1
|
Würtz M, Aumiller D, Gundelwein L, Jung P, Schütz C, Lehmann K, Tóth K, Rohr K. DNA accessibility of chromatosomes quantified by automated image analysis of AFM data. Sci Rep 2019; 9:12788. [PMID: 31484969 PMCID: PMC6726762 DOI: 10.1038/s41598-019-49163-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/19/2019] [Indexed: 12/26/2022] Open
Abstract
DNA compaction and accessibility in eukaryotes are governed by nucleosomes and orchestrated through interactions between DNA and DNA-binding proteins. Using QuantAFM, a method for automated image analysis of atomic force microscopy (AFM) data, we performed a detailed statistical analysis of structural properties of mono-nucleosomes. QuantAFM allows fast analysis of AFM images, including image preprocessing, object segmentation, and quantification of different structural parameters to assess DNA accessibility of nucleosomes. A comparison of nucleosomes reconstituted with and without linker histone H1 quantified H1's already described ability of compacting the nucleosome. We further employed nucleosomes bearing two charge-modifying mutations at position R81 and R88 in histone H2A (H2A R81E/R88E) to characterize DNA accessibility under destabilizing conditions. Upon H2A mutation, even in presence of H1, the DNA opening angle at the entry/exit site was increased and the DNA wrapping length around the histone core was reduced. Interestingly, a distinct opening of the less bendable DNA side was observed upon H2A mutation, indicating an enhancement of the intrinsic asymmetry of the Widom-601 nucleosomes. This study validates AFM as a technique to investigate structural parameters of nucleosomes and highlights how the DNA sequence, together with nucleosome modifications, can influence the DNA accessibility.
Collapse
Affiliation(s)
- Martin Würtz
- German Cancer Research Center, Division Biophysics of Macromolecules, Heidelberg, 69120, Germany
- Heidelberg University, BioQuant and IPMB, Biomedical Computer Vision Group, Heidelberg, 69120, Germany
| | - Dennis Aumiller
- Heidelberg University, Institute of Computer Science, Heidelberg, 69120, Germany
| | - Lina Gundelwein
- Heidelberg University, Institute of Computer Science, Heidelberg, 69120, Germany
| | - Philipp Jung
- Heidelberg University, Institute of Computer Science, Heidelberg, 69120, Germany
| | - Christian Schütz
- Heidelberg University, Institute of Computer Science, Heidelberg, 69120, Germany
| | - Kathrin Lehmann
- German Cancer Research Center, Division Biophysics of Macromolecules, Heidelberg, 69120, Germany
- Simon Fraser University, Department of Physics, Burnaby, BC, V5A 1S6, Canada
| | - Katalin Tóth
- German Cancer Research Center, Division Biophysics of Macromolecules, Heidelberg, 69120, Germany
| | - Karl Rohr
- Heidelberg University, BioQuant and IPMB, Biomedical Computer Vision Group, Heidelberg, 69120, Germany.
- German Cancer Research Center, Heidelberg, 69120, Germany.
| |
Collapse
|