Niwa H. How is pluripotency determined and maintained? Development. 2007;134:635–46.
Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663–76.
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.
Masui S, Nakatake Y, Toyooka Y, Shimosato D, Yagi R, Takahashi K, Okochi H, Okuda A, Matoba R, Sharov AA, et al. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol. 2007;9:625–35.
Cartwright P, McLean C, Sheppard A, Rivett D, Jones K, Dalton S. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development. 2005;132:885–96.
Jiang J, Chan YS, Loh YH, Cai J, Tong GQ, Lim CA, Robson P, Zhong S, Ng HH. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol. 2008;10:353–60.
Niwa H, Ogawa K, Shimosato D, Adachi K. A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature. 2009;460:118–22.
Smith KN, Singh AM, Dalton S. Myc represses primitive endoderm differentiation in pluripotent stem cells. Cell Stem Cell. 2010;7:343–54.
Okabayashi K, Asashima M. Tissue generation from amphibian animal caps. Curr Opin Genet Dev. 2003;13:502–7.
Venuti JM, Jeffery WR. Cell lineage and determination of cell fate in ascidian embryos. Int J Dev Biol. 1989;33:197–212.
Niwa H, Sekita Y, Tsend-Ayush E, Grutzner F. Platypus Pou5f1 reveals the first steps in the evolution of trophectoderm differentiation and pluripotency in mammals. Evol Dev. 2008;10:671–82.
Frankenberg S, Pask A, Renfree MB. The evolution of class V POU domain transcription factors in vertebrates and their characterisation in a marsupial. Dev Biol. 2010;337:162–70.
Frankenberg S, Renfree MB. On the origin of POU5F1. BMC Biol. 2013;11:56.
Kamachi Y, Kondoh H. Sox proteins: regulators of cell fate specification and differentiation. Development. 2013;140:4129–44.
Sharov AA, Masui S, Sharova LV, Piao Y, Aiba K, Matoba R, Xin L, Niwa H, Ko MS. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics. 2008;9:269.
Yuan H, Corbi N, Basilico C, Dailey L. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev. 1995;9:2635–45.
Soriano NS, Russell S. The Drosophila SOX-domain protein Dichaete is required for the development of the central nervous system midline. Development. 1998;125:3989–96.
Schepers GE, Teasdale RD, Koopman P. Twenty pairs of sox: extent, homology, and nomenclature of the mouse and human sox transcription factor gene families. Dev Cell. 2002;3:167–70.
Bowles J, Schepers G, Koopman P. Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol. 2000;227:239–55.
Guo G, Yang J, Nichols J, Hall JS, Eyres I, Mansfield W, Smith A. Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development. 2009;136:1063–9.
Kinoshita M, Shimosato D, Yamane M, Niwa H. Sox7 is dispensable for primitive endoderm differentiation from mouse ES cells. BMC Dev Biol. 2015;15:37.
Jauch R, Aksoy I, Hutchins AP, Ng CK, Tian XF, Chen J, Palasingam P, Robson P, Stanton LW, Kolatkar PR. Conversion of Sox17 into a pluripotency reprogramming factor by reengineering its association with Oct4 on DNA. Stem Cells. 2011;29:940–51.
Brunetti R, Gissi C, Pennati R, Caicci F, Gasparini F, Manni L. Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis. J Zool Syst Evol Res. 2015;53:186–93.
Phochanukul N, Russell S. No backbone but lots of Sox: Invertebrate Sox genes. Int J Biochem Cell Biol. 2010;42:453–64.
Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR, Wilmanns M. 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.
Uchikawa M, Kamachi Y, Kondoh H. Two distinct subgroups of Group B Sox genes for transcriptional activators and repressors: their expression during embryonic organogenesis of the chicken. Mech Dev. 1999;84:103–20.
Hemmrich G, Khalturin K, Boehm AM, Puchert M, Anton-Erxleben F, Wittlieb J, Klostermeier UC, Rosenstiel P, Oberg HH, Domazet-Loso T, et al. Molecular signatures of the three stem cell lineages in hydra and the emergence of stem cell function at the base of multicellularity. Mol Biol Evol. 2012;29:3267–80.
Gehring WJ. The master control gene for morphogenesis and evolution of the eye. Genes Cells. 1996;1:11–5.
Ranganayakulu G, Elliott DA, Harvey RP, Olson EN. Divergent roles for NK-2 class homeobox genes in cardiogenesis in flies and mice. Development. 1998;125:3037–48.
Cossais F, Sock E, Hornig J, Schreiner S, Kellerer S, Bosl MR, Russell S, Wegner M. Replacement of mouse Sox10 by the Drosophila ortholog Sox100B provides evidence for co-option of SoxE proteins into vertebrate-specific gene-regulatory networks through altered expression. Dev Biol. 2010;341:267–81.
Tomioka M, Nishimoto M, Miyagi S, Katayanagi T, Fukui N, Niwa H, Muramatsu M, Okuda A. Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex. Nucleic Acids Res. 2002;30:3202–13.
Uchikawa M, Ishida Y, Takemoto T, Kamachi Y, Kondoh H. Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals. Dev Cell. 2003;4:509–19.
Iwafuchi M, Yoshida Y, Onichtchouk D. M leichsenring, W Driever, T Takemoto, M Uchikawa, Y Kamachi, H Kondoh: The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates. Dev Biol. 2011;352:354–66.
Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B. CRISPE reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS One. 2014;9:e114485.
Zhou HY, Katsman Y, Dhaliwal NK, Davidson S, Macpherson NN, Sakthidevi M, Collura F, Mitchell JA. A Sox2 distal enhancer cluster regulates emrbyonic stem cell differentiation potential. Genes Dev. 2014;28:2699–711.
Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR, Niwa H. Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells. Mol Cell. 2012;52:380–92.