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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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Subramanian K, Weigert M, Borsch O, Petzold H, Garcia-Ulloa A, Myers EW, Ader M, Solovei I, Kreysing M. Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice. eLife 2019; 8:49542. [PMID: 31825309 PMCID: PMC6974353 DOI: 10.7554/elife.49542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/11/2019] [Indexed: 01/06/2023] Open
Abstract
Rod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and the underlying mechanisms remains unclear. It is widely assumed that improvements in nocturnal vision would depend on maximization of photon capture at the expense of image detail. Here, we show that retinal optical quality improves 2-fold during terminal development, and that this enhancement is caused by nuclear inversion. We further demonstrate that improved retinal contrast transmission, rather than photon-budget or resolution, enhances scotopic contrast sensitivity by 18–27%, and improves motion detection capabilities up to 10-fold in dim environments. Our findings therefore add functional significance to a prominent exception of nuclear organization and establish retinal contrast transmission as a decisive determinant of mammalian visual perception.
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Affiliation(s)
- Kaushikaram Subramanian
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Oliver Borsch
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heike Petzold
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany.,Department of Computer Science, Technische Universität Dresden, Dresden, Germany
| | - Marius Ader
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Irina Solovei
- Biozentrum, Ludwig Maximilians Universität, München, Germany
| | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
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Lattanzi G, Ortolani M, Columbaro M, Prencipe S, Mattioli E, Lanzarini C, Maraldi NM, Cenni V, Garagnani P, Salvioli S, Storci G, Bonafè M, Capanni C, Franceschi C. Lamins are rapamycin targets that impact human longevity: a study in centenarians. J Cell Sci 2013; 127:147-57. [PMID: 24155329 DOI: 10.1242/jcs.133983] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The dynamic organisation of the cell nucleus is profoundly modified during growth, development and senescence as a result of changes in chromatin arrangement and gene transcription. A plethora of data suggests that the nuclear lamina is a key player in chromatin dynamics and argues in favour of a major involvement of prelamin A in fundamental mechanisms regulating cellular senescence and organism ageing. As the best model to analyse the role of prelamin A in normal ageing, we used cells from centenarian subjects. We show that prelamin A is accumulated in fibroblasts from centenarians owing to downregulation of its specific endoprotease ZMPSTE24, whereas other nuclear envelope constituents are mostly unaffected and cells do not enter senescence. Accumulation of prelamin A in nuclei of cells from centenarians elicits loss of heterochromatin, as well as recruitment of the inactive form of 53BP1, associated with rapid response to oxidative stress. These effects, including the prelamin-A-mediated increase of nuclear 53BP1, can be reproduced by rapamycin treatment of cells from younger individuals. These data identify prelamin A and 53BP1 as new targets of rapamycin that are associated with human longevity. We propose that the reported mechanisms safeguard healthy ageing in humans through adaptation of the nuclear environment to stress stimuli.
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Affiliation(s)
- Giovanna Lattanzi
- National Research Council of Italy, Institute of Molecular Genetics, Unit of Bologna IOR, 40136 Bologna, Italy
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