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

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...

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Autores principales:	Martin Würtz, Dennis Aumiller, Lina Gundelwein, Philipp Jung, Christian Schütz, Kathrin Lehmann, Katalin Tóth, Karl Rohr
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/24a686c0245a404ebd42063bf6a81db9
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spelling	oai:doaj.org-article:24a686c0245a404ebd42063bf6a81db92021-12-02T15:09:20ZDNA accessibility of chromatosomes quantified by automated image analysis of AFM data10.1038/s41598-019-49163-42045-2322https://doaj.org/article/24a686c0245a404ebd42063bf6a81db92019-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-49163-4https://doaj.org/toc/2045-2322Abstract 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.Martin WürtzDennis AumillerLina GundelweinPhilipp JungChristian SchützKathrin LehmannKatalin TóthKarl RohrNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-12 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Martin Würtz Dennis Aumiller Lina Gundelwein Philipp Jung Christian Schütz Kathrin Lehmann Katalin Tóth Karl Rohr DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
description	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.
format	article
author	Martin Würtz Dennis Aumiller Lina Gundelwein Philipp Jung Christian Schütz Kathrin Lehmann Katalin Tóth Karl Rohr
author_facet	Martin Würtz Dennis Aumiller Lina Gundelwein Philipp Jung Christian Schütz Kathrin Lehmann Katalin Tóth Karl Rohr
author_sort	Martin Würtz
title	DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
title_short	DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
title_full	DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
title_fullStr	DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
title_full_unstemmed	DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
title_sort	dna accessibility of chromatosomes quantified by automated image analysis of afm data
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/24a686c0245a404ebd42063bf6a81db9
work_keys_str_mv	AT martinwurtz dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT dennisaumiller dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT linagundelwein dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT philippjung dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT christianschutz dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT kathrinlehmann dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT katalintoth dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata AT karlrohr dnaaccessibilityofchromatosomesquantifiedbyautomatedimageanalysisofafmdata
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DNA accessibility of chromatosomes quantified by automated image analysis of AFM data

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