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Pennacchio FA, Poli A, Pramotton FM, Lavore S, Rancati I, Cinquanta M, Vorselen D, Prina E, Romano OM, Ferrari A, Piel M, Cosentino Lagomarsino M, Maiuri P. N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells. Nat Commun 2024; 15:1070. [PMID: 38326317 PMCID: PMC10850064 DOI: 10.1038/s41467-024-45168-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
In eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, current methods to measure cytoplasmic and nuclear volumes, including confocal 3D reconstruction, have limitations, such as relying on two-dimensional projections or poor vertical resolution. Here, to overcome these limitations, we describe a method, N2FXm, to jointly measure cytoplasmic and nuclear volumes in single cultured adhering human cells, in real time, and across cell cycles. We find that this method accurately provides joint size over dynamic measurements and at different time resolutions. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we show that N2FXm can give relevant insights on how mechanical forces exerted by the cytoskeleton on the nuclear envelope can affect the growth of nucleus volume by biasing nuclear import. Our method, by allowing for accurate joint nuclear and cytoplasmic volume dynamic measurements at different time resolutions, highlights the non-constancy of the nucleus/cytoplasm ratio along the cell cycle.
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Affiliation(s)
- Fabrizio A Pennacchio
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Alessandro Poli
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Francesca Michela Pramotton
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Stefania Lavore
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Ilaria Rancati
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mario Cinquanta
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Daan Vorselen
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98105, USA
| | - Elisabetta Prina
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Orso Maria Romano
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Aldo Ferrari
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, and I.N.F.N., Via Celoria 16, 20133, Milan, Italy
| | - Paolo Maiuri
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy.
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Maiuri P, Andrea Pennacchio F, Poli A, Pramotton FM, Ferrari A, Lavore S, Rancati I, Cosentino-Lagomarsino M, Maria Romano O. Nuclear envelope tension impacts on nuclear volume. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Romano OM, Cosentino Lagomarsino M. Single rod-shaped cell fluctuations from stochastic surface and volume growth rates. Phys Rev E 2020; 101:042403. [PMID: 32422852 DOI: 10.1103/physreve.101.042403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/10/2020] [Indexed: 11/07/2022]
Abstract
Growing rod-shaped bacterial cells need to modulate the production rates of different surface and bulk components. Population data show that the balance between these rates is central for cell physiology and affects cell shape, but we still know little about these processes in single cells. We study a minimal stochastic model where single cells grow by two fluctuating volume-specific surface and volume growth rates, solving for the steady-state distributions and the correlation functions of the main geometric features. Our predictions allow us to address the detectability of different scenarios for the intrinsic coupling between the allocation of resources to surface and bulk growth.
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Affiliation(s)
- Orso Maria Romano
- IFOM, The FIRC Institute of Molecular Oncology, via Adamello 16, 20139, Milan, Italy
| | - Marco Cosentino Lagomarsino
- IFOM, The FIRC Institute of Molecular Oncology, via Adamello 16, 20139, Milan, Italy.,Dipartimento di Fisica, Università degli Studi di Milano, and INFN, via Celoria 16, Milan, Italy
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Agier N, Romano OM, Touzain F, Cosentino Lagomarsino M, Fischer G. The spatiotemporal program of replication in the genome of Lachancea kluyveri. Genome Biol Evol 2013; 5:370-88. [PMID: 23355306 PMCID: PMC3590768 DOI: 10.1093/gbe/evt014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2013] [Indexed: 12/11/2022] Open
Abstract
We generated a genome-wide replication profile in the genome of Lachancea kluyveri and assessed the relationship between replication and base composition. This species diverged from Saccharomyces cerevisiae before the ancestral whole genome duplication. The genome comprises eight chromosomes among which a chromosomal arm of 1 Mb has a G + C-content much higher than the rest of the genome. We identified 252 active replication origins in L. kluyveri and found considerable divergence in origin location with S. cerevisiae and with Lachancea waltii. Although some global features of S. cerevisiae replication are conserved: Centromeres replicate early, whereas telomeres replicate late, we found that replication origins both in L. kluyveri and L. waltii do not behave as evolutionary fragile sites. In L. kluyveri, replication timing along chromosomes alternates between regions of early and late activating origins, except for the 1 Mb GC-rich chromosomal arm. This chromosomal arm contains an origin consensus motif different from other chromosomes and is replicated early during S-phase. We showed that precocious replication results from the specific absence of late firing origins in this chromosomal arm. In addition, we found a correlation between GC-content and distance from replication origins as well as a lack of replication-associated compositional skew between leading and lagging strands specifically in this GC-rich chromosomal arm. These findings suggest that the unusual base composition in the genome of L. kluyveri could be linked to replication.
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Affiliation(s)
- Nicolas Agier
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
| | | | - Fabrice Touzain
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
- Present address: ANSES, Ploufragan/Plouzané Laboratory Viral Genomics and Biosecurity Unit (GVB), Ploufragan, France
| | - Marco Cosentino Lagomarsino
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
| | - Gilles Fischer
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
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