Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)

• Verfasst von: Weidner, Jonas [VerfasserIn]
• Verfasst von: Neitzel, Charlotte [VerfasserIn]
• Verfasst von: Gote, Martin [VerfasserIn]
• Verfasst von: Deck, Jeanette [VerfasserIn]
• Verfasst von: Küntzelmann, Kim [VerfasserIn]
• Verfasst von: Pilarczyk, Götz [VerfasserIn]
• Verfasst von: Falk, Martin [VerfasserIn]
• Verfasst von: Hausmann, Michael [VerfasserIn]
• Titel: Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)
• Verf.angabe: Jonas Weidner, Charlotte Neitzel, Martin Gote, Jeanette Deck, Kim Küntzelmann, Götz Pilarczyk, Martin Falk, Michael Hausmann
• E-Jahr: 2023
• Jahr: 16 March 2023
• Umfang: 17 S.
• Fussnoten: Online verfügbar 9. März 2023, Artikelversion 16. März 2023 ; Gesehen am 21.04.2023
• Titel Quelle: Enthalten in: Computational and structural biotechnology journal
• Ort Quelle: Gotenburg : Research Network of Computational and Structural Biotechnology (RNCSB), 2012
• Jahr Quelle: 2023
• Band/Heft Quelle: 21(2023) vom: März, Seite 2018-2034
• ISSN Quelle: 2001-0370
• DOI: doi:10.1016/j.csbj.2023.03.009
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: Application of mathematical analysis tools to chromatin organization and DNA repair processes
• Sach-SW: Persistent homology
• Sach-SW: Persistent image
• Sach-SW: Principal component analysis
• Sach-SW: Ripley distance frequency histograms
• Sach-SW: Single molecule localization microscopy (SMLM)
• K10plus-PPN: 1843333414

Abstract

The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the relationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, persistent ‘imaging’, principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein trafficking in the cytosol, offers broad flexibility of use.