A unique Oct4 interface is crucial for reprogramming to pluripotency

Nature Cell Biology

Volumn 15, Issue 3, 2013, Pages 295-301

  Esch, Daniel ^a   Vahokoski, Juha ^b   Groves, Matthew R ^b   Pogenberg, Vivian ^b   Cojocaru, Vlad ^a   Vom Bruch, Hermann ^a   Han, Dong ^a   Drexler, Hannes C A ^a   Araúzo Bravo, Marcos J ^a   Ng, Calista K L ^c,d   Jauch, Ralf ^c   Wilmanns, Matthias ^b   Schöler, Hans R ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR BIOMEDICINE   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c GENOME INSTITUTE OF SINGAPORE   (Singapore)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

OCTAMER TRANSCRIPTION FACTOR 1; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR POU;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; BIOLOGICAL ACTIVITY; CELL ASSAY; CONTROLLED STUDY; EMBRYO; EPIGENETICS; GENE TARGETING; HYDROGEN BOND; MASS SPECTROMETRY; MOLECULAR INTERACTION; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BLOTTING, WESTERN; CELL DIFFERENTIATION; CELLS, CULTURED; CRYSTALLOGRAPHY, X-RAY; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; FIBROBLASTS; HUMANS; LUCIFERASES; MICE; MOLECULAR SEQUENCE DATA; NUCLEAR REPROGRAMMING; OCTAMER TRANSCRIPTION FACTOR-3; PLURIPOTENT STEM CELLS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84874659144     PISSN: 14657392     EISSN: 14764679     Source Type: Journal    
DOI: 10.1038/ncb2680     Document Type: Article

References (39)

1. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult-broblast cultures by de-ned factors. Cell 126, 663-676 (2006).
2. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917-1920 (2007).
3. Shi, Y. et al. Induction of pluripotent stem cells from mouse embryonic-broblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell 3, 568-574 (2008).
4. Nakagawa, M. et al. Generation of induced pluripotent stem cells without Myc from mouse and human-broblasts. Nat. Biotechnol. 26, 101-106 (2008).
5. Feng, B. et al. Reprogramming of-broblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol. 11, 197-203 (2009).
6. Klemm, J. D., Rould, M. A., Aurora, R., Herr, W. & Pabo, C. O. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77, 21-32 (1994).
7. Reményi, A. et al. Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol. Cell 8, 569-580 (2001).
8. Reményi, A. et al. Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev. 17, 2048-2059 (2003).
9. Williams, D. C. Jr, Cai, M. & Clore, G. M. Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex. J. Biol. Chem. 279, 1449-1457 (2004).
10. Jauch, R., Choo, S. H., Ng, C. K. & Kolatkar, P. R. Crystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA. Proteins 79, 674-677 (2011).
11. Nishimoto, M. et al. Oct-3/4 maintains the proliferative embryonic stem cell state via speci-c binding to a variant octamer sequence in the regulatory region of the UTF1 locus. Mol. Cell Biol. 25, 5084-5094 (2005).
12. Pesce, M., Gross, M. K. & Schöler, H. R. In line with our ancestors: Oct-4 and the mammalian germ. Bioessays 20, 722-732 (1998).
13. Kehler, J. et al. Oct4 is required for primordial germ cell survival. EMBO Rep. 5, 1078-1083 (2004).
14. Klemm, J. D. & Pabo, C. O. Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. Genes Dev. 10, 27-36 (1996).
15. Van den Berg, D. L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem. Cell 6, 369-381 (2010).
16. Pardo, M. et al. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6, 382-395 (2010).
17. Ding, J., Xu, H., Faiola, F., Ma'ayan, A. & Wang, J. Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res. 22, 155-167 (2012).
18. Singhal, N. et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943-955 (2010).
19. Trotter, K. W. & Archer, T. K. The BRG1 transcriptional coregulator. Nucl. Recept. Signal. 6, e004 (2008).
20. Hu, G. & Wade, P. A. NuRD and pluripotency: a complex balancing act. Cell Stem Cell 10, 497-503 (2012).
21. Rai, K. et al. DNA demethylation in zebra-sh involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135, 1201-1212 (2008).
22. Bhutani, N. et al. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463, 1042-1047 (2010).
23. Niwa, H., Miyazaki, J. & Smith, A. G. Quantitative expression of Oct-3/4 de-nes differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372-376 (2000).
24. Adachi, K. & Schöler, H. R. Directing reprogramming to pluripotency by transcription factors. Curr. Opin. Genet. Dev. 22, 416-422 (2012).
25. Schöler, H. R., Balling, R., Hatzopoulos, A. K., Suzuki, N. & Gruss, P. Octamer binding proteins confer transcriptional activity in early mouse embryogenesis. EMBO J. 8, 2551-2557 (1989).
26. Mueller-Dieckmann, J. The open-access high-throughput crystallization facility at EMBL Hamburg. Acta Crystallogr. D 62, 1446-1452 (2006).
27. Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a positionsensitive detector. J. Appl. Crystallogr. 21, 916-924 (1988).
28. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
29. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
30. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Re-nement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
31. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486-501 (2010).
32. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12-21 (2010).
33. Sauter, P. & Matthias, P. Coactivator OBF-1 makes selective contacts with both the POU-speci-c domain and the POU homeodomain and acts as a molecular clamp on DNA. Mol. Cell Biol. 18, 7397-7409 (1998).
34. Tomilin, A. et al. Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a speci-c POU dimer con-guration. Cell 103, 853-864 (2000).
35. Kim, J. B. et al. Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature 454, 646-650 (2008).
36. Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362 (2009).
37. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670 (2003).
38. Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993).
39. Fiser, A., Do, R. K. & Sali, A. Modeling of loops in protein structures. Protein Sci. 9, 1753-1773 (2000).