1
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Cisneros-Soberanis F, Simpson EL, Beckett AJ, Pucekova N, Corless S, Kochanova NY, Prior IA, Booth DG, Earnshaw WC. Near millimolar concentration of nucleosomes in mitotic chromosomes from late prometaphase into anaphase. J Cell Biol 2024; 223:e202403165. [PMID: 39186086 PMCID: PMC11346515 DOI: 10.1083/jcb.202403165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/05/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024] Open
Abstract
Chromosome compaction is a key feature of mitosis and critical for accurate chromosome segregation. However, a precise quantitative analysis of chromosome geometry during mitotic progression is lacking. Here, we use volume electron microscopy to map, with nanometer precision, chromosomes from prometaphase through telophase in human RPE1 cells. During prometaphase, chromosomes acquire a smoother surface, their arms shorten, and the primary centromeric constriction is formed. The chromatin is progressively compacted, ultimately reaching a remarkable nucleosome concentration of over 750 µM in late prometaphase that remains relatively constant during metaphase and early anaphase. Surprisingly, chromosomes then increase their volume in late anaphase prior to deposition of the nuclear envelope. The plateau of total chromosome volume from late prometaphase through early anaphase described here is consistent with proposals that the final stages of chromatin condensation in mitosis involve a limit density, such as might be expected for a process involving phase separation.
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Affiliation(s)
| | - Eva L Simpson
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Alison J Beckett
- Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nina Pucekova
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel Corless
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Ian A Prior
- Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel G Booth
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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2
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Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg J, Šarić A, Cuylen-Haering S. A liquid-like coat mediates chromosome clustering during mitotic exit. Mol Cell 2024; 84:3254-3270.e9. [PMID: 39153474 DOI: 10.1016/j.molcel.2024.07.022] [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: 10/26/2023] [Revised: 06/04/2024] [Accepted: 07/24/2024] [Indexed: 08/19/2024]
Abstract
The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis.
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Affiliation(s)
- Alberto Hernandez-Armendariz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Valerio Sorichetti
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Yuki Hayashi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Zuzana Koskova
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Andreas Brunner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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3
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Iida S, Ide S, Tamura S, Sasai M, Tani T, Goto T, Shribak M, Maeshima K. Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation. Proc Natl Acad Sci U S A 2024; 121:e2403153121. [PMID: 39190347 PMCID: PMC11388287 DOI: 10.1073/pnas.2403153121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024] Open
Abstract
Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masaki Sasai
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- Department of Complex Systems Science, Nagoya University, Nagoya 464-8603, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | | | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
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4
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Norman RX, Chen YC, Recchia EE, Loi J, Rosemarie Q, Lesko SL, Patel S, Sherer N, Takaku M, Burkard ME, Suzuki A. One step 4x and 12x 3D-ExM: robust super-resolution microscopy in cell biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607782. [PMID: 39185153 PMCID: PMC11343106 DOI: 10.1101/2024.08.13.607782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Super-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared to traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4x and 12x 3D-ExM). 3D-ExM is a straightforward expansion microscopy method featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12x 3D-ExM achieves a lateral resolution of under 30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein-Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.
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Affiliation(s)
- Roshan X Norman
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, Hematology/Oncology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Yu-Chia Chen
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Emma E Recchia
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jonathan Loi
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Quincy Rosemarie
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sydney L Lesko
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Smit Patel
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| | - Nathan Sherer
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Motoki Takaku
- Department of Biomedical Science, University of North Dakota School of Medicine and Health Science, Grand Forks, North Dakota, USA
| | - Mark E Burkard
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Medicine, Hematology/Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Aussie Suzuki
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
- Lead Contact
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5
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Li P, Yu X. The role of rRNA in maintaining genome stability. DNA Repair (Amst) 2024; 139:103692. [PMID: 38759435 DOI: 10.1016/j.dnarep.2024.103692] [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: 03/25/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
Over the past few decades, unbiased approaches such as genetic screening and protein affinity purification have unveiled numerous proteins involved in DNA double-strand break (DSB) repair and maintaining genome stability. However, despite our knowledge of these protein factors, the underlying molecular mechanisms governing key cellular events during DSB repair remain elusive. Recent evidence has shed light on the role of non-protein factors, such as RNA, in several pivotal steps of DSB repair. In this review, we provide a comprehensive summary of these recent findings, highlighting the significance of ribosomal RNA (rRNA) as a critical mediator of DNA damage response, meiosis, and mitosis. Moreover, we discuss potential mechanisms through which rRNA may influence genome integrity.
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Affiliation(s)
- Peng Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiaochun Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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6
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Neděla V, Tihlaříková E, Cápal P, Doležel J. Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state. Sci Rep 2024; 14:12998. [PMID: 38844535 PMCID: PMC11156959 DOI: 10.1038/s41598-024-63515-9] [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: 02/19/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
The challenge of in-situ handling and high-resolution low-dose imaging of intact, sensitive and wet samples in their native state at nanometer scale, including live samples is met by Advanced Environmental Scanning Electron Microscopy (A-ESEM). This new generation of ESEM utilises machine learning-based optimization of thermodynamic conditions with respect to sample specifics to employ a low temperature method and an ionization secondary electron detector with an electrostatic separator. A modified electron microscope was used, equipped with temperature, humidity and gas pressure sensors for in-situ and real-time monitoring of the sample. A transparent ultra-thin film of ionic liquid is used to increase thermal and electrical conductivity of the samples and to minimize sample damage by free radicals. To validate the power of the new method, we analyze condensed mitotic metaphase chromosomes to reveal new structural features of their perichromosomal layer, and the organization of chromatin fibers, not observed before by any microscopic technique. The ability to resolve nano-structural details of chromosomes using A-ESEM is validated by measuring gold nanoparticles with achievable resolution in the lower nanometre units.
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Affiliation(s)
- Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic.
| | - Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
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7
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Jiang Y, Sun S, Liu X, Su K, Zhang C, Zhang P, Zhao Z, Su Y, Wang C, Du X. U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis. Cell Death Dis 2024; 15:342. [PMID: 38760378 PMCID: PMC11101645 DOI: 10.1038/s41419-024-06725-3] [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: 12/05/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
U3 snoRNA is essential for ribosome biogenesis during interphase. Upon mitotic onset, the nucleolus disassembles and U3 snoRNA relocates to the perichromosomal region (PR) to be considered as a chromosome passenger. Whether U3 controls mitosis remains unknown. Here, we demonstrate that U3 snoRNA is required for mitotic progression. We identified DDX21 as the predominant U3-binding protein during mitosis and confirmed that U3 snoRNA colocalizes with DDX21 in the PR. DDX21 knockdown induces mitotic catastrophe and similar mitotic defects caused by U3 snoRNA depletion. Interestingly, the uniform PR distribution of U3 snoRNA and DDX21 is interdependent. DDX21 functions in mitosis depending on its PR localization. Mechanistically, U3 snoRNA regulates DDX21 PR localization through maintaining its mobility. Moreover, Cy5-U3 snoRNA downsizes the fibrous condensates of His-DDX21 at proper molecular ratios in vitro. This work highlights the importance of the equilibrium between U3 snoRNA and DDX21 in PR formation and reveals the potential relationship between the PR assembly and mitotic regulation.
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Affiliation(s)
- Yang Jiang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Shiqi Sun
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaofeng Liu
- Hepatopancreatobiliary Surgery Department I, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Cancer Hospital & Institute, Peking University, Beijing, 100142, China
| | - Kunqi Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chunfeng Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Peipei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Zhuochen Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Ya Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chang Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
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8
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Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590027. [PMID: 38659940 PMCID: PMC11042376 DOI: 10.1101/2024.04.18.590027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity and interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for SMC complexes that are critical for allowing cells to refold interphase chromatin into mitotic chromosomes. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. Studies of mitotic chromosomes formed by cohesin, condensin II and condensin I alone or in combination allow us to develop new models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins do not freely pass one another but stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase loops are extruded in vivo at ~1-3 kb/sec by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.
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Affiliation(s)
- Kumiko Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Sameer Abraham
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | | | - Itaru Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Alison J. Beckett
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Nina Pučeková
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Maria Alba Abad
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Bethan Medina-Pritchard
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - James R. Paulson
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - A. Arockia Jeyaprakash
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
- Gene Center Munich, Ludwig-Maximilians-Universität München; Munich, Germany
| | - Ian A. Prior
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Leonid A. Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | | | - William C. Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
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9
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Stamatiou K, Huguet F, Serapinas LV, Spanos C, Rappsilber J, Vagnarelli P. Ki-67 is necessary during DNA replication for fork protection and genome stability. Genome Biol 2024; 25:105. [PMID: 38649976 PMCID: PMC11034166 DOI: 10.1186/s13059-024-03243-5] [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: 03/28/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin organisation and gene transcription. However, how the different roles for Ki-67 across the cell cycle are regulated and coordinated remain poorly understood. The progress towards understanding Ki-67 function have been limited by the tools available to deplete the protein, coupled to its abundance and fluctuation during the cell cycle. RESULTS Here, we use a doxycycline-inducible E3 ligase together with an auxin-inducible degron tag to achieve a rapid, acute and homogeneous degradation of Ki-67 in HCT116 cells. This system, coupled with APEX2 proteomics and phospho-proteomics approaches, allows us to show that Ki-67 plays a role during DNA replication. In its absence, DNA replication is severely delayed, the replication machinery is unloaded, causing DNA damage that is not sensed by the canonical pathways and dependent on HUWE1 ligase. This leads to defects in replication and sister chromatids cohesion, but it also triggers an interferon response mediated by the cGAS/STING pathway in all the cell lines tested. CONCLUSIONS We unveil a new function of Ki-67 in DNA replication and genome maintenance that is independent of its previously known role in mitosis and gene regulation.
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Affiliation(s)
- Konstantinos Stamatiou
- College of Health, Medicine and Life Science, Brunel University London, London, UB8 3PH, UK
| | - Florentin Huguet
- College of Health, Medicine and Life Science, Brunel University London, London, UB8 3PH, UK
| | - Lukas V Serapinas
- College of Health, Medicine and Life Science, Brunel University London, London, UB8 3PH, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Technische Universitat Berlin, Berlin, 13355, Germany
| | - Paola Vagnarelli
- College of Health, Medicine and Life Science, Brunel University London, London, UB8 3PH, UK.
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10
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Iida S, Ide S, Tamura S, Tani T, Goto T, Shribak M, Maeshima K. Orientation-Independent-DIC imaging reveals that a transient rise in depletion force contributes to mitotic chromosome condensation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566679. [PMID: 37986866 PMCID: PMC10659371 DOI: 10.1101/2023.11.11.566679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion force/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using orientation-independent-differential interference contrast (OI-DIC) module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prometaphase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like, with further condensation. These results suggest that a transient rise in depletion force, likely triggered by the relocation of macromolecules (proteins, RNAs and others) via nuclear envelope breakdown and also by a subsequent decrease in cell-volumes, contributes to mitotic chromosome condensation, shedding light on a new aspect of the condensation mechanism in living human cells.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine and Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Michael Shribak
- Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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11
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Sayago C, Sánchez-Wandelmer J, García F, Hurtado B, Lafarga V, Prieto P, Zarzuela E, Ximénez-Embún P, Ortega S, Megías D, Fernández-Capetillo O, Malumbres M, Munoz J. Decoding protein methylation function with thermal stability analysis. Nat Commun 2023; 14:3016. [PMID: 37230995 DOI: 10.1038/s41467-023-38863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Protein methylation is an important modification beyond epigenetics. However, systems analyses of protein methylation lag behind compared to other modifications. Recently, thermal stability analyses have been developed which provide a proxy of a protein functional status. Here, we show that molecular and functional events closely linked to protein methylation can be revealed by the analysis of thermal stability. Using mouse embryonic stem cells as a model, we show that Prmt5 regulates mRNA binding proteins that are enriched in intrinsically disordered regions and involved in liquid-liquid phase separation mechanisms, including the formation of stress granules. Moreover, we reveal a non-canonical function of Ezh2 in mitotic chromosomes and the perichromosomal layer, and identify Mki67 as a putative Ezh2 substrate. Our approach provides an opportunity to systematically explore protein methylation function and represents a rich resource for understanding its role in pluripotency.
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Affiliation(s)
- Cristina Sayago
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Fernando García
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Begoña Hurtado
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Cancer Cell Cycle group, Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Patricia Prieto
- Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Sagrario Ortega
- Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Cancer Cell Cycle group, Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
| | - Javier Munoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain.
- Cell Signaling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain.
- Ikerbasque, Basque foundation for science, 48011, Bilbao, Spain.
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12
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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13
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Soujanya M, Bihani A, Hajirnis N, Pathak RU, Mishra RK. Nuclear architecture and the structural basis of mitotic memory. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:8. [PMID: 36725757 DOI: 10.1007/s10577-023-09714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/13/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
The nucleus is a complex organelle that hosts the genome and is essential for vital processes like DNA replication, DNA repair, transcription, and splicing. The genome is non-randomly organized in the three-dimensional space of the nucleus. This functional sub-compartmentalization was thought to be organized on the framework of nuclear matrix (NuMat), a non-chromatin scaffold that functions as a substratum for various molecular processes of the nucleus. More recently, nuclear bodies or membrane-less subcompartments of the nucleus are thought to arise due to phase separation of chromatin, RNA, and proteins. The nuclear architecture is an amalgamation of the relative organization of chromatin, epigenetic landscape, the nuclear bodies, and the nucleoskeleton in the three-dimensional space of the nucleus. During mitosis, the nucleus undergoes drastic changes in morphology to the degree that it ceases to exist as such; various nuclear components, including the envelope that defines the nucleus, disintegrate, and the chromatin acquires mitosis-specific epigenetic marks and condenses to form chromosome. Upon mitotic exit, chromosomes are decondensed, re-establish hierarchical genome organization, and regain epigenetic and transcriptional status similar to that of the mother cell. How this mitotic memory is inherited during cell division remains a puzzle. NuMat components that are a part of the mitotic chromosome in the form of mitotic chromosome scaffold (MiCS) could potentially be the seeds that guide the relative re-establishment of the epigenome, chromosome territories, and the nuclear bodies. Here, we synthesize the advances towards understanding cellular memory of nuclear architecture across mitosis and propose a hypothesis that a subset of NuMat proteome essential for nucleation of various nuclear bodies are retained in MiCS to serve as seeds of mitotic memory, thus ensuring the daughter cells re-establish the complex status of nuclear architecture similar to that of the mother cells, thereby maintaining the pre-mitotic transcriptional status.
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Affiliation(s)
- Mamilla Soujanya
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ashish Bihani
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Nikhil Hajirnis
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | - Rashmi U Pathak
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India.
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India.
- TIGS - Tata Institute for Genetics and Society, Bangalore, India.
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14
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Stamatiou K, Chmielewska A, Ohta S, Earnshaw WC, Vagnarelli P. CCDC86 is a novel Ki-67-interacting protein important for cell division. J Cell Sci 2023; 136:286751. [PMID: 36695333 PMCID: PMC10022746 DOI: 10.1242/jcs.260391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/08/2022] [Indexed: 01/26/2023] Open
Abstract
The chromosome periphery is a network of proteins and RNAs that coats the outer surface of mitotic chromosomes. Despite the identification of new components, the functions of this complex compartment are poorly characterised. In this study, we identified a novel chromosome periphery-associated protein, CCDC86 (also known as cyclon). Using a combination of RNA interference, microscopy and biochemistry, we studied the functions of CCDC86 in mitosis. CCDC86 depletion resulted in partial disorganisation of the chromosome periphery with alterations in the localisation of Ki-67 (also known as MKI67) and nucleolin (NCL), and the formation of abnormal cytoplasmic aggregates. Furthermore, CCDC86-depleted cells displayed errors in chromosome alignment, altered spindle length and increased apoptosis. These results suggest that, within the chromosome periphery, different subcomplexes that include CCDC86, nucleolin and B23 (nucleophosmin or NPM1) are required for mitotic spindle regulation and correct kinetochore-microtubule attachments, thus contributing to chromosome segregation in mitosis. Moreover, we identified CCDC86 as a MYCN-regulated gene, the expression levels of which represent a powerful marker for prognostic outcomes in neuroblastoma.
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Affiliation(s)
- Konstantinos Stamatiou
- College of Health, Medicine and Life Sciences, Department of Life Sciences, Brunel University London, London UB8 3PH, UK
| | - Aldona Chmielewska
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Shinya Ohta
- Institute for Genetic Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-Ku, Sapporo 060-0815, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Paola Vagnarelli
- College of Health, Medicine and Life Sciences, Department of Life Sciences, Brunel University London, London UB8 3PH, UK
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15
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Chen P, Levy DL. Regulation of organelle size and organization during development. Semin Cell Dev Biol 2023; 133:53-64. [PMID: 35148938 PMCID: PMC9357868 DOI: 10.1016/j.semcdb.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
During early embryogenesis, as cells divide in the developing embryo, the size of intracellular organelles generally decreases to scale with the decrease in overall cell size. Organelle size scaling is thought to be important to establish and maintain proper cellular function, and defective scaling may lead to impaired development and disease. However, how the cell regulates organelle size and organization are largely unanswered questions. In this review, we summarize the process of size scaling at both the cell and organelle levels and discuss recently discovered mechanisms that regulate this process during early embryogenesis. In addition, we describe how some recently developed techniques and Xenopus as an animal model can be used to investigate the underlying mechanisms of size regulation and to uncover the significance of proper organelle size scaling and organization.
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Affiliation(s)
- Pan Chen
- Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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16
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van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
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Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
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17
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Kakui Y, Barrington C, Kusano Y, Thadani R, Fallesen T, Hirota T, Uhlmann F. Chromosome arm length, and a species-specific determinant, define chromosome arm width. Cell Rep 2022; 41:111753. [PMID: 36476849 DOI: 10.1016/j.celrep.2022.111753] [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: 04/20/2022] [Revised: 09/05/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Mitotic chromosomes in different organisms adopt various dimensions. What defines these dimensions is scarcely understood. Here, we compare mitotic chromosomes in budding and fission yeasts harboring similarly sized genomes distributed among 16 or 3 chromosomes, respectively. Hi-C analyses and superresolution microscopy reveal that budding yeast chromosomes are characterized by shorter-ranging mitotic chromatin contacts and are thinner compared with the thicker fission yeast chromosomes that contain longer-ranging mitotic contacts. These distinctions persist even after budding yeast chromosomes are fused to form three fission-yeast-length entities, revealing a species-specific organizing principle. Species-specific widths correlate with the known binding site intervals of the chromosomal condensin complex. Unexpectedly, within each species, we find that longer chromosome arms are always thicker and harbor longer-ranging contacts, a trend that we also observe with human chromosomes. Arm length as a chromosome width determinant informs mitotic chromosome formation models.
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Affiliation(s)
- Yasutaka Kakui
- Waseda Institute for Advanced Study, Waseda University, Tokyo 169-0051, Japan; Laboratory of Cytoskeletal Logistics, Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan; Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Christopher Barrington
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Yoshiharu Kusano
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Rahul Thadani
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Todd Fallesen
- Advanced Light Microscopy Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Toru Hirota
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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18
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Shen W, Zhang Y, Shi M, Ye B, Yin M, Li P, Shi S, Jin Y, Zhang Z, Zhang MQ, Chen Y, Zhao Z. Profiling and characterization of constitutive chromatin-enriched RNAs. iScience 2022; 25:105349. [DOI: 10.1016/j.isci.2022.105349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022] Open
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19
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Flashner S, Swift M, Sowash A, Fahmy AN, Azizkhan-Clifford J. Transcription factor Sp1 regulates mitotic chromosome assembly and segregation. Chromosoma 2022; 131:175-191. [PMID: 35916925 PMCID: PMC9470683 DOI: 10.1007/s00412-022-00778-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Aneuploidy is a pervasive feature of cancer cells that results from chromosome missegregation. Several transcription factors have been associated with aneuploidy; however, no studies to date have demonstrated that mammalian transcription factors directly regulate chromosome segregation during mitosis. Here, we demonstrate that the ubiquitously expressed transcription factor specificity protein 1 (Sp1), which we have previously linked to aneuploidy, has a mitosis-specific role regulating chromosome segregation. We find that Sp1 localizes to mitotic centromeres and auxin-induced rapid Sp1 degradation at mitotic onset results in chromosome segregation errors and aberrant mitotic progression. Furthermore, rapid Sp1 degradation results in anomalous mitotic chromosome assembly characterized by loss of condensin complex I localization to mitotic chromosomes and chromosome condensation defects. Consistent with these defects, Sp1 degradation results in reduced chromosome passenger complex activity and histone H3 serine 10 phosphorylation during mitosis, which is essential for condensin complex I recruitment and chromosome condensation. Together, these data provide the first evidence of a mammalian transcription factor acting specifically during mitosis to regulate chromosome segregation.
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Affiliation(s)
- Samuel Flashner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Michelle Swift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Aislinn Sowash
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Alexander N Fahmy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA.
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20
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Shintomi K. Making Mitotic Chromosomes in a Test Tube. EPIGENOMES 2022; 6:20. [PMID: 35893016 PMCID: PMC9326633 DOI: 10.3390/epigenomes6030020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin I complex central for the chromosome assembly process was first identified, and its functions have been intensively studied. A list of chromosome-associated proteins has been almost completed, and it is now possible to reconstitute structures resembling mitotic chromosomes with a limited number of purified factors. In this review, I introduce how far we have come in understanding the mechanism of chromosome assembly using cell-free assays and reconstitution assays, and I discuss their potential applications to solve open questions.
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Affiliation(s)
- Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN, Wako 351-0198, Saitama, Japan
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21
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Lin S, Rajan S, Lemberg S, Altawil M, Anderson K, Bryant R, Cappeta S, Chin B, Hamdan I, Hamer A, Hyzny R, Karp A, Lee D, Lim A, Nayak M, Palaniappan V, Park S, Satishkumar S, Seth A, Sri Dasari U, Toppari E, Vyas A, Walker J, Weston E, Zafar A, Zielke C, Mahabeleshwar GH, Tartakoff AM. Production of nascent ribosome precursors within the nucleolar microenvironment of Saccharomyces cerevisiae. Genetics 2022; 221:iyac070. [PMID: 35657327 PMCID: PMC9252279 DOI: 10.1093/genetics/iyac070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
35S rRNA transcripts include a 5'-external transcribed spacer followed by rRNAs of the small and large ribosomal subunits. Their processing yields massive precursors that include dozens of assembly factor proteins. In Saccharomyces cerevisiae, nucleolar assembly factors form 2 coaxial layers/volumes around ribosomal DNA. Most of these factors are cyclically recruited from a latent state to an operative state, and are extensively conserved. The layers match, at least approximately, known subcompartments found in higher eukaryotic cells. ∼80% of assembly factors are essential. The number of copies of these assembly factors is comparable to the number of nascent transcripts. Moreover, they exhibit "isoelectric balance," with RNA-binding candidate "nucleator" assembly factors being notably basic. The physical properties of pre-small subunit and pre-large subunit assembly factors are similar, as are their 19 motif signatures detected by hierarchical clustering, unlike motif signatures of the 5'-external transcribed spacer rRNP. Additionally, many assembly factors lack shared motifs. Taken together with the progression of rRNP composition during subunit maturation, and the realization that the ribosomal DNA cable is initially bathed in a subunit-nonspecific assembly factor reservoir/microenvironment, we propose a "3-step subdomain assembly model": Step (1): predominantly basic assembly factors sequentially nucleate sites along nascent rRNA; Step (2): the resulting rRNPs recruit numerous less basic assembly factors along with notably basic ribosomal proteins; Step (3): rRNPs in nearby subdomains consolidate. Cleavages of rRNA then promote release of rRNPs to the nucleoplasm, likely facilitated by the persistence of assembly factors that were already associated with nucleolar precursors.
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Affiliation(s)
- Samantha Lin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Suchita Rajan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sofia Lemberg
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark Altawil
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Katherine Anderson
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth Bryant
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sebastian Cappeta
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brandon Chin
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Isabella Hamdan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Annelise Hamer
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rachel Hyzny
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Karp
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel Lee
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alexandria Lim
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Medha Nayak
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vishnu Palaniappan
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Soomin Park
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarika Satishkumar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anika Seth
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Uva Sri Dasari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Emili Toppari
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ayush Vyas
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Julianne Walker
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Evan Weston
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Atif Zafar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cecelia Zielke
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ganapati H Mahabeleshwar
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alan M Tartakoff
- Pathology Department and The Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA
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22
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Andrés-Sánchez N, Fisher D, Krasinska L. Physiological functions and roles in cancer of the proliferation marker Ki-67. J Cell Sci 2022; 135:275629. [PMID: 35674256 DOI: 10.1242/jcs.258932] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
What do we know about Ki-67, apart from its usefulness as a cell proliferation biomarker in histopathology? Discovered in 1983, the protein and its regulation of expression and localisation throughout the cell cycle have been well characterised. However, its function and molecular mechanisms have received little attention and few answers. Although Ki-67 has long been thought to be required for cell proliferation, recent genetic studies have conclusively demonstrated that this is not the case, as loss of Ki-67 has little or no impact on cell proliferation. In contrast, Ki-67 is important for localising nucleolar material to the mitotic chromosome periphery and for structuring perinucleolar heterochromatin, and emerging data indicate that it also has critical roles in cancer development. However, its mechanisms of action have not yet been fully identified. Here, we review recent findings and propose the hypothesis that Ki-67 is involved in structuring cellular sub-compartments that assemble by liquid-liquid phase separation. At the heterochromatin boundary, this may control access of chromatin regulators, with knock-on effects on gene expression programmes. These changes allow adaptation of the cell to its environment, which, for cancer cells, is a hostile one. We discuss unresolved questions and possible avenues for future exploration.
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Affiliation(s)
- Nuria Andrés-Sánchez
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, INSERM, 34293 Montpellier, France.,Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Daniel Fisher
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, INSERM, 34293 Montpellier, France.,Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Liliana Krasinska
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, INSERM, 34293 Montpellier, France.,Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, 75013 Paris, France
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23
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Ribosomal RNA regulates chromosome clustering during mitosis. Cell Discov 2022; 8:51. [PMID: 35637200 PMCID: PMC9151767 DOI: 10.1038/s41421-022-00400-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
Noncoding RNAs are known to associate with mitotic chromosomes, but the identities and functions of chromosome-associated RNAs in mitosis remain elusive. Here, we show that rRNA species associate with condensed chromosomes during mitosis. In particular, pre-rRNAs such as 45S, 32S, and 30S are highly enriched on mitotic chromosomes. Immediately following nucleolus disassembly in mitotic prophase, rRNAs are released and associate with and coat each condensed chromosome at prometaphase. Using unbiased mass spectrometry analysis, we further demonstrate that chromosome-bound rRNAs are associated with Ki-67. Moreover, the FHA domain and the repeat region of Ki-67 recognize and anchor rRNAs to chromosomes. Finally, suppression of chromosome-bound rRNAs by RNA polymerase I inhibition or by using rRNA-binding-deficient Ki-67 mutants impair mitotic chromosome dispersion during prometaphase. Our study thus reveals an important role of rRNAs in preventing chromosome clustering during mitosis.
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24
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Wang J, Hu C, Chen X, Li Y, Sun J, Czajkowsky DM, Shao Z. Single-Molecule Micromanipulation and Super-Resolution Imaging Resolve Nanodomains Underlying Chromatin Folding in Mitotic Chromosomes. ACS NANO 2022; 16:8030-8039. [PMID: 35485433 DOI: 10.1021/acsnano.2c01025] [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] [Indexed: 06/14/2023]
Abstract
The folding of interphase chromatin into highly compact mitotic chromosomes is one of the most recognizable changes during the cell cycle. However, the structural organization underlying this drastic compaction remains elusive. Here, we combine several super resolution methods, including structured illumination microscopy (SIM), binding-activated localization microscopy (BALM), and atomic force microscopy (AFM), to examine the structural details of the DNA within the mitotic chromosome, both in the native state and after up to 30-fold extension using single-molecule micromanipulation. Images of native chromosomes reveal widespread ∼125 nm compact granules (CGs) throughout the metaphase chromosome. However, at maximal extensions, we find exclusively ∼90 nm domains (mitotic nanodomains, MNDs) that are unexpectedly resistant to extensive forces of tens of nanonewtons. The DNA content of the MNDs is estimated to be predominantly ∼80 kb, which is comparable to the size of the inner loops predicted by a recent nested loop model of the mitotic chromosome. With this DNA content, the total volume expected of the human genome assuming closely packed MNDs is nearly identical to what is observed. Thus, altogether, these results suggest that these mechanically stable MNDs, and their higher-order assembly into CGs, are the dominant higher-level structures that underlie the compaction of chromatin from interphase to metaphase.
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Affiliation(s)
- Jiabin Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqian Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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25
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Ghrelin Regulates Expression of the Transcription Factor Pax6 in Hypoxic Brain Progenitor Cells and Neurons. Cells 2022; 11:cells11050782. [PMID: 35269403 PMCID: PMC8909042 DOI: 10.3390/cells11050782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
The nature of brain impairment after hypoxia is complex and recovery harnesses different mechanisms, including neuroprotection and neurogenesis. Experimental evidence suggests that hypoxia may trigger neurogenesis postnatally by influencing the expression of a variety of transcription factors. However, the existing data are controversial. As a proof-of-principle, we subjected cultured cerebral cortex neurons, cerebellar granule neurons and organotypic cerebral cortex slices from rat brains to hypoxia and treated these cultures with the hormone ghrelin, which is well-known for its neuroprotective functions. We found that hypoxia elevated the expression levels and stimulated nuclear translocation of ghrelin’s receptor GHSR1 in the cultured neurons and the acute organotypic slices, whereas ghrelin treatment reduced the receptor expression to normoxic levels. GHSR1 expression was also increased in cerebral cortex neurons of mice with induced experimental stroke. Additional quantitative analyses of immunostainings for neuronal proliferation and differentiation markers revealed that hypoxia stimulated the proliferation of neuronal progenitors, whereas ghrelin application during the phase of recovery from hypoxia counteracted these effects. At the mechanistic level, we provide a link between the described post-ischemic phenomena and the expression of the transcription factor Pax6, an important regulator of neural progenitor cell fate. In contrast to the neurogenic niches in the brain where hypoxia is known to increase Pax6 expression, the levels of the transcription factor in cultured hypoxic cerebral cortex cells were downregulated. Moreover, the application of ghrelin to hypoxic neurons normalised the expression levels of these factors. Our findings suggest that ghrelin stimulates neurogenic factors for the protection of neurons in a GHSR1-dependent manner in non-neurogenic brain areas such as the cerebral cortex after exposure to hypoxia.
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26
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Mammel AE, Huang HZ, Gunn AL, Choo E, Hatch EM. Chromosome length and gene density contribute to micronuclear membrane stability. Life Sci Alliance 2022; 5:e202101210. [PMID: 34789512 PMCID: PMC8605325 DOI: 10.26508/lsa.202101210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022] Open
Abstract
Micronuclei are derived from missegregated chromosomes and frequently lose membrane integrity, leading to DNA damage, innate immune activation, and metastatic signaling. Here, we demonstrate that two characteristics of the trapped chromosome, length and gene density, are key contributors to micronuclei membrane stability and determine the timing of micronucleus rupture. We demonstrate that these results are not due to chromosome-specific differences in spindle position or initial protein recruitment during post-mitotic nuclear envelope assembly. Micronucleus size strongly correlates with lamin B1 levels and nuclear pore density in intact micronuclei, but, unexpectedly, lamin B1 levels do not completely predict nuclear lamina organization or membrane stability. Instead, small gene-dense micronuclei have decreased nuclear lamina gaps compared to large micronuclei, despite very low levels of lamin B1. Our data strongly suggest that nuclear envelope composition defects previously correlated with membrane rupture only partly explain membrane stability in micronuclei. We propose that an unknown factor linked to gene density has a separate function that inhibits the appearance of nuclear lamina gaps and delays membrane rupture until late in the cell cycle.
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Affiliation(s)
- Anna E Mammel
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Heather Z Huang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda L Gunn
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emma Choo
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily M Hatch
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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27
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Ferguson CJ, Urso O, Bodrug T, Gassaway BM, Watson ER, Prabu JR, Lara-Gonzalez P, Martinez-Chacin RC, Wu DY, Brigatti KW, Puffenberger EG, Taylor CM, Haas-Givler B, Jinks RN, Strauss KA, Desai A, Gabel HW, Gygi SP, Schulman BA, Brown NG, Bonni A. APC7 mediates ubiquitin signaling in constitutive heterochromatin in the developing mammalian brain. Mol Cell 2022; 82:90-105.e13. [PMID: 34942119 PMCID: PMC8741739 DOI: 10.1016/j.molcel.2021.11.031] [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: 12/08/2020] [Revised: 10/14/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
Neurodevelopmental cognitive disorders provide insights into mechanisms of human brain development. Here, we report an intellectual disability syndrome caused by the loss of APC7, a core component of the E3 ubiquitin ligase anaphase promoting complex (APC). In mechanistic studies, we uncover a critical role for APC7 during the recruitment and ubiquitination of APC substrates. In proteomics analyses of the brain from mice harboring the patient-specific APC7 mutation, we identify the chromatin-associated protein Ki-67 as an APC7-dependent substrate of the APC in neurons. Conditional knockout of the APC coactivator protein Cdh1, but not Cdc20, leads to the accumulation of Ki-67 protein in neurons in vivo, suggesting that APC7 is required for the function of Cdh1-APC in the brain. Deregulated neuronal Ki-67 upon APC7 loss localizes predominantly to constitutive heterochromatin. Our findings define an essential function for APC7 and Cdh1-APC in neuronal heterochromatin regulation, with implications for understanding human brain development and disease.
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Affiliation(s)
- Cole J Ferguson
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Neuropathology Division, Physician-Scientist Training Program, Washington University, St. Louis, MO 63110, USA
| | - Olivia Urso
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | - Tatyana Bodrug
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | - Pablo Lara-Gonzalez
- Department of Cellular and Molecular Medicine, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Raquel C Martinez-Chacin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | | | | | - Cora M Taylor
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA 17837, USA
| | - Barbara Haas-Givler
- Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA 17837, USA
| | - Robert N Jinks
- Department of Biology, Franklin and Marshall College, Lancaster, PA 17603, USA
| | | | - Arshad Desai
- Department of Cellular and Molecular Medicine, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University, Boston, MA 02138, USA
| | | | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University, St. Louis, MO 63110, USA.
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28
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Stochastic chromatin packing of 3D mitotic chromosomes revealed by coherent X-rays. Proc Natl Acad Sci U S A 2021; 118:2109921118. [PMID: 34750262 DOI: 10.1073/pnas.2109921118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints. However, its three-dimensional (3D) structure remains elusive with challenges in observing native structures of specimens at tens-of-nanometers resolution. Here, using cryogenic coherent X-ray diffraction imaging, we succeeded in obtaining nanoscale 3D structures of metaphase chromosomes that exhibited a random distribution of electron density without characteristics of high-order folding structures. Scaling analysis of the chromosomes, compared with a model structure having the same density profile as the experimental results, has discovered the fractal nature of density distributions. Quantitative 3D density maps, corroborated by molecular dynamics simulations, reveal that internal structures of chromosomes conform to diffusion-limited aggregation behavior, which indicates that 3D chromatin packing occurs via stochastic processes.
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29
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Chromosome clustering in mitosis by the nuclear protein Ki-67. Biochem Soc Trans 2021; 49:2767-2776. [PMID: 34783345 PMCID: PMC8786303 DOI: 10.1042/bst20210717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Ki-67 is highly expressed in proliferating cells, a characteristic that made the protein a very important proliferation marker widely used in the clinic. However, the molecular functions and properties of Ki-67 remained quite obscure for a long time. Only recently important discoveries have shed some light on its function and shown that Ki-67 has a major role in the formation of mitotic chromosome periphery compartment, it is associated with protein phosphatase one (PP1) and regulates chromatin function in interphase and mitosis. In this review, we discuss the role of Ki-67 during cell division. Specifically, we focus on the importance of Ki-67 in chromosome individualisation at mitotic entry (prometaphase) and its contribution to chromosome clustering and nuclear remodelling during mitotic exit.
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30
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Perutka Z, Kaduchová K, Chamrád I, Beinhauer J, Lenobel R, Petrovská B, Bergougnoux V, Vrána J, Pecinka A, Doležel J, Šebela M. Proteome Analysis of Condensed Barley Mitotic Chromosomes. FRONTIERS IN PLANT SCIENCE 2021; 12:723674. [PMID: 34497629 PMCID: PMC8419432 DOI: 10.3389/fpls.2021.723674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.
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Affiliation(s)
- Zdeněk Perutka
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Kateřina Kaduchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Beáta Petrovská
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Véronique Bergougnoux
- Department of Molecular Biology, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
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31
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Garwain O, Sun X, Iyer DR, Li R, Zhu LJ, Kaufman PD. The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage. Proc Natl Acad Sci U S A 2021; 118:e2021998118. [PMID: 34353903 PMCID: PMC8364191 DOI: 10.1073/pnas.2021998118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Vertebrate mammals express a protein called Ki-67 which is most widely known as a clinically useful marker of highly proliferative cells. Previous studies of human cells indicated that acute depletion of Ki-67 can elicit a delay at the G1/S boundary of the cell cycle, dependent on induction of the checkpoint protein p21. Consistent with those observations, we show here that acute Ki-67 depletion causes hallmarks of DNA damage, and the damage occurs even in the absence of checkpoint signaling. This damage is not observed in cells traversing S phase but is instead robustly detected in mitotic cells. The C-terminal chromatin-binding domain of Ki-67 is necessary and sufficient to protect cells from this damage. We also observe synergistic effects when Ki-67 and p53 are simultaneously depleted, resulting in increased levels of chromosome bridges at anaphase, followed by the appearance of micronuclei. Therefore, these studies identify the C terminus of Ki-67 as an important module for genome stability.
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Affiliation(s)
- Osama Garwain
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiaoming Sun
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Divya Ramalingam Iyer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
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32
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Remnant L, Kochanova NY, Reid C, Cisneros-Soberanis F, Earnshaw WC. The intrinsically disorderly story of Ki-67. Open Biol 2021; 11:210120. [PMID: 34375547 PMCID: PMC8354752 DOI: 10.1098/rsob.210120] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/13/2021] [Indexed: 01/14/2023] Open
Abstract
Ki-67 is one of the most famous marker proteins used by histologists to identify proliferating cells. Indeed, over 30 000 articles referring to Ki-67 are listed on PubMed. Here, we review some of the current literature regarding the protein. Despite its clinical importance, our knowledge of the molecular biology and biochemistry of Ki-67 is far from complete, and its exact molecular function(s) remain enigmatic. Furthermore, reports describing Ki-67 function are often contradictory, and it has only recently become clear that this proliferation marker is itself dispensable for cell proliferation. We discuss the unusual organization of the protein and its mRNA and how they relate to various models for its function. In particular, we focus on ways in which the intrinsically disordered structure of Ki-67 might aid in the assembly of the still-mysterious mitotic chromosome periphery compartment by controlling liquid-liquid phase separation of nucleolar proteins and RNAs.
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Affiliation(s)
- Lucy Remnant
- Wellcome Centre for Cell Biology, University of Edinburgh, ICB, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Natalia Y. Kochanova
- Wellcome Centre for Cell Biology, University of Edinburgh, ICB, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Caitlin Reid
- Wellcome Centre for Cell Biology, University of Edinburgh, ICB, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Fernanda Cisneros-Soberanis
- Wellcome Centre for Cell Biology, University of Edinburgh, ICB, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - William C. Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, ICB, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
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33
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Kutay U, Jühlen R, Antonin W. Mitotic disassembly and reassembly of nuclear pore complexes. Trends Cell Biol 2021; 31:1019-1033. [PMID: 34294532 DOI: 10.1016/j.tcb.2021.06.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022]
Abstract
Nuclear pore complexes (NPCs) are huge protein assemblies within the nuclear envelope (NE) that serve as selective gates for macromolecular transport between nucleus and cytoplasm. When higher eukaryotic cells prepare for division, they rapidly disintegrate NPCs during NE breakdown such that nuclear and cytoplasmic components mix to enable the formation of a cytoplasmic mitotic spindle. At the end of mitosis, reassembly of NPCs is coordinated with the establishment of the NE around decondensing chromatin. We review recent progress on mitotic NPC disassembly and reassembly, focusing on vertebrate cells. We highlight novel mechanistic insights into how NPCs are rapidly disintegrated into conveniently reusable building blocks, and put divergent models of (post-)mitotic NPC assembly into a spatial and temporal context.
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Affiliation(s)
- Ulrike Kutay
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland.
| | - Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany.
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34
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Koliopoulos MG, Alfieri C. Cell cycle regulation by complex nanomachines. FEBS J 2021; 289:5100-5120. [PMID: 34143558 DOI: 10.1111/febs.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The cell cycle is the essential biological process where one cell replicates its genome and segregates the resulting two copies into the daughter cells during mitosis. Several aspects of this process have fascinated humans since the nineteenth century. Today, the cell cycle is exhaustively investigated because of its profound connections with human diseases and cancer. At the heart of the molecular network controlling the cell cycle, we find the cyclin-dependent kinases (CDKs) acting as an oscillator to impose an orderly and highly regulated progression through the different cell cycle phases. This oscillator integrates both internal and external signals via a multitude of signalling pathways involving posttranslational modifications including phosphorylation, protein ubiquitination and mechanisms of transcriptional regulation. These tasks are specifically performed by multi-subunit complexes, which are intensively studied both biochemically and structurally with the aim to unveil mechanistic insights into their molecular function. The scope of this review is to summarise the structural biology of the cell cycle machinery, with specific focus on the core cell cycle machinery involving the CDK-cyclin oscillator. We highlight the contribution of cryo-electron microscopy, which has started to revolutionise our understanding of the molecular function and dynamics of the key players of the cell cycle.
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Affiliation(s)
- Marios G Koliopoulos
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
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35
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Kramer EM, Tayjasanant PA, Cordone B. Scaling Laws for Mitotic Chromosomes. Front Cell Dev Biol 2021; 9:684278. [PMID: 34249936 PMCID: PMC8262490 DOI: 10.3389/fcell.2021.684278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
During mitosis in higher eukaryotes, each chromosome condenses into a pair of rod-shaped chromatids. This process is co-regulated by the activity of several gene families, and the underlying biophysics remains poorly understood. To better understand the factors regulating chromosome condensation, we compiled a database of mitotic chromosome size and DNA content from the tables and figures of >200 published papers. A comparison across vertebrate species shows that chromosome width, length and volume scale with DNA content to the powers ∼1/4, ∼1/2, and ∼1, respectively. Angiosperms (flowering plants) show a similar length scaling, so this result is not specific to vertebrates. Chromosome shape and size thus satisfy two conditions: (1) DNA content per unit volume is approximately constant and (2) the cross-sectional area increases proportionately with chromosome length. Since viscous drag forces during chromosome movement are expected to scale with length, we hypothesize that the cross-section increase is necessary to limit the occurrence of large chromosome elongations that could slow or stall mitosis. Lastly, we note that individual vertebrate karyotypes typically exhibit a wider range of chromosome lengths as compared with angiosperms.
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Affiliation(s)
- Eric M Kramer
- Department of Physics, Bard College at Simon's Rock, Great Barrington, MA, United States
| | - P A Tayjasanant
- Department of Physics, Bard College at Simon's Rock, Great Barrington, MA, United States
| | - Bethan Cordone
- Department of Physics, Bard College at Simon's Rock, Great Barrington, MA, United States
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36
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Sajid A, Lalani EN, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int J Mol Sci 2021; 22:ijms22115987. [PMID: 34206020 PMCID: PMC8198510 DOI: 10.3390/ijms22115987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/18/2022] Open
Abstract
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
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Affiliation(s)
- Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Key Laboratory of Performance Evolution and Control for Engineering Structures of the Ministry of Education, Tongji University, Shanghai 200092, China
| | - Teruo Hashimoto
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | | | - Archana Bhartiya
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
| | - George Thompson
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | - Ian K. Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mohammed Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Correspondence:
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37
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Midha S, Rigden DJ, Siozios S, Hurst GDD, Jackson AP. Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems. THE ISME JOURNAL 2021; 15:1680-1694. [PMID: 33452479 PMCID: PMC8163844 DOI: 10.1038/s41396-020-00879-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by which B. saltans becomes addicted to its endosymbiont. Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts of Paracaedibacter-like bacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.
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Affiliation(s)
- Samriti Midha
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill, Liverpool, L3 5RF, UK
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38
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Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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39
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Prabhakar N, Belevich I, Peurla M, Heiligenstein X, Chang HC, Sahlgren C, Jokitalo E, Rosenholm JM. Cell Volume (3D) Correlative Microscopy Facilitated by Intracellular Fluorescent Nanodiamonds as Multi-Modal Probes. NANOMATERIALS 2020; 11:nano11010014. [PMID: 33374705 PMCID: PMC7822478 DOI: 10.3390/nano11010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023]
Abstract
Three-dimensional correlative light and electron microscopy (3D CLEM) is attaining popularity as a potential technique to explore the functional aspects of a cell together with high-resolution ultrastructural details across the cell volume. To perform such a 3D CLEM experiment, there is an imperative requirement for multi-modal probes that are both fluorescent and electron-dense. These multi-modal probes will serve as landmarks in matching up the large full cell volume datasets acquired by different imaging modalities. Fluorescent nanodiamonds (FNDs) are a unique nanosized, fluorescent, and electron-dense material from the nanocarbon family. We hereby propose a novel and straightforward method for executing 3D CLEM using FNDs as multi-modal landmarks. We demonstrate that FND is biocompatible and is easily identified both in living cell fluorescence imaging and in serial block-face scanning electron microscopy (SB-EM). We illustrate the method by registering multi-modal datasets.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Correspondence:
| | - Ilya Belevich
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan;
| | - Cecilia Sahlgren
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Eija Jokitalo
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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40
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Prabhakar N, Peurla M, Shenderova O, Rosenholm JM. Fluorescent and Electron-Dense Green Color Emitting Nanodiamonds for Single-Cell Correlative Microscopy. Molecules 2020; 25:E5897. [PMID: 33322105 PMCID: PMC7764487 DOI: 10.3390/molecules25245897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is revolutionizing how cell samples are studied. CLEM provides a combination of the molecular and ultrastructural information about a cell. For the execution of CLEM experiments, multimodal fiducial landmarks are applied to precisely overlay light and electron microscopy images. Currently applied fiducials such as quantum dots and organic dye-labeled nanoparticles can be irreversibly quenched by electron beam exposure during electron microscopy. Generally, the sample is therefore investigated with a light microscope first and later with an electron microscope. A versatile fiducial landmark should offer to switch back from electron microscopy to light microscopy while preserving its fluorescent properties. Here, we evaluated green fluorescent and electron dense nanodiamonds for the execution of CLEM experiments and precisely correlated light microscopy and electron microscopy images. We demonstrated that green color emitting fluorescent nanodiamonds withstand electron beam exposure, harsh chemical treatments, heavy metal straining, and, importantly, their fluorescent properties remained intact for light microscopy.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Olga Shenderova
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Drive, Suite 120, Raleigh, NC 27617, USA;
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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41
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Ye S, Azad AA, Chambers JE, Beckett AJ, Roach L, Moorcroft SCT, Aslam Z, Prior IA, Markham AF, Coletta PL, Marciniak SJ, Evans SD. Exploring High Aspect Ratio Gold Nanotubes as Cytosolic Agents: Structural Engineering and Uptake into Mesothelioma Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003793. [PMID: 33103323 DOI: 10.1002/smll.202003793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/13/2020] [Indexed: 06/11/2023]
Abstract
The generation of effective and safe nanoagents for biological applications requires their physicochemical characteristics to be tunable, and their cellular interactions to be well characterized. Here, the controlled synthesis is developed for preparing high-aspect ratio gold nanotubes (AuNTs) with tailorable wall thickness, microstructure, composition, and optical characteristics. The modulation of optical properties generates AuNTs with strong near infrared absorption. Surface modification enhances dispersibility of AuNTs in aqueous media and results in low cytotoxicity. The uptake and trafficking of these AuNTs by primary mesothelioma cells demonstrate their accumulation in a perinuclear distribution where they are confined initially in membrane-bound vesicles from which they ultimately escape to the cytosol. This represents the first study of the cellular interactions of high-aspect ratio 1D metal nanomaterials and will facilitate the rational design of plasmonic nanoconstructs as cytosolic nanoagents for potential diagnosis and therapeutic applications.
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Affiliation(s)
- Sunjie Ye
- School of Physics and Astronomy, Woodhouse Lane, Leeds, LS2 9JT, UK
- Leeds Institute of Medical Research, St James's University Hospital, University of Leeds, Leeds, LS9 7TF, UK
| | - Arsalan A Azad
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Joseph E Chambers
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Alison J Beckett
- Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Lucien Roach
- School of Physics and Astronomy, Woodhouse Lane, Leeds, LS2 9JT, UK
| | | | - Zabeada Aslam
- Leeds Electron Microscopy and Spectroscopy Centre, School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Ian A Prior
- Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Alexander F Markham
- Leeds Institute of Medical Research, St James's University Hospital, University of Leeds, Leeds, LS9 7TF, UK
| | - P Louise Coletta
- Leeds Institute of Medical Research, St James's University Hospital, University of Leeds, Leeds, LS9 7TF, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Stephen D Evans
- School of Physics and Astronomy, Woodhouse Lane, Leeds, LS2 9JT, UK
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42
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Price RM, Budzyński MA, Kundra S, Teves SS. Advances in visualizing transcription factor - DNA interactions. Genome 2020; 64:449-466. [PMID: 33113335 DOI: 10.1139/gen-2020-0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.
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Affiliation(s)
- Rachel M Price
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Marek A Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Shivani Kundra
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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43
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Yusuf M, Farooq S, Robinson I, Lalani EN. Cryo-nanoscale chromosome imaging-future prospects. Biophys Rev 2020; 12:1257-1263. [PMID: 33006727 PMCID: PMC7575669 DOI: 10.1007/s12551-020-00757-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 01/30/2023] Open
Abstract
The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan.
| | - Safana Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Brookhaven National Lab, Upton, NY, 11973, USA
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
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44
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Chromosome clustering by Ki-67 excludes cytoplasm during nuclear assembly. Nature 2020; 587:285-290. [PMID: 32879492 PMCID: PMC7666080 DOI: 10.1038/s41586-020-2672-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/08/2020] [Indexed: 12/31/2022]
Abstract
Gene expression in eukaryotes requires the effective separation of nuclear transcription and RNA processing from cytosolic translation1. This separation is achieved by the nuclear envelope, which controls the exchange of macromolecules through nuclear pores2. During mitosis, however, the nuclear envelope in animal and plant cells disassembles, allowing cytoplasmic and nuclear components to intermix3. When the nuclear envelope is reformed, cytoplasmic components are removed from the nucleus by receptor-mediated transport through nuclear pores2. These pores have a size limit of 39 nanometres4-7, which raises the question of how larger cytoplasmic molecules are cleared from the nucleus. Here we show in HeLa cells that large cytoplasmic components are displaced before nuclear envelope assembly by the movement of chromosomes to a dense cluster. This clustering occurs when chromosomes approach the poles of anaphase spindles, and is mediated by a microtubule-independent mechanism that involves the surfactant-like protein Ki-67. Ki-67 forms repulsive molecular brushes during the early stages of mitosis8, but during mitotic exit the brushes collapse and Ki-67 promotes chromosome clustering. We show that the exclusion of mature ribosomes from the nucleus after mitosis depends on Ki-67-regulated chromosome clustering. Thus, our study reveals that chromosome mechanics help to re-establish the compartmentalization of eukaryotic cells after open mitosis.
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45
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Stenström L, Mahdessian D, Gnann C, Cesnik AJ, Ouyang W, Leonetti MD, Uhlén M, Cuylen‐Haering S, Thul PJ, Lundberg E. Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Mol Syst Biol 2020; 16:e9469. [PMID: 32744794 PMCID: PMC7397901 DOI: 10.15252/msb.20209469] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023] Open
Abstract
The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase-specific functions. We further show that the expression of MKI67 is critical for this temporal partitioning. We provide the first proteome-wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.
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Affiliation(s)
- Lovisa Stenström
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Diana Mahdessian
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Christian Gnann
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Anthony J Cesnik
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Wei Ouyang
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | | | - Mathias Uhlén
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Sara Cuylen‐Haering
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Peter J Thul
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
| | - Emma Lundberg
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSweden
- Chan Zuckerberg BiohubSan FranciscoCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
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46
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Wu M, Leung J, Liu L, Kam C, Chan KYK, Li RA, Feng S, Chen S. A Small-Molecule AIE Chromosome Periphery Probe for Cytogenetic Studies. Angew Chem Int Ed Engl 2020; 59:10327-10331. [PMID: 32163217 PMCID: PMC7318220 DOI: 10.1002/anie.201916718] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Indexed: 01/12/2023]
Abstract
The chromosome periphery (CP) is a complex network that covers the outer surface of chromosomes. It acts as a carrier of nucleolar components, helps maintain chromosome structure, and plays an important role in mitosis. Current methods for fluorescence imaging of CP largely rely on immunostaining. We herein report a small-molecule fluorescent probe, ID-IQ, which possesses aggregation-induced emission (AIE) property, for CP imaging. By labelling the CP, ID-IQ sharply highlighted the chromosome boundaries, which enabled rapid segmentation of touching and overlapping chromosomes, direct identification of the centromere, and clear visualization of chromosome morphology. ID-IQ staining was also compatible with fluorescence in situ hybridization and could assist the precise location of the gene in designated chromosome. Altogether, this study provides a versatile cytogenetic tool for improved chromosome analysis, which greatly benefits the clinical diagnostic testing and genomic research.
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Affiliation(s)
- Ming‐Yu Wu
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Jong‐Kai Leung
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Li Liu
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Chuen Kam
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Kelvin Yuen Kwong Chan
- Department of Obstetrics and GynaecologyQueen Mary HospitalHong KongChina
- Prenatal Diagnostic LaboratoryTsan Yuk HospitalHong KongChina
| | - Ronald A. Li
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- Dr. Li Dak-Sum Research CentreThe University of Hong KongHong KongChina
| | - Shun Feng
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- Dr. Li Dak-Sum Research CentreThe University of Hong KongHong KongChina
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Generation of an antibody recognizing a set of acetylated proteins, including subunits of BAF complexes. Biochem Biophys Rep 2020; 22:100720. [PMID: 32490211 PMCID: PMC7261705 DOI: 10.1016/j.bbrep.2019.100720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to generate an antibody specific to Ki-67 acetylated at lysine 3180, whose existence was reported in an acetylome study (Scholz, C., B.T. Weinert, S.A. Wagner, P. Beli, Y. Miyake, J. Qi, L.J. Jensen, W. Streicher, A.R. McCarthy, N.J. Westwood, S. Lain, J. Cox, P. Matthias, M. Mann, J.E. Bradner, and C. Choudhary. 2015). Rabbits were immunized with a synthetic acetylated peptide corresponding to acetylated lysine 3180 of Ki-67 and the residues flanking it. The obtained antibody, referred to as Ab3180 in this study, was affinity purified with the antigen peptide and characterized. Immunoblot analysis of cell extracts using Ab3180 revealed that this antibody unexpectedly recognized a set of acetylated proteins unrelated to Ki-67. Ab3180-recognizable proteins were immunoprecipitated from cell extracts in a stringent condition and identified by mass-spec analysis as subunits of BAF (mammalian SWI/SNF) chromatin remodeling complexes. The unique specificity of Ab3180 will allow this antibody to be a useful tool for analyzing the acetylation of BAF complexes and its significance to the formation/function of BAF complexes. A new antibody (Ab3180) recognizing a set of acetylated proteins was developed. The population of proteins recognized by Ab3180 increases by treating cells with NAM. Contradicting the original aim, Ab3180 doesn't recognize Ki-67 efficiently. Ab3180 recognizes BAF chromatin remodeling complexes.
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Wu M, Leung J, Liu L, Kam C, Chan KYK, Li RA, Feng S, Chen S. A Small‐Molecule AIE Chromosome Periphery Probe for Cytogenetic Studies. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ming‐Yu Wu
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Hong Kong China
- School of Life Science and Engineering Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Jong‐Kai Leung
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Hong Kong China
| | - Li Liu
- School of Life Science and Engineering Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Chuen Kam
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Hong Kong China
| | - Kelvin Yuen Kwong Chan
- Department of Obstetrics and Gynaecology Queen Mary Hospital Hong Kong China
- Prenatal Diagnostic Laboratory Tsan Yuk Hospital Hong Kong China
| | - Ronald A. Li
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Hong Kong China
- Dr. Li Dak-Sum Research Centre The University of Hong Kong Hong Kong China
| | - Shun Feng
- School of Life Science and Engineering Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine Karolinska Institutet Hong Kong China
- Dr. Li Dak-Sum Research Centre The University of Hong Kong Hong Kong China
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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Phengchat R, Hayashida M, Ohmido N, Homeniuk D, Fukui K. 3D observation of chromosome scaffold structure using a 360° electron tomography sample holder. Micron 2019; 126:102736. [PMID: 31539626 DOI: 10.1016/j.micron.2019.102736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022]
Abstract
The chromosome scaffold is considered to be a key structure of the mitotic chromosome. It plays a vital role in chromosome condensation, shaping the X-shaped structure of the mitotic chromosome, and also provides flexibility for chromosome movement during cell division. However, it remains to be elucidated how the chromosome scaffold organizes the mitotic chromosome and how it supports shaping the structure of the chromosome during metaphase. Here we present a new technique that enables the observation of the chromosome scaffold structure in metaphase chromosomes from any direction, by transferring an isolated chromosome to a 360° rotational holder for electron tomography (ET). The chromosome was stained with immunogold-labeled condensin complex, one of the major chromosome scaffold proteins and then observed in three dimensions using ET. Using the locations of gold nanoparticles to visualize the underlying structure, the tomograms we obtained reveal the patterns of chromosome scaffold organization, which appears to consist of a helical structure that serves to organize chromatin loops into the metaphase chromosome.
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Affiliation(s)
- Rinyaporn Phengchat
- Graduate School of Human development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan
| | - Misa Hayashida
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G2M9, Canada.
| | - Nobuko Ohmido
- Graduate School of Human development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan
| | - Darren Homeniuk
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G2M9, Canada
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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