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Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024; 162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.
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Affiliation(s)
- Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Agustina L Lafuente
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Alejo Vázquez Lareu
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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Devos X, Fiche JB, Bardou M, Messina O, Houbron C, Gurgo J, Schaeffer M, Götz M, Walter T, Mueller F, Nollmann M. pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging. Genome Biol 2024; 25:47. [PMID: 38351149 PMCID: PMC10863255 DOI: 10.1186/s13059-024-03178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells. pyHiM employs a modular architecture, allowing independent execution of analysis steps and customization according to sample specificity and computing resources. pyHiM aims to facilitate the democratization and standardization of spatial genomics analysis.
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Affiliation(s)
- Xavier Devos
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marion Bardou
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Olivier Messina
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Julian Gurgo
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Markus Götz
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006, Paris, France
- Institut Curie, 75248, Paris, Cedex, France
- INSERM, U900, 75248, Paris, Cedex, France
| | - Florian Mueller
- Imaging and Modeling Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France.
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