51. (Pubitemid 36858677)
4. Pesce M, Scholer HR. Oct-4: gatekeeper in the beginnings of mammalian development. Stem Cells 2001; 19:271-8. (Pubitemid 32721093)
5. Nichols J, Zevnik B, Anastassiadis K et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 1998; 95:379-91. (Pubitemid 28507326)
6. Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 2000; 24:372-6. (Pubitemid 30187435)
7. Niwa H, Toyooka Y, Shimosato D et al. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 2005; 123:917-29. (Pubitemid 41721036)
8. Avilion AA, Nicolis SK, Pevny LH et al. Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev 2003; 17:126-40. (Pubitemid 36062514)
9. Masui S, Nakatake Y, Toyooka Y et al. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol 2007; 9:625-35. (Pubitemid 47214724)
10. Kopp JL, Ormsbee BD, Desler M et al. Small increases in the level of Sox2 trigger the differentiation of mouse embryonic stem cells. Stem Cells 2008; 26:903-911.
11. Rodda DJ, Chew JL, Lim LH et al. Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem 2005;280:24731-7. (Pubitemid 40934562)
12. Kuroda T, Tada M, Kubota H et al. Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression. Mol Cell Biol 2005; 25:2475-85. (Pubitemid 40354640)
13. Ambrosetti DC, Scholer HR, Dailey L et al. Modulation of the activity of multiple transcriptional activation domains by the DNA binding domains mediates the synergistic action of Sox2 and Oct-3 on the fibroblast growth factor-4 enhancer. J Biol Chem 2000; 275:23387-97. (Pubitemid 30646242)
14. Ambrosetti DC, Basilico C, Dailey L. Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites. Mol Cell Biol 1997; 17:6321-9. (Pubitemid 27451176)
15. Botquin V, Hess H, Fuhrmann G et al. New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. Genes Dev 1998; 12:2073-90. (Pubitemid 28323880)
16. Nishimoto M, Fukushima A, Okuda A et al. The gene for the embryonic stem cell coactivatorUTFl carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Mol Cell Biol 1999; 19:5453-65. (Pubitemid 29339903)
17. Yuan H, Corbi N, Basilico C et al. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev 1995; 9:2635-45.
18. Chew JL, Loh YH, Zhang W et al. Reciprocal transcriptional regulation of Pou5fl and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol 2005; 25:6031-46. (Pubitemid 40946556)
19. Okumura-Nakanishi S, Saito M, Niwa H et al. Oct-3/4 and Sox2 Regulate Oct-3/4 Gene in Embryonic Stem Cells. J Biol Chem 2005; 280:5307-5317. (Pubitemid 40280004)
20. Remenyi A, Lins K, Nissen LJ et al. Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev 2003; 17:2048-59. (Pubitemid 36999330)
21. Williams DC, Jr., Cai M, Clore GM. Molecular basis for synergistic transcriptional activation by Octl and Sox2 revealed from the solution structure of the 42-kDa Octl.Sox2.Hoxbl-DNA ternary transcription factor complex. J Biol Chem 2004; 279:1449-57. (Pubitemid 38082673)
22. Maruyama M, Ichisaka T, Nakagawa M et al. Differential roles for Soxl5 and Sox2 in transcriptional control in mouse embryonic stem cells. J Biol Chem 2005; 280:24371-24379. (Pubitemid 40934520)
23. Mullin NP, Yates A, Rowe AJ et al. The pluripotency rheostat Nanog functions as a dimer. Biochem J 2008; 227-231. (Pubitemid 351580174)
24. Wang W, Lin C, Lu D et al. Chromosomal transposition of PiggyBac in mouse embryonic stem cells. Proc Natl Acad Sci USA 2008; 105:9290-5.
25. Chambers I, Colby D, Robertson M et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 2003; 113:643-55. (Pubitemid 36694189)
26. Mitsui K, Tokuzawa Y, Itoh H et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 2003; 113:631-42. (Pubitemid 36694188)
27. Ivanova N, Dobrin R, Lu R et al. Dissecting self-renewal in stem cells with RNA interference. Nature 2006;442:533-8. (Pubitemid 44167907)
28. Loh YH, Wu Q, Chew JL et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006; 38:431-40.
29. Chambers I, Silva J, Colby D et al. Nanog safeguards pluripotency and mediates germline development. Nature 2007; 450:1230-4.
30. Niwa H, Ogawa K, Shimosato D et al. A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature 2009; 460:118-22.
31. Kalmar T, Lim C, Hayward P et al. Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol 2009; 7:el000149.
32. Carter MG, Stagg CA, Falco G et al. An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. Gene Expr Patterns 2008; 8:181-98.
33. Silva J, Nichols J, Theunissen TW et al. Nanog is the gateway to the pluripotent ground state. Cell 2009; 138:722-37.
34. Jiang J, Chan YS, Loh YH et al. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol 2008; 10:353-60. (Pubitemid 351331023)
35. Hall J, Guo G, Wray J et al. Oct4 and LIF/Stat3 additively induce Kruppel factors to sustain embryonic stem cell self-renewal. Cell Stem Cell 2009; 5:597-609.
36. Ema M, Mori D, Niwa H et al. Kruppel-like factor 5 is essential for blastocyst development and the normal self-renewal of mouse ESCs. Cell Stem Cell 2008; 3:555-67.
37. Dejosez M, Krumenacker JS, Zitur LJ et al. Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. Cell 2008; 133:1162-74. (Pubitemid 351852919)
38. Hu G, Kim J, Xu Q et al. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 2009; 23:837-48.
39. Ding L, Paszkowski-Rogacz M, Nitzsche A et al. A genome-scale RNAi screen for Oct4 modulators defines a role of the Pafl complex for embryonic stem cell identity. Cell Stem Cell 2009; 4:403-15.
40. Gaspar-Maia A, Alajem A, Polesso F et al. Chdl regulates open chromatin and pluripotency of embryonic stem cells. Nature 2009; 460:863-8.
41. Wang J, Rao S, Chu J et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 2006; 444:364-8. (Pubitemid 44764111)
42. Wu Q, Chen X, Zhang J et al. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. J Biol Chem 2006; 281:24090-4. (Pubitemid 44274183)
43. Suzuki A, RayaA, KawakamiYetal. Nanog binds to Smadl andblocks bone morphogenetic protein-induced differentiation of embryonic stem cells. Proc Natl Acad Sci USA 2006; 103:10294-9. (Pubitemid 44051160)
44. Torres J, Watt FM. Nanog maintains pluripotency of mouse embryonic stem cells by inhibiting NFkappaB and cooperating with Stat3. Nat Cell Biol 2008; 10:194-201. (Pubitemid 351194049)
45. Araki R, Fukumura R, Sasaki N et al. More than 40,000 transcripts, including novel and noncoding transcripts, in mouse embryonic stem cells. Stem Cells 2006; 24:2522-8. (Pubitemid 44674313)
46. Sharov AA, Piao Y, Matoba R et al. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 2003; 1:E74.
47. Nagalakshmi U, Wang Z, Waern K et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008; 320:1344-9. (Pubitemid 351929471)
48. Wilhelm BT, Marguerat S, Watt S et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008; 453:1239-43. (Pubitemid 351913597)
49. Ozsolak F, Piatt AR, Jones DR et al. Direct RNA sequencing. Nature 2009; 461:814-8.
50. Boyer LA, Lee TI, Cole MF et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005; 122:947-56. (Pubitemid 41345211)
51. Kim J, Chu J, Shen X et al. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008; 132:1049-1061. (Pubitemid 351381745)
52. Chen X, Xu H, Yuan P et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008; 133:1106-17. (Pubitemid 351787745)
53. Johnson DS, Mortazavi A, Myers RM et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007;316:1497-502. (Pubitemid 46906620)
54. Jothi R, Cuddapah S, Barski A et al. Genome-wide identification of in vivo protein-DNA binding sites from ChlP-Seq data. Nucleic Acids Res 2008; 36:5221-31.
55. Zhou Q, Chipperfield H, Melton DA et al. A gene regulatory network in mouse embryonic stem cells. Proc Natl Acad Sci USA 2007; 104:16438-43.
56. Walker E, Ohishi M, Davey RE et al. Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell 2007; 1:71-86. (Pubitemid 46865803)
57. Matoba R, Niwa H, Masui S et al. Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PLoS ONE 2006; l:e26.
58. Thanos D, Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 1995; 83:1091-100. (Pubitemid 26007801)
59. Du W, Thanos D, Maniatis T. Mechanisms of transcriptional synergism between distinct virus-inducible enhancer elements. Cell 1993; 74:887-98. (Pubitemid 23270608)
60. Faiola F, Liu X, Lo S et al. Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol Cell Biol 2005; 25:10220-34. (Pubitemid 41681950)
61. Ying QL, Wray J, Nichols J et al. The ground state of embryonic stem cell self-renewal. Nature 2008; 453:519-23. (Pubitemid 351733324)
62. Brons IG, Smithers LE, Trotter MW et al. Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature 2007; 448:191-5. (Pubitemid 47067373)
63. Tesar PJ, Chenoweth JG, Brook FA et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 2007; 448:196-9. (Pubitemid 47067378)
64. Sato N, Meijer L, Skaltsounis L et al. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat Med 2004; 10:55-63. (Pubitemid 38524699)
65. Cole MF, Johnstone SE, Newman JJ et al. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 2008; 22:746-55. (Pubitemid 351439106)
66. Pereira L, Yi F, Merrill BJ. Repression of Nanog gene transcription by Tcf3 limits embryonic stem cell self-renewal. Mol Cell Biol 2006; 26:7479-91.
67. Tarn WL, Lim CY, Han J et al. T-cell factor 3 regulates embryonic stem cell pluripotency and self-renewal by the transcriptional control of multiple lineage pathways. Stem Cells 2008; 26:2019-31.
68. Efroni S, Duttagupta R, Cheng J et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2008; 2:437-47. (Pubitemid 351598083)
69. Meshorer E, Yellajoshula D, George E et al. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 2006; 10:105-16. (Pubitemid 43025681)
70. Cao R, Wang L, Wang H et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002;298:1039-43. (Pubitemid 35247314)
71. Endoh M, Endo TA, Endoh T et al. Polycomb group proteins RinglA/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development 2008; 135:1513-24. (Pubitemid 351753641)
72. Liang J, Wan M, Zhang Y et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol 2008; 10:731-9. (Pubitemid 351772939)
73. Yeap LS, Hayashi K, Surani MA. ERG-associated protein with SET domain (ESET)-Oct4 interaction regulates pluripotency and represses the trophectoderm lineage. Epigenetics Chromatin 2009; 2:12.
74. Yuan P, Han J, Guo G et al. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev 2009; 23:2507-20.
75. Bilodeau S, Kagey MH, Frampton GM et al. SetDB 1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 2009; 23:2484-9.
76. Loh YH, Zhang W, Chen X et al. Jmjdla and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 2007; 21:2545-57. (Pubitemid 47607666)