Journal Article

DKFZ-2019-02313

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png DNA accessibility of chromatosomes quantified by automated image analysis of AFM data.

Würtz, M. (First author)DKFZ* ; Aumiller, D. ; Gundelwein, L. ; Jung, P. ; Schütz, C. ; Lehmann, K.DKFZ* ; Toth, K.DKFZ* ; Rohr, K. (Last author)DKFZ*

2019
Macmillan Publishers Limited, part of Springer Nature [London]

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Please use a persistent id in citations: doi:10.1038/s41598-019-49163-4

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.

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Contributing Institute(s):

1. Biophysik der Makromoleküle (B040)
2. Theoretische Bioinformatik (B080)

Research Program(s):

1. 312 - Functional and structural genomics (POF3-312) (POF3-312)

Appears in the scientific report 2019

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