Sox Transcription Factors Require Selective Interactions with Oct4 and Specific Transactivation Functions to Mediate Reprogramming

The unique ability of Sox2 to cooperate with Oct4 at selective binding sites in the genome is critical for reprogramming somatic cells into induced pluripotent stem cells (iPSCs). We have recently demonstrated that Sox17 can be converted into a reprogramming factor by alteration of a single amino acid (Sox17EK) within its DNA binding HMG domain. Here we expanded this study by introducing analogous mutations to 10 other Sox proteins and interrogated the role of N‐and C‐termini on the reprogramming efficiency. We found that point‐mutated Sox7 and Sox17 can convert human and mouse fibroblasts into iPSCs, but Sox4, Sox5, Sox6, Sox8, Sox9, Sox11, Sox12, Sox13, and Sox18 cannot. Next we studied regions outside the HMG domain and found that the C‐terminal transactivation domain of Sox17 and Sox7 enhances the potency of Sox2 in iPSC assays and confers weak reprogramming potential to the otherwise inactive Sox4EK and Sox18EK proteins. These results suggest that the glutamate (E) to lysine (K) mutation in the HMG domain is necessary but insufficient to swap the function of Sox factors. Moreover, the HMG domain alone fused to the VP16 transactivation domain is able to induce reprogramming, albeit at low efficiency. By molecular dissection of the C‐terminus of Sox17, we found that the β‐catenin interaction region contributes to the enhanced reprogramming efficiency of Sox17EK. To mechanistically understand the enhanced reprogramming potential of Sox17EK, we analyzed ChIP‐sequencing and expression data and identified a subset of candidate genes specifically regulated by Sox17EK and not by Sox2. Stem Cells 2013;31:2632–2646

[1]  Tristan Frum,et al.  Oct4 cell-autonomously promotes primitive endoderm development in the mouse blastocyst. , 2013, Developmental cell.

[2]  L. Stanton,et al.  Pluripotency-regulating networks provide basis for reprogramming. , 2013, Current molecular medicine.

[3]  Mauro J. Muraro,et al.  Concise Review: The Dynamics of Induced Pluripotency and Its Behavior Captured in Gene Network Motifs , 2013, Stem cells.

[4]  P. Robson,et al.  Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm , 2013, The EMBO journal.

[5]  Qi-Long Ying,et al.  Gbx2, a LIF/Stat3 target, promotes reprogramming to and retention of the pluripotent ground state , 2013, Journal of Cell Science.

[6]  Prasanna R Kolatkar,et al.  The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition. , 2012, The Biochemical journal.

[7]  Shyam Prabhakar,et al.  Deciphering the Sox-Oct partner code by quantitative cooperativity measurements , 2012, Nucleic acids research.

[8]  P. Robson,et al.  Conversion of Sox17 into a Pluripotency Reprogramming Factor by Reengineering Its Association with Oct4 on DNA , 2011, Stem cells.

[9]  M. Goodheart,et al.  Sox17 modulates Wnt3A/beta-catenin-mediated transcriptional activation of the Lef-1 promoter. , 2010, American journal of physiology. Lung cellular and molecular physiology.

[10]  P. Kraus,et al.  A more cost effective and rapid high percentage germ‐line transmitting chimeric mouse generation procedure via microinjection of 2‐cell, 4‐cell, and 8‐cell embryos with ES and iPS cells , 2010, Genesis.

[11]  Robin Lovell-Badge,et al.  The early history of the Sox genes. , 2010, The international journal of biochemistry & cell biology.

[12]  M. Beltrame,et al.  SoxF genes: Key players in the development of the cardio-vascular system. , 2010, The international journal of biochemistry & cell biology.

[13]  Kit T. Rodolfa,et al.  Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. , 2010, Genes & development.

[14]  Yang Yang,et al.  Kruppel-like Factor 4 (Klf4) Prevents Embryonic Stem (ES) Cell Differentiation by Regulating Nanog Gene Expression* , 2010, The Journal of Biological Chemistry.

[15]  Marc W. Kirschner,et al.  Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling , 2009, Nature.

[16]  R. Nusse,et al.  Towards an integrated view of Wnt signaling in development , 2009, Development.

[17]  Deepak M. Gupta,et al.  Feeder-free derivation of induced pluripotent stem cells from adult human adipose stem cells , 2009, Proceedings of the National Academy of Sciences.

[18]  Chad A. Cowan,et al.  Interplay of Oct4 with Sox2 and Sox17: a molecular switch from stem cell pluripotency to specifying a cardiac fate , 2009, The Journal of cell biology.

[19]  Raivo Kolde,et al.  The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation , 2009, PloS one.

[20]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[21]  P. Kolatkar,et al.  The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms. , 2009, Journal of molecular biology.

[22]  Thomas Lufkin,et al.  Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb , 2009, Nature Cell Biology.

[23]  F. Orsenigo,et al.  Sox18 induces development of the lymphatic vasculature in mice , 2008, Nature.

[24]  Wenjun Guo,et al.  Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2 , 2008, Nature Biotechnology.

[25]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[26]  J. Rossant,et al.  Establishment of endoderm progenitors by SOX transcription factor expression in human embryonic stem cells. , 2008, Cell stem cell.

[27]  Jie Pan,et al.  Sox17 facilitates the differentiation of mouse embryonic stem cells into primitive and definitive endoderm in vitro , 2008, Development, growth & differentiation.

[28]  Wenjun Guo,et al.  Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds , 2008, Nature Biotechnology.

[29]  A. Rizzino,et al.  Small Increases in the Level of Sox2 Trigger the Differentiation of Mouse Embryonic Stem Cells , 2008, Stem cells.

[30]  Richard A Young,et al.  Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. , 2008, Genes & development.

[31]  Marius Wernig,et al.  c-Myc is dispensable for direct reprogramming of mouse fibroblasts. , 2008, Cell stem cell.

[32]  Shulan Tian,et al.  Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells , 2007, Science.

[33]  Marielle Afanassieff,et al.  Self‐Renewal of Murine Embryonic Stem Cells Is Supported by the Serine/Threonine Kinases Pim‐1 and Pim‐3 , 2007, Stem cells.

[34]  Aaron M. Zorn,et al.  Sox17 and Sox4 Differentially Regulate β-Catenin/T-Cell Factor Activity and Proliferation of Colon Carcinoma Cells , 2007, Molecular and Cellular Biology.

[35]  Y. Saijoh,et al.  Redundant roles of Sox17 and Sox18 in early cardiovascular development of mouse embryos. , 2007, Biochemical and biophysical research communications.

[36]  J. Kiefer,et al.  Back to basics: Sox genes , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

[37]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[38]  H. Niwa,et al.  Synergistic action of Wnt and LIF in maintaining pluripotency of mouse ES cells. , 2006, Biochemical and biophysical research communications.

[39]  X. Chen,et al.  The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells , 2006, Nature Genetics.

[40]  Dongxin Zhao,et al.  WNT/β-catenin pathway up-regulates Stat3 and converges on LIF to prevent differentiation of mouse embryonic stem cells , 2006 .

[41]  Megan F. Cole,et al.  Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells , 2005, Cell.

[42]  P. Robson,et al.  Transcriptional Regulation of Nanog by OCT4 and SOX2* , 2005, Journal of Biological Chemistry.

[43]  X. Chen,et al.  Reciprocal Transcriptional Regulation of Pou5f1 and Sox2 via the Oct4/Sox2 Complex in Embryonic Stem Cells , 2005, Molecular and Cellular Biology.

[44]  M. Tada,et al.  Octamer and Sox Elements Are Required for Transcriptional cis Regulation of Nanog Gene Expression , 2005, Molecular and Cellular Biology.

[45]  I. Chambers The molecular basis of pluripotency in mouse embryonic stem cells. , 2004, Cloning and stem cells.

[46]  H. Hamada,et al.  Interplay of SOX and POU Factors in Regulation of the Nestin Gene in Neural Primordial Cells , 2004, Molecular and Cellular Biology.

[47]  A. Zorn,et al.  Sox17 and β-catenin cooperate to regulate the transcription of endodermal genes , 2004 .

[48]  Matthias Wilmanns,et al.  Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. , 2003, Genes & development.

[49]  P. Koopman,et al.  Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators. , 2002, Current opinion in genetics & development.

[50]  Yoshiakira Kanai,et al.  Depletion of definitive gut endoderm in Sox17-null mutant mice. , 2002, Development.

[51]  L. Mirny,et al.  Using orthologous and paralogous proteins to identify specificity determining residues , 2002, Genome Biology.

[52]  J. Cañizares,et al.  SOX7 transcription factor: sequence, chromosomal localisation, expression, transactivation and interference with Wnt signalling. , 2001, Nucleic Acids Research.

[53]  H. Kondoh,et al.  Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. , 2001, Genes & development.

[54]  J. Bowles,et al.  Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. , 2000, Developmental biology.

[55]  H. Kondoh,et al.  Pairing SOX off: with partners in the regulation of embryonic development. , 2000, Trends in genetics : TIG.

[56]  Akihiko Okuda,et al.  The Gene for the Embryonic Stem Cell Coactivator UTF1 Carries a Regulatory Element Which Selectively Interacts with a Complex Composed of Oct-3/4 and Sox-2 , 1999, Molecular and Cellular Biology.

[57]  M. Wegner,et al.  From head to toes: the multiple facets of Sox proteins. , 1999, Nucleic acids research.

[58]  H. Kondoh,et al.  Mechanism of Regulatory Target Selection by the SOX High-Mobility-Group Domain Proteins as Revealed by Comparison of SOX1/2/3 and SOX9 , 1999, Molecular and Cellular Biology.

[59]  H. Schöler,et al.  Formation of Pluripotent Stem Cells in the Mammalian Embryo Depends on the POU Transcription Factor Oct4 , 1998, Cell.

[60]  M. Wegner,et al.  Cooperative Function of POU Proteins and SOX Proteins in Glial Cells* , 1998, The Journal of Biological Chemistry.

[61]  M. Wegner,et al.  Sox10, a Novel Transcriptional Modulator in Glial Cells , 1998, The Journal of Neuroscience.

[62]  D. Ambrosetti,et al.  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 , 1997, Molecular and cellular biology.

[63]  M. Rosenfeld,et al.  POU domain family values: flexibility, partnerships, and developmental codes. , 1997, Genes & development.

[64]  N. Corbi,et al.  Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. , 1995, Genes & development.

[65]  A. Gronenborn,et al.  Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex , 1995, Cell.

[66]  H. Clevers,et al.  Sox‐4, an Sry‐like HMG box protein, is a transcriptional activator in lymphocytes. , 1993, The EMBO journal.

[67]  G. Ruvkun,et al.  The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. , 1988, Genes & development.

[68]  Xiaoxiao Zhang,et al.  Gene Regulatory Networks Mediating Canonical Wnt Signal‐Directed Control of Pluripotency and Differentiation in Embryo Stem Cells , 2013, Stem cells.

[69]  Takashi Aoi,et al.  Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts , 2008, Nature Biotechnology.

[70]  V. Lefebvre,et al.  Control of cell fate and differentiation by Sry-related high-mobility-group box (Sox) transcription factors. , 2007, The international journal of biochemistry & cell biology.

[71]  Dongxin Zhao,et al.  WNT/beta-catenin pathway up-regulates Stat3 and converges on LIF to prevent differentiation of mouse embryonic stem cells. , 2006, Developmental biology.

[72]  A. Zorn,et al.  Sox17 and beta-catenin cooperate to regulate the transcription of endodermal genes. , 2004, Development.

[73]  R. Lovell-Badge,et al.  Multipotent cell lineages in early mouse development depend on SOX2 function. , 2003, Genes & development.

[74]  C. Lottaz,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[75]  Herbert Schulz,et al.  Novel STAT3 Target Genes Exert Distinct Roles in the Inhibition of Mesoderm and Endoderm Differentiation in Cooperation with Nanog , 2009, Stem cells.