1
|
Roudot P, Legant WR, Zou Q, Dean KM, Isogai T, Welf ES, David AF, Gerlich DW, Fiolka R, Betzig E, Danuser G. u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions. Cell Rep Methods 2023; 3:100655. [PMID: 38042149 PMCID: PMC10783629 DOI: 10.1016/j.crmeth.2023.100655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/04/2023]
Abstract
We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.
Collapse
Affiliation(s)
- Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA; Aix Marseille University, CNRS, Centrale Marseille, I2M, Turing Centre for Living Systems, Marseille, France.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ana F David
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Eric Betzig
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
2
|
Nagasaka K, Davidson IF, Stocsits RR, Tang W, Wutz G, Batty P, Panarotto M, Litos G, Schleiffer A, Gerlich DW, Peters JM. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms. Mol Cell 2023; 83:3049-3063.e6. [PMID: 37591243 DOI: 10.1016/j.molcel.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/28/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.
Collapse
Affiliation(s)
- Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Melanie Panarotto
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.
| |
Collapse
|
3
|
Batty P, Langer CCH, Takács Z, Tang W, Blaukopf C, Peters J, Gerlich DW. Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase. EMBO J 2023; 42:e113475. [PMID: 37357575 PMCID: PMC10425840 DOI: 10.15252/embj.2023113475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.
Collapse
Affiliation(s)
- Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Christoph CH Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Zsuzsanna Takács
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Jan‐Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| |
Collapse
|
4
|
Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
Collapse
Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
| |
Collapse
|
5
|
Langer CCH, Mitter M, Stocsits RR, Gerlich DW. HiCognition: a visual exploration and hypothesis testing tool for 3D genomics. Genome Biol 2023; 24:158. [PMID: 37408019 DOI: 10.1186/s13059-023-02996-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information. We present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, enabling detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcription and cohesion subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition help to understand the relationship between the structure and function of the genome.
Collapse
Affiliation(s)
- Christoph C H Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
6
|
Gibson BA, Blaukopf C, Lou T, Chen L, Doolittle LK, Finkelstein I, Narlikar GJ, Gerlich DW, Rosen MK. In diverse conditions, intrinsic chromatin condensates have liquid-like material properties. Proc Natl Acad Sci U S A 2023; 120:e2218085120. [PMID: 37094140 PMCID: PMC10161002 DOI: 10.1073/pnas.2218085120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Nuclear DNA in eukaryotes is wrapped around histone proteins to form nucleosomes on a chromatin fiber. Dynamic folding of the chromatin fiber into loops and variations in the degree of chromatin compaction regulate essential processes such as transcription, recombination, and mitotic chromosome segregation. Our understanding of the physical properties that allow chromatin to be dynamically remodeled even in highly compacted states is limited. Previously, we reported that chromatin has an intrinsic capacity to phase separate and form dynamic liquid-like condensates, which can be regulated by cellular factors [B. A. Gibson et al., Cell 179, 470-484.e421 (2019)]. Recent contradictory reports claim that a specific set of solution conditions is required for fluidity in condensates that would otherwise be solid [J. C. Hansen, K. Maeshima, M. J. Hendzel, Epigenetics Chromatin 14, 50 (2021); H. Strickfaden et al., Cell 183, 1772-1784.e1713 (2020)]. We sought to resolve these discrepancies, as our ability to translate with confidence these biophysical observations to cells requires their precise characterization. Moreover, whether chromatin assemblies are dynamic or static affects how processes such as transcription, loop extrusion, and remodeling will engage them inside cells. Here, we show in diverse conditions and without specific buffering components that chromatin fragments form phase separated fluids in vitro. We also explore how sample preparation and imaging affect the experimental observation of chromatin condensate dynamics. Last, we describe how liquid-like in vitro behaviors can translate to the locally dynamic but globally constrained chromatin movement observed in cells.
Collapse
Affiliation(s)
- Bryan A Gibson
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Tracy Lou
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Lifeng Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lynda K Doolittle
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ilya Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Michael K Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| |
Collapse
|
7
|
Skok J, Gerlich DW. Editorial: From chromatin to dynamic loops and liquid-like phases: New views on the cell nucleus. Curr Opin Cell Biol 2021; 70:iii-v. [PMID: 33810967 DOI: 10.1016/j.ceb.2021.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jane Skok
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria.
| |
Collapse
|
8
|
Mitter M, Gerlich DW. Mapping Sister Chromatid Conformation in Replicated Chromosomes. Trends Biochem Sci 2020; 46:169-170. [PMID: 33342665 DOI: 10.1016/j.tibs.2020.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
9
|
Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW. Conformation of sister chromatids in the replicated human genome. Nature 2020; 586:139-144. [PMID: 32968280 PMCID: PMC7116725 DOI: 10.1038/s41586-020-2744-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)1,2 analysis has revealed a complex genomic landscape of internal chromosomal structures in vertebrate cells3-7, but the identical sequence of sister chromatids has made it difficult to determine how they topologically interact in replicated chromosomes. Here we describe sister-chromatid-sensitive Hi-C (scsHi-C), which is based on labelling of nascent DNA with 4-thio-thymidine and nucleoside conversion chemistry. Genome-wide conformation maps of human chromosomes reveal that sister-chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister-chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired and are characterized by facultative heterochromatin and insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister-chromatid topologies and our scsHi-C technology will make it possible to investigate how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.
Collapse
Affiliation(s)
- Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| | - Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Zsuzsanna Takacs
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Christoph C H Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gregor Jessberger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Charlie T Beales
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
10
|
Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell 2019; 179:470-484.e21. [PMID: 31543265 DOI: 10.1016/j.cell.2019.08.037] [Citation(s) in RCA: 546] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets. Linker histone H1 and internucleosome linker lengths shared across eukaryotes promote phase separation of chromatin, tune droplet properties, and coordinate to form condensates of consistent density in manners that parallel chromatin behavior in cells. Histone acetylation by p300 antagonizes chromatin phase separation, dissolving droplets in vitro and decreasing droplet formation in nuclei. In the presence of multi-bromodomain proteins, such as BRD4, highly acetylated chromatin forms a new phase-separated state with droplets of distinct physical properties, which can be immiscible with unmodified chromatin droplets, mimicking nuclear chromatin subdomains. Our data suggest a framework, based on intrinsic phase separation of the chromatin polymer, for understanding the organization and regulation of eukaryotic genomes.
Collapse
Affiliation(s)
- Bryan A Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lynda K Doolittle
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maximillian W G Schneider
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Liv E Jensen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Henry
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
11
|
Batty P, Gerlich DW. Mitotic Chromosome Mechanics: How Cells Segregate Their Genome. Trends Cell Biol 2019; 29:717-726. [PMID: 31230958 DOI: 10.1016/j.tcb.2019.05.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 01/09/2023]
Abstract
During mitosis, replicated chromosomes segregate such that each daughter cell receives one copy of the genome. Faithful mechanical transport during mitosis requires that chromosomes undergo extensive structural changes as the cell cycle progresses, resulting in the formation of compact, cylindrical bodies. Such structural changes encompass a range of different activities, including longitudinal condensation of the chromosome axis, global chromatin compaction, resolution of sister chromatids, and individualisation of chromosomes into separate bodies. After mitosis, chromosomes undergo further reorganisation to rebuild interphase cell nuclei. Here we review the requirements for mitotic chromosomes to successfully transmit genetic information to daughter cells and the biophysical principles that underpin such requirements.
Collapse
Affiliation(s)
- Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| |
Collapse
|
12
|
David AF, Roudot P, Legant WR, Betzig E, Danuser G, Gerlich DW. Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth. J Cell Biol 2019; 218:2150-2168. [PMID: 31113824 PMCID: PMC6605806 DOI: 10.1083/jcb.201805044] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 12/19/2018] [Accepted: 04/30/2019] [Indexed: 12/31/2022] Open
Abstract
Vertebrate cells assemble mitotic spindles through multiple pathways. It is shown that Augmin-dependent, noncentrosomal nucleation generates the vast majority of microtubules in metaphase spindles. This results in a strong directional bias of microtubule growth toward individual kinetochores. Dividing cells reorganize their microtubule cytoskeleton into a bipolar spindle, which moves one set of sister chromatids to each nascent daughter cell. Early spindle assembly models postulated that spindle pole–derived microtubules search the cytoplasmic space until they randomly encounter a kinetochore to form a stable attachment. More recent work uncovered several additional, centrosome-independent microtubule generation pathways, but the contributions of each pathway to spindle assembly have remained unclear. Here, we combined live microscopy and mathematical modeling to show that most microtubules nucleate at noncentrosomal regions in dividing human cells. Using a live-cell probe that selectively labels aged microtubule lattices, we demonstrate that the distribution of growing microtubule plus ends can be almost entirely explained by Augmin-dependent amplification of long-lived microtubule lattices. By ultrafast 3D lattice light-sheet microscopy, we observed that this mechanism results in a strong directional bias of microtubule growth toward individual kinetochores. Our systematic quantification of spindle dynamics reveals highly coordinated microtubule growth during kinetochore fiber assembly.
Collapse
Affiliation(s)
- Ana F David
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Philippe Roudot
- Department of Cell Biology and Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Wesley R Legant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Gaudenz Danuser
- Department of Cell Biology and Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| |
Collapse
|
13
|
Affiliation(s)
| | - Daniel W. Gerlich
- IMBA–Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| |
Collapse
|
14
|
|
15
|
Stanyte R, Nuebler J, Blaukopf C, Hoefler R, Stocsits R, Peters JM, Gerlich DW. Dynamics of sister chromatid resolution during cell cycle progression. J Cell Biol 2018; 217:1985-2004. [PMID: 29695489 PMCID: PMC5987726 DOI: 10.1083/jcb.201801157] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/16/2018] [Accepted: 04/11/2018] [Indexed: 01/04/2023] Open
Abstract
Faithful genome transmission in dividing cells requires that the two copies of each chromosome's DNA package into separate but physically linked sister chromatids. The linkage between sister chromatids is mediated by cohesin, yet where sister chromatids are linked and how they resolve during cell cycle progression has remained unclear. In this study, we investigated sister chromatid organization in live human cells using dCas9-mEGFP labeling of endogenous genomic loci. We detected substantial sister locus separation during G2 phase irrespective of the proximity to cohesin enrichment sites. Almost all sister loci separated within a few hours after their respective replication and then rapidly equilibrated their average distances within dynamic chromatin polymers. Our findings explain why the topology of sister chromatid resolution in G2 largely reflects the DNA replication program. Furthermore, these data suggest that cohesin enrichment sites are not persistent cohesive sites in human cells. Rather, cohesion might occur at variable genomic positions within the cell population.
Collapse
Affiliation(s)
- Rugile Stanyte
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Johannes Nuebler
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Rudolf Hoefler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| |
Collapse
|
16
|
Sommer C, Hoefler R, Samwer M, Gerlich DW. A deep learning and novelty detection framework for rapid phenotyping in high-content screening. Mol Biol Cell 2017; 28:3428-3436. [PMID: 28954863 PMCID: PMC5687041 DOI: 10.1091/mbc.e17-05-0333] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/31/2017] [Accepted: 09/18/2017] [Indexed: 11/16/2022] Open
Abstract
Supervised machine learning is a powerful and widely used method for analyzing high-content screening data. Despite its accuracy, efficiency, and versatility, supervised machine learning has drawbacks, most notably its dependence on a priori knowledge of expected phenotypes and time-consuming classifier training. We provide a solution to these limitations with CellCognition Explorer, a generic novelty detection and deep learning framework. Application to several large-scale screening data sets on nuclear and mitotic cell morphologies demonstrates that CellCognition Explorer enables discovery of rare phenotypes without user training, which has broad implications for improved assay development in high-content screening.
Collapse
Affiliation(s)
- Christoph Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Rudolf Hoefler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Matthias Samwer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| |
Collapse
|
17
|
Spira F, Cuylen-Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt M, Gerlich DW. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife 2017; 6. [PMID: 29106370 PMCID: PMC5673306 DOI: 10.7554/elife.30867] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 10/28/2017] [Indexed: 12/21/2022] Open
Abstract
The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.
Collapse
Affiliation(s)
- Felix Spira
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Sara Cuylen-Haering
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Shalin Mehta
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, United States
| | - Matthias Samwer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Anne Reversat
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Amitabh Verma
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, United States
| | - Rudolf Oldenbourg
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, United States
| | - Michael Sixt
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| |
Collapse
|
18
|
Kukolj E, Kaufmann T, Dick AE, Zeillinger R, Gerlich DW, Slade D. PARP inhibition causes premature loss of cohesion in cancer cells. Oncotarget 2017; 8:103931-103951. [PMID: 29262611 PMCID: PMC5732777 DOI: 10.18632/oncotarget.21879] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) regulate various aspects of cellular function including mitotic progression. Although PARP inhibitors have been undergoing various clinical trials and the PARP1/2 inhibitor olaparib was approved as monotherapy for BRCA-mutated ovarian cancer, their mode of action in killing tumour cells is not fully understood. We investigated the effect of PARP inhibition on mitosis in cancerous (cervical, ovary, breast and osteosarcoma) and non-cancerous cells by live-cell imaging. The clinically relevant inhibitor olaparib induced strong perturbations in mitosis, including problems with chromosome alignment at the metaphase plate, anaphase delay, and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest, resulting in sister chromatid scattering. PARP1 and PARP2 depletion suppressed the phenotype while PARP2 overexpression enhanced it, suggesting that olaparib-bound PARP1 and PARP2 rather than the lack of catalytic activity causes this phenotype. Olaparib-induced mitotic chromatid scattering was observed in various cancer cell lines with increased protein levels of PARP1 and PARP2, but not in non-cancer or cancer cell lines that expressed lower levels of PARP1 or PARP2. Interestingly, the sister chromatid scattering phenotype occurred only when olaparib was added during the S-phase preceding mitosis, suggesting that PARP1 and PARP2 entrapment at replication forks impairs sister chromatid cohesion. Clinically relevant DNA-damaging agents that impair replication progression such as topoisomerase inhibitors and cisplatin were also found to induce sister chromatid scattering and metaphase plate alignment problems, suggesting that these mitotic phenotypes are a common outcome of replication perturbation.
Collapse
Affiliation(s)
- Eva Kukolj
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Tanja Kaufmann
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Amalie E Dick
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Dea Slade
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| |
Collapse
|
19
|
Samwer M, Schneider MWG, Hoefler R, Schmalhorst PS, Jude JG, Zuber J, Gerlich DW. DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes. Cell 2017; 170:956-972.e23. [PMID: 28841419 PMCID: PMC5638020 DOI: 10.1016/j.cell.2017.07.038] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/12/2017] [Accepted: 07/24/2017] [Indexed: 01/23/2023]
Abstract
Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF's association with inner nuclear membrane proteins but instead relies on BAF's ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function.
Collapse
Affiliation(s)
- Matthias Samwer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Maximilian W G Schneider
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Rudolf Hoefler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Philipp S Schmalhorst
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Julian G Jude
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria.
| |
Collapse
|
20
|
Mierzwa BE, Chiaruttini N, Redondo-Morata L, von Filseck JM, König J, Larios J, Poser I, Müller-Reichert T, Scheuring S, Roux A, Gerlich DW. Dynamic subunit turnover in ESCRT-III assemblies is regulated by Vps4 to mediate membrane remodelling during cytokinesis. Nat Cell Biol 2017; 19:787-798. [PMID: 28604678 PMCID: PMC5493987 DOI: 10.1038/ncb3559] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
Abstract
The Endosomal Sorting Complex Required for Transport (ESCRT)-III mediates membrane fission in fundamental cellular processes, including cytokinesis. ESCRT-III is thought to form persistent filaments that over time increase their curvature to constrict membranes. Unexpectedly, we found that ESCRT-III at the midbody of human cells rapidly turns over subunits with cytoplasmic pools while gradually forming larger assemblies. ESCRT-III turnover depended on the ATPase VPS4, which accumulated at the midbody simultaneously with ESCRT-III subunits, and was required for assembly of functional ESCRT-III structures. In vitro, the Vps2/Vps24 subunits of ESCRT-III formed side-by-side filaments with Snf7 and inhibited further polymerization, but the growth inhibition was alleviated by the addition of Vps4 and ATP. High-speed atomic force microscopy further revealed highly dynamic arrays of growing and shrinking ESCRT-III spirals in presence of Vps4. Continuous ESCRT-III remodeling by subunit turnover might facilitate shape adaptions to variable membrane geometries, with broad implications for diverse cellular processes.
Collapse
Affiliation(s)
- Beata E Mierzwa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), AT-1030 Vienna, Austria
| | - Nicolas Chiaruttini
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | | | | | - Julia König
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Jorge Larios
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, 13009 Marseille, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), AT-1030 Vienna, Austria
| |
Collapse
|
21
|
Fededa JP, Esk C, Mierzwa B, Stanyte R, Yuan S, Zheng H, Ebnet K, Yan W, Knoblich JA, Gerlich DW. MicroRNA-34/449 controls mitotic spindle orientation during mammalian cortex development. EMBO J 2016; 35:2386-2398. [PMID: 27707753 PMCID: PMC5109238 DOI: 10.15252/embj.201694056] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 08/18/2016] [Accepted: 09/06/2016] [Indexed: 01/07/2023] Open
Abstract
Correct orientation of the mitotic spindle determines the plane of cellular cleavage and is crucial for organ development. In the developing cerebral cortex, spindle orientation defects result in severe neurodevelopmental disorders, but the precise mechanisms that control this important event are not fully understood. Here, we use a combination of high-content screening and mouse genetics to identify the miR-34/449 family as key regulators of mitotic spindle orientation in the developing cerebral cortex. By screening through all cortically expressed miRNAs in HeLa cells, we show that several members of the miR-34/449 family control mitotic duration and spindle rotation. Analysis of miR-34/449 knockout (KO) mouse embryos demonstrates significant spindle misorientation phenotypes in cortical progenitors, resulting in an excess of radial glia cells at the expense of intermediate progenitors and a significant delay in neurogenesis. We identify the junction adhesion molecule-A (JAM-A) as a key target for miR-34/449 in the developing cortex that might be responsible for those defects. Our data indicate that miRNA-dependent regulation of mitotic spindle orientation is crucial for cell fate specification during mammalian neurogenesis.
Collapse
Affiliation(s)
- Juan Pablo Fededa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| | - Beata Mierzwa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| | - Rugile Stanyte
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | - Klaus Ebnet
- Institute-associated Research Group "Cell Adhesion and Cell Polarity", Institute of Medical Biochemistry, ZMBE, Münster, Germany
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV, USA
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Vienna, Austria
| |
Collapse
|
22
|
Cuylen S, Blaukopf C, Politi AZ, Müller-Reichert T, Neumann B, Poser I, Ellenberg J, Hyman AA, Gerlich DW. Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature 2016; 535:308-12. [PMID: 27362226 PMCID: PMC4947524 DOI: 10.1038/nature18610] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/27/2016] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are partitioned into chromosomes, which during mitosis
form compact and spatially well-separated mechanical bodies1–3.This
enables chromosomes to move independently of each other for segregation of
precisely one copy of the genome to each of the nascent daughter cells. Despite
insights into the spatial organization of mitotic chromosomes4 and the discovery of proteins at the
chromosome surface3,5,6, the molecular and
biophysical basis of mitotic chromosome individuality have remained unclear. We
report that Ki-67, a component of the mitotic chromosome periphery, prevents
chromosomes from collapsing into a single chromatin mass after nuclear envelope
disassembly, thus enabling independent chromosome motility and efficient
interactions with the mitotic spindle. The chromosome separation function of
Ki-67 is not confined within a specific protein domain but correlates with size
and net charge of truncation mutants that apparently lack secondary structure.
This suggests that Ki-67 forms a steric and electrical barrier, similar to
surface-active agents (surfactants) that disperse particles or phase-separated
liquid droplets in solvents. Fluorescence correlation spectroscopy showed a high
surface density of Ki-67 and dual-color labeling of both protein termini
revealed an extended molecular conformation, indicating brush-like arrangements
that are characteristic for polymeric surfactants. Our study thus elucidates a
biomechanical role of the mitotic chromosome periphery and suggests that natural
proteins can function as surfactants in intracellular compartmentalization.
Collapse
|
23
|
Uehara R, Kamasaki T, Hiruma S, Poser I, Yoda K, Yajima J, Gerlich DW, Goshima G. Augmin shapes the anaphase spindle for efficient cytokinetic furrow ingression and abscission. Mol Biol Cell 2016; 27:812-27. [PMID: 26764096 PMCID: PMC4803307 DOI: 10.1091/mbc.e15-02-0101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 01/07/2016] [Indexed: 11/11/2022] Open
Abstract
During anaphase, distinct populations of microtubules (MTs) form by either centrosome-dependent or augmin-dependent nucleation. It remains largely unknown whether these different MT populations contribute distinct functions to cytokinesis. Here we show that augmin-dependent MTs are required for the progression of both furrow ingression and abscission. Augmin depletion reduced the accumulation of anillin, a contractile ring regulator at the cell equator, yet centrosomal MTs were sufficient to mediate RhoA activation at the furrow. This defect in contractile ring organization, combined with incomplete spindle pole separation during anaphase, led to impaired furrow ingression. During the late stages of cytokinesis, astral MTs formed bundles in the intercellular bridge, but these failed to assemble a focused midbody structure and did not establish tight linkage to the plasma membrane, resulting in furrow regression. Thus augmin-dependent acentrosomal MTs and centrosomal MTs contribute to nonredundant targeting mechanisms of different cytokinesis factors, which are required for the formation of a functional contractile ring and midbody.
Collapse
Affiliation(s)
- Ryota Uehara
- Creative Research Institution, Hokkaido University, Sapporo 001-0021, Japan Department of Life Sciences, School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tomoko Kamasaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Shota Hiruma
- Creative Research Institution, Hokkaido University, Sapporo 001-0021, Japan
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Kinya Yoda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Junichiro Yajima
- Department of Life Sciences, School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter Campus, 1030 Vienna, Austria
| | - Gohta Goshima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| |
Collapse
|
24
|
Gentili C, Castor D, Kaden S, Lauterbach D, Gysi M, Steigemann P, Gerlich DW, Jiricny J, Ferrari S. Chromosome Missegregation Associated with RUVBL1 Deficiency. PLoS One 2015; 10:e0133576. [PMID: 26201077 PMCID: PMC4511761 DOI: 10.1371/journal.pone.0133576] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
RUVBL1 (RuvB-like1) and RUVBL2 (RuvB-like 2) are integral components of multisubunit protein complexes involved in processes ranging from cellular metabolism, transcription and chromatin remodeling to DNA repair. Here, we show that although RUVBL1 and RUVBL2 are known to form heterodimeric complexes in which they stabilize each other, the subunits separate during cytokinesis. In anaphase-to-telophase transition, RUVBL1 localizes to structures of the mitotic spindle apparatus, where it partially co-localizes with polo-like kinase 1 (PLK1). The ability of PLK1 to phosphorylate RUVBL1-but not RUVBL2-in vitro and their physical association in vivo suggest that this kinase differentially regulates the function of the RuvB-like proteins during mitosis. We further show that siRNA-mediated knock-down of RuvB-like proteins causes severe defects in chromosome alignment and segregation. In addition, we show that the ATPase activity of RUVBL1 is indispensable for cell proliferation. Our data thus demonstrate that RUVBL1 is essential for efficient mitosis and proliferation.
Collapse
Affiliation(s)
- Christian Gentili
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Dennis Castor
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Svenja Kaden
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - David Lauterbach
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Mario Gysi
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Patrick Steigemann
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Daniel W. Gerlich
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| |
Collapse
|
25
|
Rudolph D, Impagnatiello MA, Blaukopf C, Sommer C, Gerlich DW, Roth M, Tontsch-Grunt U, Wernitznig A, Savarese F, Hofmann MH, Albrecht C, Geiselmann L, Reschke M, Garin-Chesa P, Zuber J, Moll J, Adolf GR, Kraut N. Efficacy and mechanism of action of volasertib, a potent and selective inhibitor of Polo-like kinases, in preclinical models of acute myeloid leukemia. J Pharmacol Exp Ther 2015; 352:579-89. [PMID: 25576074 DOI: 10.1124/jpet.114.221150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Polo-like kinase 1 (Plk1), a member of the Polo-like kinase family of serine/threonine kinases, is a key regulator of multiple steps in mitosis. Here we report on the pharmacological profile of volasertib, a potent and selective Plk inhibitor, in multiple preclinical models of acute myeloid leukemia (AML) including established cell lines, bone marrow samples from AML patients in short-term culture, and subcutaneous as well as disseminated in vivo models in immune-deficient mice. Our results indicate that volasertib is highly efficacious as a single agent and in combination with established and emerging AML drugs, including the antimetabolite cytarabine, hypomethylating agents (decitabine, azacitidine), and quizartinib, a signal transduction inhibitor targeting FLT3. Collectively, these preclinical data support the use of volasertib as a new therapeutic approach for the treatment of AML patients, and provide a foundation for combination approaches that may further improve and prolong clinical responses.
Collapse
MESH Headings
- Animals
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/metabolism
- Cells, Cultured
- Dose-Response Relationship, Drug
- Drug Evaluation, Preclinical/methods
- Female
- HeLa Cells
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/enzymology
- Mice
- Mice, Nude
- Mice, SCID
- Mice, Transgenic
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins/metabolism
- Pteridines/pharmacology
- Pteridines/therapeutic use
- Treatment Outcome
- Xenograft Model Antitumor Assays/methods
- Polo-Like Kinase 1
Collapse
Affiliation(s)
- Dorothea Rudolph
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Maria Antonietta Impagnatiello
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Claudia Blaukopf
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Christoph Sommer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Daniel W Gerlich
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Mareike Roth
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Ulrike Tontsch-Grunt
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Andreas Wernitznig
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Fabio Savarese
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Marco H Hofmann
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Christoph Albrecht
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Lena Geiselmann
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Markus Reschke
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Pilar Garin-Chesa
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Johannes Zuber
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Jürgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Günther R Adolf
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria (D.R., M.A.I., U.T.-G., A.W., F.S., M.H.H., C.A., L.G., M.R., P.G.-C., J.M., G.R.A., N.K.); Institute of Molecular Biotechnology, Vienna, Austria (C.B., C.S., D.W.G.); and Research Institute of Molecular Pathology, Vienna, Austria (M.R., J.Z.)
| |
Collapse
|
26
|
Abstract
Cytokinesis mediates the physical separation of dividing cells after chromosome segregation. In animal cell cytokinesis, a contractile ring, mainly composed of actin and myosin filaments, ingresses a cleavage furrow midway between the two spindle poles. A distinct machinery, involving the endosomal sorting complex required for transport III (ESCRT-III), subsequently splits the plasma membrane of nascent daughter cells in a process termed abscission. Here, we provide a brief overview of early cytokinesis events in animal cells and then cover in depth recently emerging models for the assembly and function of the abscission machinery and its temporal coordination with chromosome segregation.
Collapse
Affiliation(s)
- Beata Mierzwa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria.
| |
Collapse
|
27
|
Lukinavičius G, Reymond L, D'Este E, Masharina A, Göttfert F, Ta H, Güther A, Fournier M, Rizzo S, Waldmann H, Blaukopf C, Sommer C, Gerlich DW, Arndt HD, Hell SW, Johnsson K. Fluorogenic probes for live-cell imaging of the cytoskeleton. Nat Methods 2014; 11:731-3. [PMID: 24859753 DOI: 10.1038/nmeth.2972] [Citation(s) in RCA: 526] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/24/2014] [Indexed: 12/21/2022]
Abstract
We introduce far-red, fluorogenic probes that combine minimal cytotoxicity with excellent brightness and photostability for fluorescence imaging of actin and tubulin in living cells. Applied in stimulated emission depletion (STED) microscopy, they reveal the ninefold symmetry of the centrosome and the spatial organization of actin in the axon of cultured rat neurons with a resolution unprecedented for imaging cytoskeletal structures in living cells.
Collapse
Affiliation(s)
- Gražvydas Lukinavičius
- 1] Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [2]
| | - Luc Reymond
- 1] Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [2] National Centre of Competence of Research in Chemical Biology, Lausanne, Switzerland. [3]
| | - Elisa D'Este
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anastasiya Masharina
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Fabian Göttfert
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Angelika Güther
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Jena, Germany
| | - Mathias Fournier
- Bioimaging and Optics Platform, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefano Rizzo
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Hans-Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Jena, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kai Johnsson
- 1] Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [2] National Centre of Competence of Research in Chemical Biology, Lausanne, Switzerland
| |
Collapse
|
28
|
Turgay Y, Champion L, Balazs C, Held M, Toso A, Gerlich DW, Meraldi P, Kutay U. SUN proteins facilitate the removal of membranes from chromatin during nuclear envelope breakdown. ACTA ACUST UNITED AC 2014; 204:1099-109. [PMID: 24662567 PMCID: PMC3971743 DOI: 10.1083/jcb.201310116] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
SUN proteins reside in the inner nuclear membrane and form complexes with KASH proteins of the outer nuclear membrane that connect the nuclear envelope (NE) to the cytoskeleton. These complexes have well-established functions in nuclear anchorage and migration in interphase, but little is known about their involvement in mitotic processes. Our analysis demonstrates that simultaneous depletion of human SUN1 and SUN2 delayed removal of membranes from chromatin during NE breakdown (NEBD) and impaired the formation of prophase NE invaginations (PNEIs), similar to microtubule depolymerization or down-regulation of the dynein cofactors NudE/EL. In addition, overexpression of dominant-negative SUN and KASH constructs reduced the occurrence of PNEI, indicating a requirement for functional SUN-KASH complexes in NE remodeling. Codepletion of SUN1/2 slowed cell proliferation and resulted in an accumulation of morphologically defective and disoriented mitotic spindles. Quantification of mitotic timing revealed a delay between NEBD and chromatin separation, indicating a role of SUN proteins in bipolar spindle assembly and mitotic progression.
Collapse
Affiliation(s)
- Yagmur Turgay
- Institute of Biochemistry, Department of Biology, and 2 Light Microscopy Center, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Vázquez-Novelle MD, Sansregret L, Dick AE, Smith CA, McAinsh AD, Gerlich DW, Petronczki M. Cdk1 inactivation terminates mitotic checkpoint surveillance and stabilizes kinetochore attachments in anaphase. Curr Biol 2014; 24:638-45. [PMID: 24583019 PMCID: PMC3969148 DOI: 10.1016/j.cub.2014.01.034] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/24/2013] [Accepted: 01/14/2014] [Indexed: 12/19/2022]
Abstract
Two mechanisms safeguard the bipolar attachment of chromosomes in mitosis. A correction mechanism destabilizes erroneous attachments that do not generate tension across sister kinetochores [1]. In response to unattached kinetochores, the mitotic checkpoint delays anaphase onset by inhibiting the anaphase-promoting complex/cyclosome (APC/C(Cdc20)) [2]. Upon satisfaction of both pathways, the APC/C(Cdc20) elicits the degradation of securin and cyclin B [3]. This liberates separase triggering sister chromatid disjunction and inactivates cyclin-dependent kinase 1 (Cdk1) causing mitotic exit. How eukaryotic cells avoid the engagement of attachment monitoring mechanisms when sister chromatids split and tension is lost at anaphase is poorly understood [4]. Here we show that Cdk1 inactivation disables mitotic checkpoint surveillance at anaphase onset in human cells. Preventing cyclin B1 proteolysis at the time of sister chromatid disjunction destabilizes kinetochore-microtubule attachments and triggers the engagement of the mitotic checkpoint. As a consequence, mitotic checkpoint proteins accumulate at anaphase kinetochores, the APC/C(Cdc20) is inhibited, and securin reaccumulates. Conversely, acute pharmacological inhibition of Cdk1 abrogates the engagement and maintenance of the mitotic checkpoint upon microtubule depolymerization. We propose that the simultaneous destruction of securin and cyclin B elicited by the APC/C(Cdc20) couples chromosome segregation to the dissolution of attachment monitoring mechanisms during mitotic exit.
Collapse
Affiliation(s)
- María Dolores Vázquez-Novelle
- Cell Division and Aneuploidy Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, UK.
| | - Laurent Sansregret
- Cell Division and Aneuploidy Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, UK
| | - Amalie E Dick
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Christopher A Smith
- Centre for Mechanochemical Cell Biology, Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew D McAinsh
- Centre for Mechanochemical Cell Biology, Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mark Petronczki
- Cell Division and Aneuploidy Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, UK.
| |
Collapse
|
30
|
Abstract
Recent advances in microscope automation provide new opportunities for high-throughput cell biology, such as image-based screening. High-complex image analysis tasks often make the implementation of static and predefined processing rules a cumbersome effort. Machine-learning methods, instead, seek to use intrinsic data structure, as well as the expert annotations of biologists to infer models that can be used to solve versatile data analysis tasks. Here, we explain how machine-learning methods work and what needs to be considered for their successful application in cell biology. We outline how microscopy images can be converted into a data representation suitable for machine learning, and then introduce various state-of-the-art machine-learning algorithms, highlighting recent applications in image-based screening. Our Commentary aims to provide the biologist with a guide to the application of machine learning to microscopy assays and we therefore include extensive discussion on how to optimize experimental workflow as well as the data analysis pipeline.
Collapse
Affiliation(s)
- Christoph Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | | |
Collapse
|
31
|
Abstract
Recent advances in microscope automation provide new opportunities for high-throughput cell biology, such as image-based screening. High-complex image analysis tasks often make the implementation of static and predefined processing rules a cumbersome effort. Machine-learning methods, instead, seek to use intrinsic data structure, as well as the expert annotations of biologists to infer models that can be used to solve versatile data analysis tasks. Here, we explain how machine-learning methods work and what needs to be considered for their successful application in cell biology. We outline how microscopy images can be converted into a data representation suitable for machine learning, and then introduce various state-of-the-art machine-learning algorithms, highlighting recent applications in image-based screening. Our Commentary aims to provide the biologist with a guide to the application of machine learning to microscopy assays and we therefore include extensive discussion on how to optimize experimental workflow as well as the data analysis pipeline.
Collapse
Affiliation(s)
- Christoph Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | | |
Collapse
|
32
|
Uehara R, Tsukada Y, Kamasaki T, Poser I, Yoda K, Gerlich DW, Goshima G. Aurora B and Kif2A control microtubule length for assembly of a functional central spindle during anaphase. ACTA ACUST UNITED AC 2013; 202:623-36. [PMID: 23960144 PMCID: PMC3747305 DOI: 10.1083/jcb.201302123] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A gradient of Aurora B activity determines the distribution of the microtubule depolymerase Kif2A at the central spindle and specifies the subsequent spindle structure necessary for proper cytokinesis. The central spindle is built during anaphase by coupling antiparallel microtubules (MTs) at a central overlap zone, which provides a signaling scaffold for the regulation of cytokinesis. The mechanisms underlying central spindle morphogenesis are still poorly understood. In this paper, we show that the MT depolymerase Kif2A controls the length and alignment of central spindle MTs through depolymerization at their minus ends. The distribution of Kif2A was limited to the distal ends of the central spindle through Aurora B–dependent phosphorylation and exclusion from the spindle midzone. Overactivation or inhibition of Kif2A affected interchromosomal MT length and disorganized the central spindle, resulting in uncoordinated cell division. Experimental data and model simulations suggest that the steady-state length of the central spindle and its symmetric position between segregating chromosomes are predominantly determined by the Aurora B activity gradient. On the basis of these results, we propose a robust self-organization mechanism for central spindle formation.
Collapse
Affiliation(s)
- Ryota Uehara
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
| | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
The mitotic spindle assembly checkpoint (SAC) delays anaphase onset until all chromosomes have attached to both spindle poles. Here, we investigated SAC signalling kinetics in response to acute detachment of individual chromosomes using laser microsurgery. Most detached chromosomes delayed anaphase until they had realigned to the metaphase plate. A substantial fraction of cells, however, entered anaphase in the presence of unaligned chromosomes. We identify two mechanisms by which cells can bypass the SAC: first, single unattached chromosomes inhibit the anaphase-promoting complex/cyclosome (APC/C) less efficiently than a full complement of unattached chromosomes; second, because of the relatively slow kinetics of re-imposing APC/C inhibition during metaphase, cells were unresponsive to chromosome detachment up to several minutes before anaphase onset. Our study defines when cells irreversibly commit to enter anaphase and shows that the SAC signal strength correlates with the number of unattached chromosomes. Detailed knowledge about SAC signalling kinetics is important for understanding the emergence of aneuploidy and the response of cancer cells to chemotherapeutics targeting the mitotic spindle.
Collapse
Affiliation(s)
- Amalie E Dick
- 1] Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria [2] Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland [3] Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | | |
Collapse
|
34
|
Abstract
Summary: High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms. Availability: Source code is freely available at www.github.com/cellh5 under the GPL license and at www.bioconductor.org/packages/release/bioc/html/rhdf5.html under the Artistic-2.0 license. Demo datasets and the CellH5Browser are available at www.cellh5.org. A Fiji importer for cellh5 will be released soon. Contact:daniel.gerlich@imba.oeaw.ac.at or christoph.sommer@imba.oeaw.ac.at Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Christoph Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | | | | | | | | |
Collapse
|
35
|
Wurzenberger C, Held M, Lampson MA, Poser I, Hyman AA, Gerlich DW. Sds22 and Repo-Man stabilize chromosome segregation by counteracting Aurora B on anaphase kinetochores. ACTA ACUST UNITED AC 2012; 198:173-83. [PMID: 22801782 PMCID: PMC3410419 DOI: 10.1083/jcb.201112112] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Repo-Man and Sds22 counteract Aurora B phosphorylation of Dsn1 and thus regulate the kinetochore–microtubule interface during anaphase. During mitotic spindle assembly, Aurora B kinase is part of an error correction mechanism that detaches microtubules from kinetochores that are under low mechanical tension. During anaphase, however, kinetochore–microtubule attachments must be maintained despite a drop of tension after removal of sister chromatid cohesion. Consistent with this requirement, Aurora B relocates away from chromosomes to the central spindle at the metaphase–anaphase transition. By ribonucleic acid interference screening using a phosphorylation biosensor, we identified two PP1-targeting subunits, Sds22 and Repo-Man, which counteracted Aurora B–dependent phosphorylation of the outer kinetochore component Dsn1 during anaphase. Sds22 or Repo-Man depletion induced transient pauses during poleward chromosome movement and a high incidence of chromosome missegregation. Thus, our study identifies PP1-targeting subunits that regulate the microtubule–kinetochore interface during anaphase for faithful chromosome segregation.
Collapse
Affiliation(s)
- Claudia Wurzenberger
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
36
|
Abstract
The mitosis-to-interphase transition involves dramatic cellular reorganization from a state that supports chromosome segregation to a state that complies with all functions of an interphase cell. This process, termed mitotic exit, depends on the removal of mitotic phosphorylations from a broad range of substrates. Mitotic exit regulation involves inactivation of mitotic kinases and activation of counteracting protein phosphatases. The key mitotic exit phosphatase in budding yeast, Cdc14, is now well understood. By contrast, in animal cells, it is now emerging that mitotic exit relies on distinct regulatory networks, including the protein phosphatases PP1 and PP2A.
Collapse
Affiliation(s)
- Claudia Wurzenberger
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETHZ), HPM D11.3, Schafmattstrasse 18, 8093 Zürich, Switzerland
| | | |
Collapse
|
37
|
Dobrynin G, Popp O, Romer T, Bremer S, Schmitz MHA, Gerlich DW, Meyer H. Cdc48/p97-Ufd1-Npl4 antagonizes Aurora B during chromosome segregation in HeLa cells. J Cell Sci 2011; 124:1571-80. [PMID: 21486945 DOI: 10.1242/jcs.069500] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
During exit from mitosis in Xenopus laevis egg extracts, the AAA+ ATPase Cdc48/p97 (also known as VCP in vertebrates) and its adapter Ufd1-Npl4 remove the kinase Aurora B from chromatin to allow nucleus formation. Here, we show that in HeLa cells Ufd1-Npl4 already antagonizes Aurora B on chromosomes during earlier mitotic stages and that this is crucial for proper chromosome segregation. Depletion of Ufd1-Npl4 by small interfering RNA (siRNA) caused chromosome alignment and anaphase defects resulting in missegregated chromosomes and multi-lobed nuclei. Ufd1-Npl4 depletion also led to increased levels of Aurora B on prometaphase and metaphase chromosomes. This increase was associated with higher Aurora B activity, as evidenced by the partial resistance of CENP-A phosphorylation to the Aurora B inhibitor hesperadin. Furthermore, low concentrations of hesperadin partially rescued chromosome alignment in Ufd1-depleted cells, whereas, conversely, Ufd1-depletion partially restored congression in the presence of hesperadin. These data establish Cdc48/p97-Ufd1-Npl4 as a crucial negative regulator of Aurora B early in mitosis of human somatic cells and suggest that the activity of Aurora B on chromosomes needs to be restrained to ensure faithful chromosome segregation.
Collapse
Affiliation(s)
- Grzegorz Dobrynin
- Centre for Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | | | | | | | | | | | | |
Collapse
|
38
|
Guizetti J, Schermelleh L, Mäntler J, Maar S, Poser I, Leonhardt H, Müller-Reichert T, Gerlich DW. Cortical constriction during abscission involves helices of ESCRT-III-dependent filaments. Science 2011; 331:1616-20. [PMID: 21310966 DOI: 10.1126/science.1201847] [Citation(s) in RCA: 359] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After partitioning of cytoplasmic contents by cleavage furrow ingression, animal cells remain connected by an intercellular bridge, which subsequently splits by abscission. Here, we examined intermediate stages of abscission in human cells by using live imaging, three-dimensional structured illumination microscopy, and electron tomography. We identified helices of 17-nanometer-diameter filaments, which narrowed the cortex of the intercellular bridge to a single stalk. The endosomal sorting complex required for transport (ESCRT)-III co-localized with constriction zones and was required for assembly of 17-nanometer-diameter filaments. Simultaneous spastin-mediated removal of underlying microtubules enabled full constriction at the abscission site. The identification of contractile filament helices at the intercellular bridge has broad implications for the understanding of cell division and of ESCRT-III-mediated fission of large membrane structures.
Collapse
Affiliation(s)
- Julien Guizetti
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstrasse 18, Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Piwko W, Olma MH, Held M, Bianco JN, Pedrioli PGA, Hofmann K, Pasero P, Gerlich DW, Peter M. RNAi-based screening identifies the Mms22L-Nfkbil2 complex as a novel regulator of DNA replication in human cells. EMBO J 2010; 29:4210-22. [PMID: 21113133 DOI: 10.1038/emboj.2010.304] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/05/2010] [Indexed: 01/08/2023] Open
Abstract
Cullin 4 (Cul4)-based ubiquitin ligases emerged as critical regulators of DNA replication and repair. Over 50 Cul4-specific adaptors (DNA damage-binding 1 (Ddb1)-Cul4-associated factors; DCAFs) have been identified and are thought to assemble functionally distinct Cul4 complexes. Using a live-cell imaging-based RNAi screen, we analysed the function of DCAFs and Cul4-linked proteins, and identified specific subsets required for progression through G1 and S phase. We discovered C6orf167/Mms22-like protein (Mms22L) as a putative human orthologue of budding yeast Mms22, which, together with cullin Rtt101, regulates genome stability by promoting DNA replication through natural pause sites and damaged templates. Loss of Mms22L function in human cells results in S phase-dependent genomic instability characterised by spontaneous double-strand breaks and DNA damage checkpoint activation. Unlike yeast Mms22, human Mms22L does not stably bind to Cul4, but is degraded in a Cul4-dependent manner and upon replication stress. Mms22L physically and functionally interacts with the scaffold-like protein Nfkbil2 that co-purifies with histones, several chromatin remodelling and DNA replication/repair factors. Together, our results strongly suggest that the Mms22L-Nfkbil2 complex contributes to genome stability by regulating the chromatin state at stalled replication forks.
Collapse
Affiliation(s)
- Wojciech Piwko
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Abstract
Cytokinesis leads to the separation of dividing cells, which in animal cells involves the contraction of an actin-myosin ring and subsequent fission during abscission. Abscission requires a series of dynamic events, including midbody-targeted vesicle secretion, specialization of plasma membrane domains, disassembly of midbody-associated microtubule bundles and plasma membrane fission. A large number of molecular factors required for abscission have been identified through localization, loss-of-function and proteomics studies, but their coordinate function in abscission is still poorly understood. Here, we review the structural elements and molecular factors known to contribute to abscission, and discuss their potential role in the context of proposed models for the abscission mechanism.
Collapse
Affiliation(s)
- Julien Guizetti
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Zurich, Switzerland
| | | |
Collapse
|
41
|
Lacroix B, van Dijk J, Gold ND, Guizetti J, Aldrian-Herrada G, Rogowski K, Gerlich DW, Janke C. Tubulin polyglutamylation stimulates spastin-mediated microtubule severing. ACTA ACUST UNITED AC 2010; 189:945-54. [PMID: 20530212 PMCID: PMC2886356 DOI: 10.1083/jcb.201001024] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microtubules with long polyglutamylated C-terminal tails are more prone to severing by spastin, establishing the importance of tubulin posttranslational modifications. Posttranslational glutamylation of tubulin is present on selected subsets of microtubules in cells. Although the modification is expected to contribute to the spatial and temporal organization of the cytoskeleton, hardly anything is known about its functional relevance. Here we demonstrate that glutamylation, and in particular the generation of long glutamate side chains, promotes the severing of microtubules. In human cells, the generation of long side chains induces spastin-dependent microtubule disassembly and, consistently, only microtubules modified by long glutamate side chains are efficiently severed by spastin in vitro. Our study reveals a novel control mechanism for microtubule mass and stability, which is of fundamental importance to cellular physiology and might have implications for diseases related to microtubule severing.
Collapse
Affiliation(s)
- Benjamin Lacroix
- Centre de Recherche de Biochimie Macromoléculaire, Université Montpellier 2 and 1, Centre National de la Recherche Scientifique UMR 5237, Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Lekomtsev S, Guizetti J, Pozniakovsky A, Gerlich DW, Petronczki M. Evidence that the tumor-suppressor protein BRCA2 does not regulate cytokinesis in human cells. J Cell Sci 2010; 123:1395-400. [DOI: 10.1242/jcs.068015] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Germline mutations in the tumor-suppressor gene BRCA2 predispose to breast and ovarian cancer. BRCA2 plays a well-established role in maintaining genome stability by regulating homologous recombination. BRCA2 has more recently been implicated in cytokinesis, the final step of cell division, but the molecular basis for this remains unknown. We have used time-lapse microscopy, recently developed cytokinesis assays and BAC recombineering (bacterial artificial chromosome recombinogenic engineering) to investigate the function and localization of BRCA2 during cell division. Our analysis suggests that BRCA2 does not regulate cytokinesis in human cells. Thus, cytokinesis defects are unlikely to contribute to chromosomal instability and tumorigenesis in BRCA2-related cancers.
Collapse
Affiliation(s)
- Sergey Lekomtsev
- Cell Division and Aneuploidy Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire, EN6 3LD, UK
| | - Julien Guizetti
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstrasse 18, CH-8093 Zurich, Switzerland
| | - Andrei Pozniakovsky
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
| | - Daniel W. Gerlich
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstrasse 18, CH-8093 Zurich, Switzerland
| | - Mark Petronczki
- Cell Division and Aneuploidy Laboratory, Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire, EN6 3LD, UK
| |
Collapse
|
43
|
Abstract
Fluorescence microscopy is one of the most powerful tools to investigate complex cellular processes such as cell division, cell motility, or intracellular trafficking. The availability of RNA interference (RNAi) technology and automated microscopy has opened the possibility to perform cellular imaging in functional genomics and other large-scale applications. Although imaging often dramatically increases the content of a screening assay, it poses new challenges to achieve accurate quantitative annotation and therefore needs to be carefully adjusted to the specific needs of individual screening applications. In this review, we discuss principles of assay design, large-scale RNAi, microscope automation, and computational data analysis. We highlight strategies for imaging-based RNAi screening adapted to different library and assay designs.
Collapse
Affiliation(s)
- Christian Conrad
- Advanced Light Microscopy Core Facility, European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany.
| | | |
Collapse
|
44
|
Maerki S, Olma MH, Staubli T, Steigemann P, Gerlich DW, Quadroni M, Sumara I, Peter M. The Cul3-KLHL21 E3 ubiquitin ligase targets aurora B to midzone microtubules in anaphase and is required for cytokinesis. ACTA ACUST UNITED AC 2010; 187:791-800. [PMID: 19995937 PMCID: PMC2806313 DOI: 10.1083/jcb.200906117] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selective ubiquitination of Aurora B by different Cul3 adaptors targets it at the correct time to the correct place during mitosis. Cul3 (Cullin3)-based E3 ubiquitin ligases recently emerged as critical regulators of mitosis. In this study, we identify two mammalian BTB (Bric-a-brac–Tramtrack–Broad complex)-Kelch proteins, KLHL21 and KLHL22, that interact with Cul3 and are required for efficient chromosome alignment. Interestingly, KLHL21 but not KLHL22 is necessary for cytokinesis and regulates translocation of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase, similar to the previously described BTB-Kelch proteins KLHL9 and KLHL13. KLHL21 directly binds to Aurora B and mediates ubiquitination of Aurora B in vitro. In contrast to KLHL9 and KLHL13, KLHL21 localizes to midzone microtubules in anaphase and recruits Aurora B and Cul3 to this region. Together, our results suggest that different Cul3 adaptors nonredundantly regulate Aurora B during mitosis, possibly by ubiquitinating different pools of Aurora B at distinct subcellular localizations.
Collapse
Affiliation(s)
- Sarah Maerki
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Guizetti J, Mäntler J, Müller-Reichert T, Gerlich DW. Correlative time-lapse imaging and electron microscopy to study abscission in HeLa cells. Methods Cell Biol 2010; 96:591-601. [PMID: 20869539 DOI: 10.1016/s0091-679x(10)96024-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HeLa cells are widely used as a model system to study cell division. The last step of cell division, abscission, occurs at an about 1 μm wide intercellular bridge that connects the post-mitotic sister cells. Abscission often occurs long after ingression of the cleavage furrow, and no efficient methods to synchronize cells to this stage are available. Here, we have developed a correlative fluorescence time-lapse imaging and electron microscopic approach using Aclar sheets with engraved grid patterns. This grid pattern, leaving a negative imprint on thin-layer embedded samples, allows identification of cells selected from the time-lapse imaging for serial-section electron microscopy. This method facilitates the ultrastructural analysis of specific stages of abscission.
Collapse
Affiliation(s)
- Julien Guizetti
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), CH-8093 Zurich, Switzerland
| | | | | | | |
Collapse
|
46
|
Bollen M, Gerlich DW, Lesage B. Mitotic phosphatases: from entry guards to exit guides. Trends Cell Biol 2009; 19:531-41. [PMID: 19734049 DOI: 10.1016/j.tcb.2009.06.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 06/25/2009] [Accepted: 06/25/2009] [Indexed: 12/16/2022]
Abstract
While the importance of protein kinases for the spatial and temporal control of mitotic events has long been recognized, mitotic phosphatases have only recently come into the limelight. It is now well established that protein phosphatases counteract mitotic kinases, so contributing to the generation of switch-like responses at mitotic stage transitions. In addition, the timely dephosphorylation of mitotic phosphoproteins by tightly regulated phosphatases is required for the assembly and stability of the mitotic spindle, the initiation of anaphase, and exit from mitosis. Mitotic phosphatases also emerge as effectors of the DNA damage and spindle assembly checkpoints. These new findings show that protein phosphatases regulate every step of mitosis and provide novel insights into the dynamic and versatile nature of mitotic phosphoregulation.
Collapse
Affiliation(s)
- Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Molecular Cell Biology, University of Leuven, B-3000 Leuven, Belgium.
| | | | | |
Collapse
|
47
|
Steigemann P, Gerlich DW. Cytokinetic abscission: cellular dynamics at the midbody. Trends Cell Biol 2009; 19:606-16. [PMID: 19733077 DOI: 10.1016/j.tcb.2009.07.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 07/18/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
The intercellular canal containing the midbody is one of the most prominent structures in dividing animal cells, yet its function in the completion of cytokinesis by abscission remains largely unknown. This is because of its small size, which makes it difficult to investigate the cytoskeletal and membrane dynamics underlying abscission by standard light microscopy. The advent of new fluorescent probes and imaging technologies, along with sophisticated perturbation tools, provides new possibilities to elucidate the molecular control of this essential cell biological process. Here we discuss the control of midbody assembly and current models for the mechanism of abscission in animal cells. We highlight new methodologies that will facilitate testing and refining of these models.
Collapse
Affiliation(s)
- Patrick Steigemann
- Institute of Biochemistry, Swiss Federal Institute of Technology Zurich (ETHZ), Schafmattstr. 18, CH-8093 Zurich, Switzerland
| | | |
Collapse
|
48
|
Abstract
The dynamic reorganization of chromatin into rigid and compact mitotic chromosomes is of fundamental importance for faithful chromosome segregation. Owing to the difficulty of investigating this process under physiological conditions, the exact morphological transitions and the molecular machinery driving chromosome condensation remain poorly defined. Here, we review how imaging-based methods can be used to quantitate chromosome condensation in vivo, focusing on yeast and animal tissue culture cells as widely used model systems. We discuss approaches how to address structural dynamics of condensing chromosomes and chromosome segments, as well as to probe for mechanical properties of mitotic chromosomes. Application of such methods to systematic perturbation studies will provide a means to reveal the molecular networks underlying the regulation of mitotic chromosome condensation.
Collapse
Affiliation(s)
- Gabriel Neurohr
- Institute of Biochemistry, Swiss Institute of Technology Zurich (ETHZ), Schafmattstr. 18, CH-8093 Zurich, Switzerland
| | | |
Collapse
|
49
|
Steigemann P, Gerlich DW. An evolutionary conserved checkpoint controls abscission timing. Cell Cycle 2009; 8:1814-1815. [PMID: 19471121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
|
50
|
Chan YW, Fava LL, Uldschmid A, Schmitz MHA, Gerlich DW, Nigg EA, Santamaria A. Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly. ACTA ACUST UNITED AC 2009; 185:859-74. [PMID: 19468067 PMCID: PMC2711594 DOI: 10.1083/jcb.200812167] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitotic spindle formation and chromosome segregation depend critically on kinetochore-microtubule (KT-MT) interactions. A new protein, termed Spindly in Drosophila and SPDL-1 in C. elegans, was recently shown to regulate KT localization of dynein, but depletion phenotypes revealed striking differences, suggesting evolutionarily diverse roles of mitotic dynein. By characterizing the function of Spindly in human cells, we identify specific functions for KT dynein. We show that localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B. hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment. Moreover, depletion of hSpindly induces a striking spindle rotation, which can be rescued by co-depletion of dynein. However, in contrast to Drosophila, hSpindly depletion does not abolish the removal of MAD2 and ZW10 from KTs. Collectively, our data reveal hSpindly-mediated dynein functions and highlight a critical role of KT dynein in spindle orientation.
Collapse
Affiliation(s)
- Ying Wai Chan
- Department of Cell Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | | | | | | | | | | | | |
Collapse
|