Mechanism of opening and closing of nucleosomes: single molecule fluorescence studies
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
(See online at https://dx.doi.org/10.1093/nar/gkq1279) - Role of histone tails in nucleosome stability. (2011) PLoS Comp Biol 7(12), e1002279
M. Biswas, K. Voltz, J.C. Smith, J. Langowski
(See online at https://dx.doi.org/10.1371/journal.pcbi.1002279) - 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.
(See online at https://doi.org/10.1038/NMETH.2222) - 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.
(See online at https://doi.org/10.1002/cphc.201100822) - 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.
(See online at https://doi.org/10.1002/cphc.201100897) - 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
(See online at https://doi.org/10.1016/j.bpj.2011.11.4028) - 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
(See online at https://doi.org/10.1371/journal.pone.0057018) - 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
(See online at https://doi.org/10.1002/cyto.a.22320) - 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
(See online at https://doi.org/10.1093/nar/gku423) - 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
(See online at https://doi.org/10.1016/j.bpj.2014.10.065) - 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
(See online at https://doi.org/10.1016/j.bpj.2015.07.004) - 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
(See online at https://doi.org/10.1093/nar/gku1354) - Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter-nucleosome Interaction. (2016) Biophysical Journal
R. Zhang, J. Erler, J. Langowski
(See online at https://doi.org/10.1016/j.bpj.2016.11.015) - 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.
(See online at https://doi.org/10.1016/j.sbi.2016.11.012)
