Takahashi K, Yamanaka S: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006, 126: 663-676. 10.1016/j.cell.2006.07.024.
Article
CAS
PubMed
Google Scholar
Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Gifford W, Martin G, Kupriyanov S, Baldwin KK: Adult mice generated from induced pluripotent stem cells. Nature. 2009, 461: 91-94. 10.1038/nature08310.
Article
CAS
PubMed
Google Scholar
Kang L, Wang J, Zhang Y, Kou Z, Gao S: iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell. 2009, 5: 135-138. 10.1016/j.stem.2009.07.001.
Article
CAS
PubMed
Google Scholar
Zhao XY, Li W, Lv Z, Liu L, Tong M, Hai T, Hao J, Guo CL, Ma QW, Wang L, Zeng F, Zhou Q: iPS cells produce viable mice through tetraploid complementation. Nature. 2009, 461: 86-90. 10.1038/nature08267.
Article
CAS
PubMed
Google Scholar
Gao Y, Chen J, Li K, Wu T, Huang B, Liu W, Kou X, Zhang Y, Huang H, Jiang Y, Yao C, Liu X, Lu Z, Xu Z, Kang L, Chen J, Wang H, Cai T, Gao S: Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming. Cell Stem Cell. 2013, 12: 453-469. 10.1016/j.stem.2013.02.005.
Article
CAS
PubMed
Google Scholar
Chen J, Liu H, Liu J, Qi J, Wei B, Yang J, Liang H, Chen Y, Wu Y, Guo L, Zhu J, Zhao X, Peng T, Zhang Y, Chen S, Li X, Li D, Wang T, Pei D: H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet. 2013, 45: 34-42. 10.1038/ng.2491.
Article
CAS
PubMed
Google Scholar
Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, Young RA: Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell. 2010, 7: 249-257. 10.1016/j.stem.2010.06.015.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jiang C, Pugh BF: Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet. 2009, 10: 161-172. 10.1038/nrg2522.
Article
CAS
PubMed
Google Scholar
Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M: Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol. 2011, 12: 36-47. 10.1038/nrm3036.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kou Z, Kang L, Yuan Y, Tao Y, Zhang Y, Wu T, He J, Wang J, Liu Z, Gao S: Mice cloned from induced pluripotent stem cells (iPSCs). Biol Reprod. 2010, 83: 238-243. 10.1095/biolreprod.110.084731.
Article
CAS
PubMed
Google Scholar
Kang L, Wu T, Tao Y, Yuan Y, He J, Zhang Y, Luo T, Kou Z, Gao S: Viable mice produced from three-factor induced pluripotent stem (iPS) cells through tetraploid complementation. Cell Res. 2011, 21: 546-549. 10.1038/cr.2010.164.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ahmed K, Dehghani H, Rugg-Gunn P, Fussner E, Rossant J, Bazett-Jones DP: Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo. PLoS One. 2010, 5: e10531-10.1371/journal.pone.0010531.
Article
PubMed Central
PubMed
Google Scholar
Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, Bazett-Jones DP, Le Grice S, McKay RD, Buetow KH, Gingeras TR, Misteli T, Meshorer E: Global transcription in pluripotent embryonic stem cells. Cell Stem Cell. 2008, 2: 437-447. 10.1016/j.stem.2008.03.021.
Article
CAS
PubMed Central
PubMed
Google Scholar
Park SH, Kook MC, Kim EY, Park S, Lim JH: Ultrastructure of human embryonic stem cells and spontaneous and retinoic acid-induced differentiating cells. Ultrastruct Pathol. 2004, 28: 229-238. 10.1080/01913120490515595.
Article
PubMed
Google Scholar
Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Hofer T, Rippe K: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res. 2014, 24: 1285-1295. 10.1101/gr.164418.113.
Article
CAS
PubMed Central
PubMed
Google Scholar
Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Hofer T, Rippe K: Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol. 2012, 19: 1185-1192. 10.1038/nsmb.2419.
Article
CAS
PubMed
Google Scholar
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature. 2007, 446: 572-576. 10.1038/nature05632.
Article
CAS
PubMed
Google Scholar
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF: Nucleosome organization in the Drosophila genome. Nature. 2008, 453: 358-362. 10.1038/nature06929.
Article
CAS
PubMed Central
PubMed
Google Scholar
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K: Dynamic regulation of nucleosome positioning in the human genome. Cell. 2008, 132: 887-898. 10.1016/j.cell.2008.02.022.
Article
CAS
PubMed
Google Scholar
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH: Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008, 133: 1106-1117. 10.1016/j.cell.2008.04.043.
Article
CAS
PubMed
Google Scholar
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B: A map of the cis-regulatory sequences in the mouse genome. Nature. 2012, 488: 116-120. 10.1038/nature11243.
Article
CAS
PubMed Central
PubMed
Google Scholar
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC: CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 2010, 6: e1001023-10.1371/journal.pgen.1001023.
Article
PubMed Central
PubMed
Google Scholar
Orkin SH, Hochedlinger K: Chromatin connections to pluripotency and cellular reprogramming. Cell. 2011, 145: 835-850. 10.1016/j.cell.2011.05.019.
Article
CAS
PubMed
Google Scholar
Soufi A, Donahue G, Zaret KS: Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell. 2012, 151: 994-1004. 10.1016/j.cell.2012.09.045.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K: Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 2009, 19: 24-32. 10.1101/gr.082800.108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC: Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PLoS One. 2010, 5: e8975-10.1371/journal.pone.0008975.
Article
PubMed Central
PubMed
Google Scholar
Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE: Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009, 5: 111-123. 10.1016/j.stem.2009.06.008.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M: Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011, 13: 541-549. 10.1038/ncb2239.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, Plongthongkum N, Kumar S, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Kan NG, Schöler HR, Mercola M, Zhang K, Izpisua Belmonte JC: Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proc Natl Acad Sci U S A. 2012, 109: 16196-16201. 10.1073/pnas.1202352109.
Article
CAS
PubMed Central
PubMed
Google Scholar
Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ: Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011, 8: 821-827. 10.1038/nmeth.1699.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009, 462: 315-322. 10.1038/nature08514.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B: Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010, 6: 479-491. 10.1016/j.stem.2010.03.018.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ben-David U, Benvenisty N: The tumorigenicity of human embryonic and induced pluripotent stem cells. Nat Rev Cancer. 2011, 11: 268-277. 10.1038/nrc3034.
Article
CAS
PubMed
Google Scholar
Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K: Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011, 471: 63-67. 10.1038/nature09805.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Narva E, Ng S, Sourour M, Hamalainen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T: Copy number variation and selection during reprogramming to pluripotency. Nature. 2011, 471: 58-62. 10.1038/nature09871.
Article
CAS
PubMed
Google Scholar
Zheng B, Cao B, Li G, Huard J: Mouse adipose-derived stem cells undergo multilineage differentiation in vitro but primarily osteogenic and chondrogenic differentiation in vivo. Tissue Eng. 2006, 12: 1891-1901. 10.1089/ten.2006.12.1891.
Article
CAS
PubMed
Google Scholar
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: 699-702. 10.1126/science.1154884.
Article
CAS
PubMed
Google Scholar
Jensen KB, Driskell RR, Watt FM: Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis. Nat Protoc. 2010, 5: 898-911. 10.1038/nprot.2010.39.
Article
CAS
PubMed
Google Scholar