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DNA accessibility of chromatosomes quantified by automated image analysis of AFM data

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 structur...

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Bibliographic Details
Main Authors: Würtz, Martin (Author) , Aumiller, Dennis (Author) , Gundelwein, Lina (Author) , Jung, Philipp (Author) , Schütz, Christian (Author) , Lehmann, Kathrin (Author) , Tóth, Katalin (Author) , Rohr, Karl (Author)
Format: Article (Journal)
Language:English
Published: 04 September 2019
In: Scientific reports
Year: 2019, Volume: 9
ISSN:2045-2322
DOI:10.1038/s41598-019-49163-4
Online Access:Verlag, Volltext: https://doi.org/10.1038/s41598-019-49163-4
Verlag: https://www.nature.com/articles/s41598-019-49163-4
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Author Notes:Martin Würtz, Dennis Aumiller, Lina Gundelwein, Philipp Jung, Christian Schütz, Kathrin Lehmann, Katalin Tóth & Karl Rohr
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Summary: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.
Item Description:Gesehen am 03.12.2019
Physical Description:Online Resource
ISSN:2045-2322
DOI:10.1038/s41598-019-49163-4

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