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Laghmach R, Di Pierro M, Potoyan DA. Four-Dimensional Mesoscale Liquid Model of Nucleus Resolves Chromatin's Radial Organization. PRX LIFE 2024; 2:013006. [PMID: 38601142 PMCID: PMC11005002 DOI: 10.1103/prxlife.2.013006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Recent advances chromatin capture, imaging techniques, and polymer modeling have dramatically enhanced quantitative understanding of chromosomal folding. However, the dynamism inherent in genome architectures due to physical and biochemical forces and their impact on nuclear architecture and cellular functions remains elusive. While imaging of chromatin in four dimensions is becoming more common, there is a conspicuous lack of physics-based computational tools appropriate for revealing the forces that shape nuclear architecture and dynamics. To this end, we have developed a multiphase liquid model of the nucleus, which can resolve chromosomal territories, compartments, and nuclear lamina using a physics-based and data-informed free-energy function. The model enables rapid hypothesis-driven prototyping of nuclear dynamics in four dimensions, thereby facilitating comparison with whole nucleus imaging experiments. As an application, we model the Drosophila nucleus and map phase diagram of various possible nuclear morphologies. We shed light on the interplay of adhesive and cohesive interactions which give rise to distinct radial organization seen in conventional, inverted, and senescent nuclear architectures. The results also show the highly dynamic nature of the radial organization, the disruption of which leads to significant variability in domain coarsening dynamics and consequently variability of chromatin architecture. The model also highlights the impact of oblate nuclear geometry and heterochromatin-subtype interactions on the global chromatin architecture and local asymmetry of chromatin compartments.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Davit A. Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA and Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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2
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Kuang H, Li Y, Wang Y, Shi M, Duan R, Xiao Q, She H, Liu Y, Liang Q, Teng Y, Zhou M, Liang D, Li Z, Wu L. A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder. Cell Rep 2023; 42:113445. [PMID: 37980560 DOI: 10.1016/j.celrep.2023.113445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/15/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023] Open
Abstract
The INTS11 endonuclease is crucial in modulating gene expression and has only recently been linked to human neurodevelopmental disorders (NDDs). However, how INTS11 participates in human development and disease remains unclear. Here, we identify a homozygous INTS11 variant in two siblings with a severe NDD. The variant impairs INTS11 catalytic activity, supported by its substrate's accumulation, and causes G2/M arrest in patient cells with length-dependent dysregulation of genes involved in mitosis and neural development, including the NDD gene CDKL5. The mutant knockin (KI) in induced pluripotent stem cells (iPSCs) disturbs their mitotic spindle organization and thus leads to slow proliferation and increased apoptosis, possibly through the decreased neurally functional CDKL5-induced extracellular signal-regulated kinase (ERK) pathway inhibition. The generation of neural progenitor cells (NPCs) from the mutant iPSCs is also delayed, with long transcript loss concerning neurogenesis. Our work reveals a mechanism underlying INTS11 dysfunction-caused human NDD and provides an iPSC model for this disease.
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Affiliation(s)
- Hanzhe Kuang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yunlong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yixuan Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Meizhen Shi
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ranhui Duan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Qiao Xiao
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Haoyuan She
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yingdi Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Qiaowei Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China
| | - Yanling Teng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Miaojin Zhou
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China.
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China.
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China.
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3
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Yamashita M, Tamamitsu M, Kirisako H, Goda Y, Chen X, Hattori K, Ota S. High-Throughput 3D Imaging Flow Cytometry of Suspended Adherent 3D Cell Cultures. SMALL METHODS 2023:e2301318. [PMID: 38133483 DOI: 10.1002/smtd.202301318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Indexed: 12/23/2023]
Abstract
3D cell cultures are indispensable in recapitulating in vivo environments. Among the many 3D culture methods, culturing adherent cells on hydrogel beads to form spheroid-like structures is a powerful strategy for maintaining high cell viability and functions in the adherent states. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high throughput, scalable 3D imaging flow cytometry platform for analyzing spheroid models. This platform is realized by integrating a single objective fluorescence light-sheet microscopy with a microfluidic device that combines hydrodynamic and acoustofluidic focusing techniques. This integration enabled unprecedentedly high-throughput and scalable optofluidic 3D imaging, processing 1310 spheroids consisting of 28 117 cells min-1 . The large dataset obtained enables precise quantification and comparison of the nuclear morphology of adhering and suspended cells, revealing that the adhering cells have smaller nuclei with less rounded surfaces. This platform's high throughput, robustness, and precision for analyzing the morphology of subcellular structures in 3D culture models hold promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.
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Affiliation(s)
- Minato Yamashita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Miu Tamamitsu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiromi Kirisako
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Yuki Goda
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Xiaoyao Chen
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Kazuki Hattori
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Sadao Ota
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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Wang N, Wang Z, Tzourtzou S, Wang X, Bi X, Leimeister J, Xu L, Sakamoto T, Matsunaga S, Schaller A, Jiang H, Liu C. The plant nuclear lamina disassembles to regulate genome folding in stress conditions. NATURE PLANTS 2023:10.1038/s41477-023-01457-2. [PMID: 37400513 PMCID: PMC10356608 DOI: 10.1038/s41477-023-01457-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
The nuclear lamina is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana, nuclear matrix constituent proteins (NMCPs) are essential components of the nuclear lamina and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein-coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei is flexible and responds to various developmental cues and environmental stimuli. On the basis of these observations in Arabidopsis, and given the role of NMCP genes (CRWN1 and CRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin-nuclear lamina interactions when the global chromatin organization patterns are being altered in plants. Here we report the highly flexible nature of the plant nuclear lamina, which disassembles substantially under various stress conditions. Focusing on heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. By investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional coregulator to modulate the shift of the plant transcriptome profile in response to heat stress.
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Affiliation(s)
- Nan Wang
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Zhidan Wang
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sofia Tzourtzou
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Wang
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Xiuli Bi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, China
| | - Julia Leimeister
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Linhao Xu
- Applied Chromosome Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hua Jiang
- Applied Chromosome Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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5
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Schvarzstein M, Alam F, Toure M, Yanowitz JL. An Emerging Animal Model for Querying the Role of Whole Genome Duplication in Development, Evolution, and Disease. J Dev Biol 2023; 11:26. [PMID: 37367480 PMCID: PMC10299280 DOI: 10.3390/jdb11020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Whole genome duplication (WGD) or polyploidization can occur at the cellular, tissue, and organismal levels. At the cellular level, tetraploidization has been proposed as a driver of aneuploidy and genome instability and correlates strongly with cancer progression, metastasis, and the development of drug resistance. WGD is also a key developmental strategy for regulating cell size, metabolism, and cellular function. In specific tissues, WGD is involved in normal development (e.g., organogenesis), tissue homeostasis, wound healing, and regeneration. At the organismal level, WGD propels evolutionary processes such as adaptation, speciation, and crop domestication. An essential strategy to further our understanding of the mechanisms promoting WGD and its effects is to compare isogenic strains that differ only in their ploidy. Caenorhabditis elegans (C. elegans) is emerging as an animal model for these comparisons, in part because relatively stable and fertile tetraploid strains can be produced rapidly from nearly any diploid strain. Here, we review the use of Caenorhabditis polyploids as tools to understand important developmental processes (e.g., sex determination, dosage compensation, and allometric relationships) and cellular processes (e.g., cell cycle regulation and chromosome dynamics during meiosis). We also discuss how the unique characteristics of the C. elegans WGD model will enable significant advances in our understanding of the mechanisms of polyploidization and its role in development and disease.
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Affiliation(s)
- Mara Schvarzstein
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
- Biology Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
- Biochemistry Department, The Graduate Center at the City University of New York, New York, NY 10016, USA
| | - Fatema Alam
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Muhammad Toure
- Biology Department, Brooklyn College at the City University of New York, Brooklyn, NY 11210, USA
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA;
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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6
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Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S. Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis. J Cell Sci 2023; 136:286881. [PMID: 36695178 DOI: 10.1242/jcs.260568] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.
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Affiliation(s)
- Sherman Foo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
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Pasternak T, Kircher S, Pérez-Pérez JM, Palme K. A simple pipeline for cell cycle kinetic studies in the root apical meristem. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4683-4695. [PMID: 35312781 DOI: 10.1093/jxb/erac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification. Based on this approach, we characterized differences in cell volume, nucleus volume, and nucleus shape across different domains of the Arabidopsis RAM. We found that DNA replication patterns were cell layer and region dependent. G2 phase duration, which varied from 3.5 h in the pericycle to more than 4.5 h in the epidermis, was found to be associated with some features of nucleus geometry. Endocycle duration was determined as the time required to achieve 100% EdU-positive cells in the elongation zone and, as such, it was estimated to be in the region of 5 h for the epidermis and cortex. This experimental pipeline could be used to precisely map cell cycle duration in the RAM of mutants and in response to environmental stress in several plant species without the need for introgressing molecular cell cycle markers.
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Affiliation(s)
- Taras Pasternak
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Stefan Kircher
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
| | | | - Klaus Palme
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, China
- ScreenSYS GmbH, Engesserstr. 4, 79108 Freiburg, Germany
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Abstract
Cells adopt a size that is optimal for their function, and pushing them beyond this limit can cause cell aging and death by senescence or reduce proliferative potential. However, by increasing their genome copy number (ploidy), cells can increase their size dramatically and homeostatically maintain physiological properties such as biosynthesis rate. Recent studies investigating the relationship between cell size and rates of biosynthesis and metabolism under normal, polyploid, and pathological conditions are revealing new insights into how cells attain the best function or fitness for their size by tuning processes including transcription, translation, and mitochondrial respiration. A new frontier is to connect single-cell scaling relationships with tissue and whole-organism physiology, which promises to reveal molecular and evolutionary principles underlying the astonishing diversity of size observed across the tree of life.
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Affiliation(s)
- Clotilde Cadart
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
| | - Rebecca Heald
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
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9
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Mechanisms of cellular mRNA transcript homeostasis. Trends Cell Biol 2022; 32:655-668. [PMID: 35660047 DOI: 10.1016/j.tcb.2022.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
For most genes, mRNA transcript abundance scales with cell size to ensure a constant concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with regulation of the activity and abundance of RNA polymerase II (Pol II) now emerging as a key point of control. However, there is also considerable evidence for feedback mechanisms that kinetically couple the rates of mRNA synthesis, nuclear export, and degradation to allow cells to compensate for changes in one by adjusting the others. Researchers are beginning to integrate results from these different fields to reveal the mechanisms underlying transcript homeostasis. This will be crucial for moving beyond our current understanding of relative gene expression towards an appreciation of how absolute transcript levels are linked to other aspects of the cellular phenotype.
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