In silico approaches to untangle the structural mechanisms of the combinatorial regulation of transcription by the pluripotency marker Oct4

• Applicant: Vlad Cojocaru, Ph.D.
• Subject Area: Structural Biology ; Biophysics
• Term: from 2011 to 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 195122149

• Final Report Year: 2014

Final Report Abstract

We applied state-of-the-art computational biophysics methods to understand the structural details that contribute to the ability of OCT4 to adapt its function to the biological environment. In this process, a major role is played by the interaction partners and enhancer elements available in different biological contexts. First, we studied how OCT4 and SOX2 cooperate to recognize the canonical composite motif which is formed by the juxtaposition of the individual binding sites and is the predominant OCT4 binding site in pluripotent cells. Strikingly, we found that SOX2 modifies the orientation and dynamics of both DNA-binding domains of OCT4, the POU- specific and POU-homeodomain, despite interacting directly only with the first. Moreover, SOX2 inverts the relative strength of their DNA-binding affinities, modifying their roles in exploring the DNA. Ultimately, we found that the OCT4-SOX2 cooperativity is modulated through the opposing effects of physical interactions and DNA-mediated allostery. This is an unexpected mechanism for the modulation of cooperative DNA recognition. Second, we studied the structural details underlying the SOX-dependent motif preference of OCT4. We revealed the structure of the OCT4-SOX17-compressed complex that has been shown to form during commitment of pluripotent stem cells to the primitive endoderm lineage. From our simulations, we designed a SOX2 mutant that we predicted and confirmed experimentally to act as SOX17. Furthermore, we found a good correlation between estimated and measured relative cooperative binding free energies, demonstrating that structural-base design of interfaces between transcription factors is attainable and can be used to alter transcriptional circuitries even when experimentallyderived structures for the DNA-bound complexes are not available. We consider the interaction between OCT4 and SOX factors as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions. Our studies contribute to the understanding of the assembly of multi-protein complexes on DNA regulatory regions which ultimately provides specificity to transcriptional regulation.

Publications

• (2012). Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins. Nature Communications 3:1279
  Tapia N, Reinhardt P, Duemmler A, Wu G, Araúzo-Bravo MJ, Esch D, Greber B, Cojocaru V, Rascon CA, Tazaki A, Kump K, Voss R, Tanaka EM, Schöler HR
  
• (2013). A unique Oct4 interface is crucial for reprogramming to pluripotency. Nature Cell Biology 15(3):295-301
  Esch D, Vahokoski J, Groves MR, Pogenberg V, Cojocaru V, Vom Bruch H, Han D, Drexler HC, Araúzo-Bravo MJ, Ng CK, Jauch R, Wilmanns M, Schöler HR
  
• (2014). OCT4: dynamic DNA binding pioneers stem cell pluripotency. Biochimica Biophysica Acta 1839(3):138-54
  Jerabek S, Merino F, Schöler HR, Cojocaru V
  
• (2014). Structural basis for the SOX-dependent redistribution of Oct4 during stem cell differentiation. Structure
  Merino F, Ng C, Veerapandian V, Schöler HR, Jauch R, Cojocaru V