Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Cell

Volumn 133, Issue 6, 2008, Pages 1106-1117

  Chen, Xi ^a,b   Xu, Han ^a   Yuan, Ping ^a   Fang, Fang ^a,b   Huss, Mikael ^a   Vega, Vinsensius B ^a   Wong, Eleanor ^a   Orlov, Yuriy L ^a   Zhang, Weiwei ^a,b   Jiang, Jianming ^a,b   Loh, Yuin Han ^a,b   Yeo, Hock Chuan ^a   Yeo, Zhen Xuan ^a   Narang, Vipin ^a   Govindarajan, Kunde Ramamoorthy ^a   Leong, Bernard ^a   Shahab, Atif ^a   Ruan, Yijun ^a   Bourque, Guillaume ^a   Sung, Wing Kin ^a   Clarke, Neil D ^a   Wei, Chia Lin ^a   Ng, Huck Hui ^a,b   more..

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

DNA; PROTEINS; STEMCELL

Indexed keywords

HISTONE ACETYLTRANSFERASE PCAF; KRUPPEL LIKE FACTOR 4; OCTAMER TRANSCRIPTION FACTOR 4; PROCOLLAGEN C PROTEINASE; SMAD1 PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

ANIMAL CELL; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CYTOLOGY; DNA SEQUENCE; EMBRYONIC STEM CELL; GENE FUNCTION; GENOME; MOUSE; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

EID: 44649117905     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2008.04.043     Document Type: Article

References (50)

1. Arnosti D.N., and Kulkarni M.M. Transcriptional enhancers: intelligent enhanceosomes or flexible billboards?. J. Cell. Biochem. 94 (2005) 890-898
2. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
3. Bieda M., Xu X., Singer M.A., Green R., and Farnham P.J. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16 (2006) 595-605
4. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
5. Boiani M., and Schöler H.R. Regulatory networks in embryo-derived pluripotent stem cells. Nat. Rev. Mol. Cell Biol. 6 (2005) 872-884
6. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., Guenther M.G., Kumar R.M., Murray H.L., Jenner R.G., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
7. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441 (2006) 349-353
8. Cartwright P., McLean C., Sheppard A., Rivett D., Jones K., and Dalton S. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development 132 (2005) 885-896
9. Cawley S., Bekiranov S., Ng H.H., Kapranov P., Sekinger E.A., Kampa D., Piccolboni A., Sementchenko V., Cheng J., Williams A.J., et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116 (2004) 499-509
10. Chambers I., Colby D., Robertson M., Nichols J., Lee S., Tweedie S., and Smith A. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113 (2003) 643-655
11. Chew J.L., Loh Y.H., Zhang W., Chen X., Tam W.L., Yeap L.S., Li P., Ang Y.S., Lim B., Robson P., et al. Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol. Cell. Biol. 25 (2005) 6031-6046
12. Ehret G.B., Reichenbach P., Schindler U., Horvath C.M., Fritz S., Nabholz M., and Bucher P. DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites. J. Biol. Chem. 276 (2001) 6675-6688
13. Faiola F., Liu X., Lo S., Pan S., Zhang K., Lymar E., Farina A., and Martinez E. Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol. Cell. Biol. 25 (2005) 10220-10234
14. Galan-Caridad J.M., Harel S., Arenzana T.L., Hou Z.E., Doetsch F.K., Mirny L.A., and Reizis B. Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 129 (2007) 345-357
15. Heintzman N.D., Stuart R.K., Hon G., Fu Y., Ching C.W., Hawkins R.D., Barrera L.O., Van Calcar S., Qu C., Ching K.A., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39 (2007) 311-318
16. Ivanova N., Dobrin R., Lu R., Kotenko I., Levorse J., DeCoste C., Schafer X., Lun Y., and Lemischka I.R. Dissecting self-renewal in stem cells with RNA interference. Nature 442 (2006) 533-538
17. Ivanova N.B., Dimos J.T., Schaniel C., Hackney J.A., Moore K.A., and Lemischka I.R. A stem cell molecular signature. Science 298 (2002) 601-604
18. Jiang J., Chan Y.S., Loh Y.H., Cai J., Tong G.Q., Lim C.A., Robson P., Zhong S., and Ng H.H. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat. Cell Biol. 10 (2008) 353-360
19. Johnson D.S., Mortazavi A., Myers R.M., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
20. Kaczynski J., Cook T., and Urrutia R. Sp1- and Kruppel-like transcription factors. Genome Biol. 4 (2003) 206
21. Kim J., Chu J., Shen X., Wang J., and Orkin S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132 (2008) 1049-1061
22. Kim T.H., Abdullaev Z.K., Smith A.D., Ching K.A., Loukinov D.I., Green R.D., Zhang M.Q., Lobanenkov V.V., and Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128 (2007) 1231-1245
23. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
24. Loh Y.H., Wu Q., Chew J.L., Vega V.B., Zhang W., Chen X., Bourque G., George J., Leong B., Liu J., et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38 (2006) 431-440
25. Maherali N., Sridharan R., Xie W., Utikal J., Eminli S., Arnold K., Stadtfeld M., Yachechko R., Tchieu J., Jaenisch R., et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1 (2007) 55-70
26. Merika M., Williams A.J., Chen G., Collins T., and Thanos D. Recruitment of CBP/p300 by the IFN β enhanceosome is required for synergistic activation of transcription. Mol. Cell 1 (1998) 277-287
27. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
28. Mitsui K., Tokuzawa Y., Itoh H., Segawa K., Murakami M., Takahashi K., Maruyama M., Maeda M., and Yamanaka S. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113 (2003) 631-642
29. Nichols J., Zevnik B., Anastassiadis K., Niwa H., Klewe-Nebenius D., Chambers I., Schöler H., and Smith A. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95 (1998) 379-391
30. Niwa H., Burdon T., Chambers I., and Smith A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev. 12 (1998) 2048-2060
31. Ogryzko V.V., Schiltz R.L., Russanova V., Howard B.H., and Nakatani Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87 (1996) 953-959
32. Okita K., Ichisaka T., and Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature 448 (2007) 313-317
33. Panne D., Maniatis T., and Harrison S.C. An atomic model of the interferon-β enhanceosome. Cell 129 (2007) 1111-1123
34. Pavesi G., Mauri G., and Pesole G. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17 Suppl 1 (2001) S207-S214
35. Pettersson K., Svensson K., Mattsson R., Carlsson B., Ohlsson R., and Berkenstam A. Expression of a novel member of estrogen response element-binding nuclear receptors is restricted to the early stages of chorion formation during mouse embryogenesis. Mech. Dev. 54 (1996) 211-223
36. Ramalho-Santos M., Yoon S., Matsuzaki Y., Mulligan R.C., and Melton D.A. "Stemness": transcriptional profiling of embryonic and adult stem cells. Science 298 (2002) 597-600
37. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., Zeng T., Euskirchen G., Bernier B., Varhol R., Delaney A., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4 (2007) 651-657
38. Smith A.G. Embryo-derived stem cells: of mice and men. Annu. Rev. Cell Dev. Biol. 17 (2001) 435-462
39. Struhl K. Gene regulation. A paradigm for precision. Science 293 (2001) 1054-1055
40. Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol. 14 (2007) 103-105
41. Suzuki A., Raya A., Kawakami Y., Morita M., Matsui T., Nakashima K., Gage F.H., Rodriguez-Esteban C., and Izpisua Belmonte J.C. Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells. Proc. Natl. Acad. Sci. USA 103 (2006) 10294-10299
42. Takahashi K., and Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126 (2006) 663-676
43. Thanos D., and Maniatis T. Virus induction of human IFN β gene expression requires the assembly of an enhanceosome. Cell 83 (1995) 1091-1100
44. Thomas K.R., and Capecchi M.R. Introduction of homologous DNA sequences into mammalian cells induces mutations in the cognate gene. Nature 324 (1986) 34-38
45. Wang J., Rao S., Chu J., Shen X., Levasseur D.N., Theunissen T.W., and Orkin S.H. A protein interaction network for pluripotency of embryonic stem cells. Nature 444 (2006) 364-368
46. Wathelet M.G., Lin C.H., Parekh B.S., Ronco L.V., Howley P.M., and Maniatis T. Virus infection induces the assembly of coordinately activated transcription factors on the IFN-β enhancer in vivo. Mol. Cell 1 (1998) 507-518
47. Wernig M., Meissner A., Foreman R., Brambrink T., Ku M., Hochedlinger K., Bernstein B.E., and Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448 (2007) 318-324
48. Ying Q.L., Nichols J., Chambers I., and Smith A. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell 115 (2003) 281-292
49. Zeller K.I., Zhao X., Lee C.W., Chiu K.P., Yao F., Yustein J.T., Ooi H.S., Orlov Y.L., Shahab A., Yong H.C., et al. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc. Natl. Acad. Sci. USA 103 (2006) 17834-17839
50. Zhou Q., Chipperfield H., Melton D.A., and Wong W.H. A gene regulatory network in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 104 (2007) 16438-16443