Mechanism of opening and closing of nucleosomes: single molecule fluorescence studies

• Applicants: Professor Dr. Jörg Langowski (†); Professor Dr. Claus Seidel
• Subject Area: Biophysics
• Term: from 2011 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 196798826

• Final Report Year: 2017

Final Report Abstract

These sophisticated single-molecule FRET measurements of nucleosomes at physiological conditions studies allowed us for the first time to unravel the disassembly process into single steps, starting from the opening of the protein core via sequential dissociation of histone proteins to total unwrapping of the DNA, and identify their characteristic time constants ranging from microseconds to seconds. We combined this quantitative kinetic description with a detailed analysis of the FRET data to characterize the intermediates structurally so that we can provide a unified view of nucleosome disassembly and identify important molecular determinants for this process. This study gives us a detailed picture of the fundamental nucleosome motions that play a dual role in compacting the genome and regulating access to specific DNA sequences. The results are timely; there is a very active debate in the literature about the mechanism of nucleosome unfolding and the role of structural intermediates. This knowledge allowed us to study nucleosome arrays with significantly higher complexity. Finally, the technological boost in the Seidel group put one applicant in the position to submit the project proposal "hybridFRET" for an ERC Advanced Grant 2014, that is actually funded.

Publications

• Nucleosomal DNA accessibility governed by the dimer/tetramer interface. (2011) Nucl. Acids Res., 39, 3093-3102
  V. Böhm, A. Gansen, A. Hieb, K. Tóth, A. Andrews, K. Luger, J. Langowski
  
• Role of histone tails in nucleosome stability. (2011) PLoS Comp Biol 7(12), e1002279
  M. Biswas, K. Voltz, J.C. Smith, J. Langowski
  
• A toolkit and benchmark study for FRET-restrained highprecision structural modeling. Nat. Methods 9, 1218-1225 (2012)
  Kalinin, S., Peulen, Th.-O., Sindbert, S., Rothwell, P. J., Berger, S., Restle, T., Goody, R. S., Gohlke, H., Seidel, C. A. M.
  
• Combining MFD and PIE for accurate single-pair Förster Resonance Energy Transfer measurements. ChemPhysChem 13, 1060-1078 (2012)
  Kudryavtsev, V., Sikor, M., Kalinin, S., Mokranjac, D., Seidel, C. A. M., Lamb, D. C.
  
• Filtered FCS: Species auto and cross correlation functions highlight binding and dynamics in biomolecules. ChemPhysChem 13, 1036-1053 (2012)
  Felekyan, S., Kalinin, S., Sanabria, H., Valeri, A., Seidel, C. A. M.
  
• Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study. (2012) Biophys. J. 102 (4), 849-858
  K. Voltz, J. Trylska, J.C. Smith, J. Langowski
  
• Closing the gap between singlemolecule and bulk FRET analysis of nucleosomes. (2013) PLoS ONE 8(4):e57018
  A. Gansen, A.R. Hieb, V. Böhm, K. Tóth, J. Langowski
  
• Histone- and DNA sequence-dependent stability of nucleosomes
studied by single pair FRET. (2013) Cytometry A 83(9):839-46
  K. Tóth, V. Böhm, C. Sellmann, M. Danner, J. Hanne, M. Berg, I. Barz, A. Gansen, J. Langowski
  
• The conformational state of the nucleosome entry-exit site modulates TATA-box specific TBP binding. (2014) Nucl. Acids Res.,42(12):7561-76
  A.R. Hieb, A. Gansen, V. Böhm, J. Langowski
  
• The role of histone tails in the nucleosome: A computational study. (2014) Biophysical Journal, 107(12), 2911-22
  J. Erler, R. Zhang, L. Petridis, X. Cheng, J.C. Smith, J. Langowski
  
• Nucleosome core particle stability and disassembly and assembly kinetics studied using single-molecule fluorescence. (2015) Biophys. J., 109, 1676-1685
  N.P. Hazan, T.E. Tomov, R. Tsukanov, Y. Berger, R. Masoud, K. Tóth, J. Langowski, E. Nir
  
• Opposing roles of H3 and H4 acetylation in the regulation of nucleosome structure – a FRET study. (2015) Nucl. Acids Res., 43(3),1433- 43
  A. Gansen, K. Tóth, N. Schwarz, J. Langowski
  
• Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter-nucleosome Interaction. (2016) Biophysical Journal
  R. Zhang, J. Erler, J. Langowski
  
• Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr. Opin. Struct. Biol. 40, 163–185 (2016)
  Dimura, M., Peulen, T. O., Hanke, C. A., Prakash, A., Gohlke, H., Seidel, C. A. M.