1
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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2
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Dulin D. An Introduction to Magnetic Tweezers. Methods Mol Biol 2024; 2694:375-401. [PMID: 37824014 DOI: 10.1007/978-1-0716-3377-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Magnetic tweezers are a single-molecule force and torque spectroscopy technique that enable the mechanical interrogation in vitro of biomolecules, such as nucleic acids and proteins. They use a magnetic field originating from either permanent magnets or electromagnets to attract a magnetic particle, thus stretching the tethering biomolecule. They nicely complement other force spectroscopy techniques such as optical tweezers and atomic force microscopy (AFM) as they operate as a very stable force clamp, enabling long-duration experiments over a very broad range of forces spanning from 10 fN to 1 nN, with 1-10 milliseconds time and sub-nanometer spatial resolution. Their simplicity, robustness, and versatility have made magnetic tweezers a key technique within the field of single-molecule biophysics, being broadly applied to study the mechanical properties of, e.g., nucleic acids, genome processing molecular motors, protein folding, and nucleoprotein filaments. Furthermore, magnetic tweezers allow for high-throughput single-molecule measurements by tracking hundreds of biomolecules simultaneously both in real-time and at high spatiotemporal resolution. Magnetic tweezers naturally combine with surface-based fluorescence spectroscopy techniques, such as total internal reflection fluorescence microscopy, enabling correlative fluorescence and force/torque spectroscopy on biomolecules. This chapter presents an introduction to magnetic tweezers including a description of the hardware, the theory behind force calibration, its spatiotemporal resolution, combining it with other techniques, and a (non-exhaustive) overview of biological applications.
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Affiliation(s)
- David Dulin
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
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3
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Wang C, Manders F, Groh L, Oldenkamp R, Logie C. Corticosteroid-induced chromatin loop dynamics at the FKBP5 gene. Ann N Y Acad Sci 2023; 1529:109-119. [PMID: 37796452 DOI: 10.1111/nyas.15064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
FKBP5 is a 115-kb-long glucocorticoid-inducible gene implicated in psychiatric disorders. To investigate the complexities of chromatin interaction frequencies at the FKBP5 topologically associated domain (TAD), we deployed 15 one-to-all chromatin capture viewpoints near gene promoters, enhancers, introns, and CTCF-loop anchors. This revealed a "one-TAD-one-gene" structure encompassing the FKBP5 promoter and its enhancers. The FKBP5 promoter and its two glucocorticoid-stimulated enhancers roam the entire TAD while displaying subtle cell type-specific interactomes. The FKBP5 TAD consists of two nested CTCF loops that are coordinated by one CTCF site in the eighth intron of FKBP5 and another beyond its polyadenylation site, 61 kb further. Loop extension correlates with transcription increases through the intronic CTCF site. This is efficiently compensated for, since the short loop is restored even under high transcription regimes. The boundaries of the FKBP5 TAD consist of divergent CTCF site patterns, harbor multiple smaller genes, and are resilient to glucocorticoid stimulation. Interestingly, both FKBP5 TAD boundaries harbor H3K27me3-marked heterochromatin blocks that may reinforce them. We propose that cis-acting genetic and epigenetic polymorphisms underlying FKBP5 expression variation are likely to reside within a 240-kb region that consists of the FKBP5 TAD, its left sub-TAD, and both its boundaries.
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Affiliation(s)
- Cheng Wang
- Department of Molecular Biology, Radboud Institute for Molecular Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Freek Manders
- Department of Molecular Biology, Radboud Institute for Molecular Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands
- Gendx, Utrecht, The Netherlands
| | - Laszlo Groh
- Department of Molecular Biology, Radboud Institute for Molecular Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Roel Oldenkamp
- Department of Molecular Biology, Radboud Institute for Molecular Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Colin Logie
- Department of Molecular Biology, Radboud Institute for Molecular Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands
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4
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Moon KW, Ryu JK. Current working models of SMC-driven DNA-loop extrusion. Biochem Soc Trans 2023; 51:1801-1810. [PMID: 37767565 DOI: 10.1042/bst20220898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Structural maintenance of chromosome (SMC) proteins play a key roles in the chromosome organization by condensing two meters of DNA into cell-sized structures considered as the SMC protein extrudes DNA loop. Recent sequencing-based high-throughput chromosome conformation capture technique (Hi-C) and single-molecule experiments have provided direct evidence of DNA-loop extrusion. However, the molecular mechanism by which SMCs extrude a DNA loop is still under debate. Here, we review DNA-loop extrusion studies with single-molecule assays and introduce recent structural studies of how the ATP-hydrolysis cycle is coupled to the conformational changes of SMCs for DNA-loop extrusion. In addition, we explain the conservation of the DNA-binding sites that are vital for dynamic DNA-loop extrusion by comparing Cryo-EM structures of SMC complexes. Based on this information, we compare and discuss four compelling working models that explain how the SMC complex extrudes a DNA loop.
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Affiliation(s)
- Kyoung-Wook Moon
- Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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5
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Pobegalov G, Chu LY, Peters JM, Molodtsov MI. Single cohesin molecules generate force by two distinct mechanisms. Nat Commun 2023; 14:3946. [PMID: 37402740 DOI: 10.1038/s41467-023-39696-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Spatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
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Affiliation(s)
- Georgii Pobegalov
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Lee-Ya Chu
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria
| | - Maxim I Molodtsov
- The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria.
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6
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Martínez‐García B, Dyson S, Segura J, Ayats A, Cutts EE, Gutierrez‐Escribano P, Aragón L, Roca J. Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage. EMBO J 2023; 42:e111913. [PMID: 36533296 PMCID: PMC9890231 DOI: 10.15252/embj.2022111913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain positive DNA supercoils. However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of -0.4. This ∆Lk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. We propose that this loop is the feeding segment of DNA that is subsequently merged to enlarge an extruding loop. Such a "pinch and merge" mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop.
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Affiliation(s)
| | - Sílvia Dyson
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Joana Segura
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Alba Ayats
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Erin E Cutts
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | | | - Luís Aragón
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | - Joaquim Roca
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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7
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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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8
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Reeling it in: how DNA topology drives loop extrusion by condensin. Nat Struct Mol Biol 2022; 29:623-625. [PMID: 35835869 PMCID: PMC9871954 DOI: 10.1038/s41594-022-00805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes such as condensin regulate chromosome organization by extruding loops. A new study uses single-molecule imaging of condensin on supercoiled DNA to understand how condensins navigate the under- and overwound DNA states common throughout the genome.
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9
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Condensin-driven loop extrusion on supercoiled DNA. Nat Struct Mol Biol 2022; 29:719-727. [PMID: 35835864 DOI: 10.1038/s41594-022-00802-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping are stimulated by positively supercoiled DNA, and condensin preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.
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10
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Nomidis SK, Carlon E, Gruber S, Marko JF. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nucleic Acids Res 2022; 50:4974-4987. [PMID: 35474142 PMCID: PMC9122525 DOI: 10.1093/nar/gkac268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 12/19/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced ‘power stroke’ to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site (‘safety belt’), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.
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Affiliation(s)
- Stefanos K Nomidis
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
| | - John F Marko
- To whom correspondence should be addressed. Tel: +1 847 467 1276; Fax: +1 847 467 1380;
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11
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Ryu JK, Rah SH, Janissen R, Kerssemakers JWJ, Bonato A, Michieletto D, Dekker C. Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events. Nucleic Acids Res 2021; 50:820-832. [PMID: 34951453 PMCID: PMC8789078 DOI: 10.1093/nar/gkab1268] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 10/22/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022] Open
Abstract
The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. The measured median step sizes range between 20–40 nm at forces of 1.0–0.2 pN, respectively, comparable with the holocomplex size. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ∼200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sang-Hyun Rah
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Andrea Bonato
- University of Edinburgh, SUPA, School of Physics and Astronomy, EH9 3FD, Edinburgh, UK
| | - Davide Michieletto
- University of Edinburgh, SUPA, School of Physics and Astronomy, EH9 3FD, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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12
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Roca J, Dyson S, Segura J, Valdés A, Martínez-García B. Keeping intracellular DNA untangled: A new role for condensin? Bioessays 2021; 44:e2100187. [PMID: 34761394 DOI: 10.1002/bies.202100187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022]
Abstract
The DNA-passage activity of topoisomerase II accidentally produces DNA knots and interlinks within and between chromatin fibers. Fortunately, these unwanted DNA entanglements are actively removed by some mechanism. Here we present an outline on DNA knot formation and discuss recent studies that have investigated how intracellular DNA knots are removed. First, although topoisomerase II is able to minimize DNA entanglements in vitro to below equilibrium values, it is unclear whether such capacity performs equally in vivo in chromatinized DNA. Second, DNA supercoiling could bias topoisomerase II to untangle the DNA. However, experimental evidence indicates that transcriptional supercoiling of intracellular DNA boosts knot formation. Last, cohesin and condensin could tighten DNA entanglements via DNA loop extrusion (LE) and force their dissolution by topoisomerase II. Recent observations indicate that condensin activity promotes the removal of DNA knots during interphase and mitosis. This activity might facilitate the spatial organization and dynamics of chromatin.
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Affiliation(s)
- Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Silvia Dyson
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Antonio Valdés
- Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
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13
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Loeff L, Kerssemakers JWJ, Joo C, Dekker C. AutoStepfinder: A fast and automated step detection method for single-molecule analysis. PATTERNS 2021; 2:100256. [PMID: 34036291 PMCID: PMC8134948 DOI: 10.1016/j.patter.2021.100256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 01/05/2023]
Abstract
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour. Fast, automated, and bias-free detection of steps within single-molecule trajectories Robust step detection without any prior knowledge on the data A dual-pass strategy for the detection of steps over a wide variety of scales A user-friendly interface for a simplified step fitting procedure
Single-molecule techniques have made it possible to track individual protein complexes in real time with a nanometer spatial resolution and a millisecond timescale. Accurate determination of the dynamic states within single-molecule time traces provides valuable kinetic information that underlie the function of biological macromolecules. Here, we present a new automated step detection method called AutoStepfinder, a versatile, robust, and easy-to-use algorithm that allows researchers to determine the kinetic states within single-molecule time trajectories without any bias.
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Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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14
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Birnie A, Dekker C. Genome-in-a-Box: Building a Chromosome from the Bottom Up. ACS NANO 2021; 15:111-124. [PMID: 33347266 PMCID: PMC7844827 DOI: 10.1021/acsnano.0c07397] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box" (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.
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Affiliation(s)
- Anthony Birnie
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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15
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Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
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Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
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16
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Dyson S, Segura J, Martínez‐García B, Valdés A, Roca J. Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo. EMBO J 2021; 40:e105393. [PMID: 33155682 PMCID: PMC7780148 DOI: 10.15252/embj.2020105393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
The juxtaposition of intracellular DNA segments, together with the DNA-passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.
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Grants
- BFU2015-67007-P Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- PID2019-109482GB-I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2016-077806 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2012-061167 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2015-071597 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
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Affiliation(s)
- Sílvia Dyson
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Belén Martínez‐García
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
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17
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Gutierrez-Escribano P, Hormeño S, Madariaga-Marcos J, Solé-Soler R, O'Reilly FJ, Morris K, Aicart-Ramos C, Aramayo R, Montoya A, Kramer H, Rappsilber J, Torres-Rosell J, Moreno-Herrero F, Aragon L. Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction. Mol Cell 2020; 80:1039-1054.e6. [PMID: 33301732 PMCID: PMC7758880 DOI: 10.1016/j.molcel.2020.11.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/03/2023]
Abstract
Eukaryotic SMC complexes, cohesin, condensin, and Smc5/6, use ATP hydrolysis to power a plethora of functions requiring organization and restructuring of eukaryotic chromosomes in interphase and during mitosis. The Smc5/6 mechanism of action and its activity on DNA are largely unknown. Here we purified the budding yeast Smc5/6 holocomplex and characterized its core biochemical and biophysical activities. Purified Smc5/6 exhibits DNA-dependent ATP hydrolysis and SUMO E3 ligase activity. We show that Smc5/6 binds DNA topologically with affinity for supercoiled and catenated DNA templates. Employing single-molecule assays to analyze the functional and dynamic characteristics of Smc5/6 bound to DNA, we show that Smc5/6 locks DNA plectonemes and can compact DNA in an ATP-dependent manner. These results demonstrate that the Smc5/6 complex recognizes DNA tertiary structures involving juxtaposed helices and might modulate DNA topology by plectoneme stabilization and local compaction.
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Affiliation(s)
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roger Solé-Soler
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kyle Morris
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ricardo Aramayo
- Microscopy Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jordi Torres-Rosell
- Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Department of Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Luis Aragon
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK.
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18
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The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Mol Cell 2020; 80:1025-1038.e5. [PMID: 33301731 DOI: 10.1016/j.molcel.2020.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
The structural organization of chromosomes is a crucial feature that defines the functional state of genes and genomes. The extent of structural changes experienced by genomes of eukaryotic cells can be dramatic and spans several orders of magnitude. At the core of these changes lies a unique group of ATPases-the SMC proteins-that act as major effectors of chromosome behavior in cells. The Smc5/6 proteins play essential roles in the maintenance of genome stability, yet their mode of action is not fully understood. Here we show that the human Smc5/6 complex recognizes unusual DNA configurations and uses the energy of ATP hydrolysis to promote their compaction. Structural analyses reveal subunit interfaces responsible for the functionality of the Smc5/6 complex and how mutations in these regions may lead to chromosome breakage syndromes in humans. Collectively, our results suggest that the Smc5/6 complex promotes genome stability as a DNA micro-compaction machine.
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19
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Cutts EE, Vannini A. Condensin complexes: understanding loop extrusion one conformational change at a time. Biochem Soc Trans 2020; 48:2089-2100. [PMID: 33005926 PMCID: PMC7609036 DOI: 10.1042/bst20200241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Condensin and cohesin, both members of the structural maintenance of chromosome (SMC) family, contribute to the regulation and structure of chromatin. Recent work has shown both condensin and cohesin extrude DNA loops and most likely work via a conserved mechanism. This review focuses on condensin complexes, highlighting recent in vitro work characterising DNA loop formation and protein structure. We discuss similarities between condensin and cohesin complexes to derive a possible mechanistic model, as well as discuss differences that exist between the different condensin isoforms found in higher eukaryotes.
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Affiliation(s)
- Erin E. Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
- Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy
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20
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The condensin holocomplex cycles dynamically between open and collapsed states. Nat Struct Mol Biol 2020; 27:1134-1141. [PMID: 32989304 DOI: 10.1038/s41594-020-0508-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
Structural maintenance of chromosome (SMC) protein complexes are the key organizers of the spatiotemporal structure of chromosomes. The condensin SMC complex has recently been shown to be a molecular motor that extrudes large loops of DNA, but the mechanism of this unique motor remains elusive. Using atomic force microscopy, we show that budding yeast condensin exhibits mainly open 'O' shapes and collapsed 'B' shapes, and it cycles dynamically between these two states over time, with ATP binding inducing the O to B transition. Condensin binds DNA via its globular domain and also via the hinge domain. We observe a single condensin complex at the stem of extruded DNA loops, where the neck size of the DNA loop correlates with the width of the condensin complex. The results are indicative of a type of scrunching model in which condensin extrudes DNA by a cyclic switching of its conformation between O and B shapes.
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21
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Finardi A, Massari LF, Visintin R. Anaphase Bridges: Not All Natural Fibers Are Healthy. Genes (Basel) 2020; 11:genes11080902. [PMID: 32784550 PMCID: PMC7464157 DOI: 10.3390/genes11080902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role.
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Affiliation(s)
- Alice Finardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Lucia F. Massari
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Rosella Visintin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5748-9859; Fax: +39-02-9437-5991
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22
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Kong M, Cutts EE, Pan D, Beuron F, Kaliyappan T, Xue C, Morris EP, Musacchio A, Vannini A, Greene EC. Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA. Mol Cell 2020; 79:99-114.e9. [PMID: 32445620 PMCID: PMC7335352 DOI: 10.1016/j.molcel.2020.04.026] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/08/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential for genome organization from bacteria to humans, but their mechanisms of action remain poorly understood. Here, we characterize human SMC complexes condensin I and II and unveil the architecture of the human condensin II complex, revealing two putative DNA-entrapment sites. Using single-molecule imaging, we demonstrate that both condensin I and II exhibit ATP-dependent motor activity and promote extensive and reversible compaction of double-stranded DNA. Nucleosomes are incorporated into DNA loops during compaction without being displaced from the DNA, indicating that condensin complexes can readily act upon nucleosome-bound DNA molecules. These observations shed light on critical processes involved in genome organization in human cells.
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Affiliation(s)
- Muwen Kong
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Thangavelu Kaliyappan
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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23
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Loop extrusion: theory meets single-molecule experiments. Curr Opin Cell Biol 2020; 64:124-138. [PMID: 32534241 DOI: 10.1016/j.ceb.2020.04.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/20/2022]
Abstract
Chromosomes are organized as chromatin loops that promote segregation, enhancer-promoter interactions, and other genomic functions. Loops were hypothesized to form by 'loop extrusion,' by which structural maintenance of chromosomes (SMC) complexes, such as condensin and cohesin, bind to chromatin, reel it in, and extrude it as a loop. However, such exotic motor activity had never been observed. Following an explosion of indirect evidence, recent single-molecule experiments directly imaged DNA loop extrusion by condensin and cohesin in vitro. These experiments observe rapid (kb/s) extrusion that requires ATP hydrolysis and stalls under pN forces. Surprisingly, condensin extrudes loops asymmetrically, challenging previous models. Extrusion by cohesin is symmetric but requires the protein Nipbl. We discuss how SMC complexes may perform their functions on chromatin in vivo.
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24
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Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. eLife 2020; 9:e53558. [PMID: 32250245 PMCID: PMC7295573 DOI: 10.7554/elife.53558] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/03/2020] [Indexed: 12/19/2022] Open
Abstract
SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a 'one-sided' manner. We therefore simulate one-sided loop extrusion to investigate whether 'one-sided' complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by 'two-sided' loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization.
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Affiliation(s)
- Edward J Banigan
- Institute for Medical Engineering & Science, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Aafke A van den Berg
- Institute for Medical Engineering & Science, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Hugo B Brandão
- Harvard Graduate Program in Biophysics, Harvard UniversityCambridgeUnited States
| | - John F Marko
- Departments of Molecular Biosciences and Physics & Astronomy, Northwestern UniversityEvanstonUnited States
| | - Leonid A Mirny
- Institute for Medical Engineering & Science, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
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25
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Kim S, Darcy IK. A topological analysis of difference topology experiments of condensin with topoisomerase II. Biol Open 2020; 9:bio048603. [PMID: 32184229 PMCID: PMC7132813 DOI: 10.1242/bio.048603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/03/2020] [Indexed: 11/20/2022] Open
Abstract
An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.
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Affiliation(s)
- Soojeong Kim
- Yonsei University, University College, Incheon 21983, South Korea
| | - Isabel K Darcy
- Department of Mathematics, University of Iowa, Iowa City 52242, USA
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26
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Ghosh SK, Jost D. Genome organization via loop extrusion, insights from polymer physics models. Brief Funct Genomics 2020; 19:119-127. [PMID: 31711163 DOI: 10.1093/bfgp/elz023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
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Affiliation(s)
- Surya K Ghosh
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007 Lyon, France
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27
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Elbatsh AMO, Kim E, Eeftens JM, Raaijmakers JA, van der Weide RH, García-Nieto A, Bravo S, Ganji M, Uit de Bos J, Teunissen H, Medema RH, de Wit E, Haering CH, Dekker C, Rowland BD. Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation. Mol Cell 2019; 76:724-737.e5. [PMID: 31629658 PMCID: PMC6900782 DOI: 10.1016/j.molcel.2019.09.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/17/2019] [Accepted: 09/13/2019] [Indexed: 01/19/2023]
Abstract
Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild-type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.
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Affiliation(s)
- Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jonne A Raaijmakers
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Robin H van der Weide
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alberto García-Nieto
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jelmi Uit de Bos
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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28
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29
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Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. Proc Natl Acad Sci U S A 2019; 116:24956-24965. [PMID: 31757850 DOI: 10.1073/pnas.1906355116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryote cell division features a chromosome compaction-decompaction cycle that is synchronized with their physical and topological segregation. It has been proposed that lengthwise compaction of chromatin into mitotic chromosomes via loop extrusion underlies the compaction-segregation/resolution process. We analyze this disentanglement scheme via considering the chromosome to be a succession of DNA/chromatin loops-a polymer "brush"-where active extrusion of loops controls the brush structure. Given type-II DNA topoisomerase (Topo II)-catalyzed topology fluctuations, we find that interchromosome entanglements are minimized for a certain "optimal" loop that scales with the chromosome size. The optimal loop organization is in accord with experimental data across species, suggesting an important structural role of genomic loops in maintaining a less entangled genome. Application of the model to the interphase genome indicates that active loop extrusion can maintain a level of chromosome compaction with suppressed entanglements; the transition to the metaphase state requires higher lengthwise compaction and drives complete topological segregation. Optimized genomic loops may provide a means for evolutionary propagation of gene-expression patterns while simultaneously maintaining a disentangled genome. We also find that compact metaphase chromosomes have a densely packed core along their cylindrical axes that explains their observed mechanical stiffness. Our model connects chromosome structural reorganization to topological resolution through the cell cycle and highlights a mechanism of directing Topo II-mediated strand passage via loop extrusion-driven lengthwise compaction.
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Gutierrez-Escribano P, Newton MD, Llauró A, Huber J, Tanasie L, Davy J, Aly I, Aramayo R, Montoya A, Kramer H, Stigler J, Rueda DS, Aragon L. A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules. SCIENCE ADVANCES 2019; 5:eaay6804. [PMID: 31807710 PMCID: PMC6881171 DOI: 10.1126/sciadv.aay6804] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/22/2019] [Indexed: 05/13/2023]
Abstract
Sister chromatid cohesion requires cohesin to act as a protein linker to hold chromatids together. How cohesin tethers chromatids remains poorly understood. We have used optical tweezers to visualize cohesin as it holds DNA molecules. We show that cohesin complexes tether DNAs in the presence of Scc2/Scc4 and ATP demonstrating a conserved activity from yeast to humans. Cohesin forms two classes of tethers: a "permanent bridge" resisting forces over 80 pN and a force-sensitive "reversible bridge." The establishment of bridges requires physical proximity of dsDNA segments and occurs in a single step. "Permanent" cohesin bridges slide when they occur in trans, but cannot be removed when in cis. Therefore, DNAs occupy separate physical compartments in cohesin molecules. We finally demonstrate that cohesin tetramers can compact linear DNA molecules stretched by very low force (below 1 pN), consistent with the possibility that, like condensin, cohesin is also capable of loop extrusion.
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Affiliation(s)
- Pilar Gutierrez-Escribano
- Cell Cycle Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Matthew D. Newton
- Single Molecule Imaging Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
- Molecular Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Aida Llauró
- LUMICKS, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands
| | - Jonas Huber
- Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Loredana Tanasie
- Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Joseph Davy
- Cell Cycle Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Isabel Aly
- Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Ricardo Aramayo
- Microscopy Facility, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Johannes Stigler
- Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - David S. Rueda
- Single Molecule Imaging Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
- Molecular Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Luis Aragon
- Cell Cycle Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
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31
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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32
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Abstract
Protein complexes built of structural maintenance of chromosomes (SMC) and kleisin subunits, including cohesin, condensin and the Smc5/6 complex, are master organizers of genome architecture in all kingdoms of life. How these large ring-shaped molecular machines use the energy of ATP hydrolysis to change the topology of chromatin fibers has remained a central unresolved question of chromosome biology. A currently emerging concept suggests that the common principle that underlies the essential functions of SMC protein complexes in the control of gene expression, chromosome segregation or DNA damage repair is their ability to expand DNA into large loop structures. Here, we review the current knowledge about the biochemical and structural properties of SMC protein complexes that might enable them to extrude DNA loops and compare their action to other motor proteins and nucleic acid translocases. We evaluate the currently predominant models of active loop extrusion and propose a detailed version of a 'scrunching' model, which reconciles much of the available mechanistic data and provides an elegant explanation for how SMC protein complexes fulfill an array of seemingly diverse tasks during the organization of genomes.
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33
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Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proc Natl Acad Sci U S A 2019; 116:20489-20499. [PMID: 31548377 PMCID: PMC6789630 DOI: 10.1073/pnas.1907009116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.
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Affiliation(s)
- Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138
| | - Payel Paul
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Aafke A van den Berg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138;
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
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34
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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35
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Marko JF, De Los Rios P, Barducci A, Gruber S. DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes. Nucleic Acids Res 2019; 47:6956-6972. [PMID: 31175837 PMCID: PMC6649773 DOI: 10.1093/nar/gkz497] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 05/20/2019] [Accepted: 06/06/2019] [Indexed: 01/08/2023] Open
Abstract
Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a 'loop extrusion' process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor 'track'-in this case DNA-are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with 'stalling' occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (Escherichia coli MukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.
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Affiliation(s)
- John F Marko
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Paolo De Los Rios
- Laboratory of Statistical Biophysics, Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Switzerland
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
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36
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Mirny LA, Imakaev M, Abdennur N. Two major mechanisms of chromosome organization. Curr Opin Cell Biol 2019; 58:142-152. [PMID: 31228682 DOI: 10.1016/j.ceb.2019.05.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/14/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
The spatial organization of chromosomes has long been connected to their polymeric nature and is believed to be important for their biological functions, including the control of interactions between genomic elements, the maintenance of genetic information, and the compaction and safe transfer of chromosomes to cellular progeny. chromosome conformation capture techniques, particularly Hi-C, have provided a comprehensive picture of spatial chromosome organization and revealed new features and elements of chromosome folding. Furthermore, recent advances in microscopy have made it possible to obtain distance maps for extensive regions of chromosomes (Bintu et al., 2018; Nir et al., 2018 [2••,3]), providing information complementary to, and in excellent agreement with, Hi-C maps. Not only has the resolution of both techniques advanced significantly, but new perturbation data generated in the last two years have led to the identification of molecular mechanisms behind large-scale genome organization. Two major mechanisms that have been proposed to govern chromosome organization are (i) the active (ATP-dependent) process of loop extrusion by Structural Maintenance of Chromosomes (SMC) complexes, and (ii) the spatial compartmentalization of the genome, which is likely mediated by affinity interactions between heterochromatic regions (Falk et al., 2019 [76••]) rather than by ATP-dependent processes. Here, we review existing evidence that these two processes operate together to fold chromosomes in interphase and that loop extrusion alone drives mitotic compaction. We discuss possible implications of these mechanisms for chromosome function.
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Affiliation(s)
- Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
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37
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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38
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Loop formation by SMC complexes: turning heads, bending elbows, and fixed anchors. Curr Opin Genet Dev 2019; 55:11-18. [PMID: 31108424 DOI: 10.1016/j.gde.2019.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/24/2022]
Abstract
From the dynamic interphase genome to compacted mitotic chromosomes, DNA is organized by the conserved SMC complexes cohesin and condensin. The picture is emerging that these complexes structure the genome through a shared basic principle that involves the formation and processive enlargement of chromatin loops. This appears to be an asymmetric process, in which the complex anchors at the base of a loop and then enlarges the loop in a one-sided manner. We discuss the latest insights into how ATPase-driven conformational changes within these complexes may enlarge loops, and consider how asymmetric DNA reeling can bring together genomic elements in a symmetric manner.
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39
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Unraveling quiescence-specific repressive chromatin domains. Curr Genet 2019; 65:1145-1151. [PMID: 31055637 DOI: 10.1007/s00294-019-00985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 01/30/2023]
Abstract
Quiescence is a highly conserved inactive life stage in which the cell reversibly exits the cell cycle in response to external cues. Quiescence is essential for diverse processes such as the maintenance of adult stem cell stores, stress resistance, and longevity, and its misregulation has been implicated in cancer. Although the non-cycling nature of quiescent cells has made obtaining sufficient quantities of quiescent cells for study difficult, the development of a Saccharomyces cerevisiae model of quiescence has recently enabled detailed investigation into mechanisms underlying the quiescent state. Like their metazoan counterparts, quiescent budding yeast exhibit widespread transcriptional silencing and dramatic chromatin condensation. We have recently found that the structural maintenance of chromosomes (SMC) complex condensin binds throughout the quiescent budding yeast genome and induces the formation of large chromatin loop domains. In the absence of condensin, quiescent cell chromatin is decondensed and transcription is de-repressed. Here, we briefly discuss our findings in the larger context of the genome organization field.
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40
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Takahashi M, Hirota T. Folding the genome into mitotic chromosomes. Curr Opin Cell Biol 2019; 60:19-26. [PMID: 30999230 DOI: 10.1016/j.ceb.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
Abstract
How linear DNA molecules are packaged into compact cylindrical chromosomes in preparation for cell division has remained one of the central outstanding questions in cell biology. Condensin is a highly conserved protein complex that universally determines large-scale DNA geometry during mitotic chromosome assembly. A wide range of recently developed approaches, including super resolution microscopy, single molecule imaging, Hi-C analyses and computational modeling, have profoundly changed how we view mitotic chromosomes. This review highlights recent discoveries on chromosome architecture and condensin function.
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Affiliation(s)
- Motoko Takahashi
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Toru Hirota
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.
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41
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Abstract
Condensins and cohesins are highly conserved complexes that tether together DNA loci within a single DNA molecule to produce DNA loops. Condensin and cohesin structures, however, are different, and the DNA loops produced by each underlie distinct cell processes. Condensin rods compact chromosomes during mitosis, with condensin I and II complexes producing spatially defined and nested looping in metazoan cells. Structurally adaptive cohesin rings produce loops, which organize the genome during interphase. Cohesin-mediated loops, termed topologically associating domains or TADs, antagonize the formation of epigenetically defined but untethered DNA volumes, termed compartments. While condensin complexes formed through cis-interactions must maintain chromatin compaction throughout mitosis, cohesins remain highly dynamic during interphase to allow for transcription-mediated responses to external cues and the execution of developmental programs. Here, I review differences in condensin and cohesin structures, and highlight recent advances regarding the intramolecular or cis-based tetherings through which condensins compact DNA during mitosis and cohesins organize the genome during interphase.
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Affiliation(s)
- Robert V Skibbens
- Department of Biological Sciences, 111 Research Drive, Lehigh University, Bethlehem, PA 18015, USA
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42
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Baxter J, Oliver AW, Schalbetter SA. Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact. Bioessays 2018; 41:e1800182. [PMID: 30506702 DOI: 10.1002/bies.201800182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Indexed: 01/24/2023]
Abstract
The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome-wide contact frequency analyses indicate that intra-chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle. DNA loop extrusion has emerged as a unifying model for how chromosome loops are formed in cis in different genomic contexts and cell cycle stages. The highly conserved family of SMC complexes have been found to be required for DNA cis-looping and have been suggested to be the enzymatic core of loop extruding machines. Here, the current body of evidence available for the in vivo and in vitro action of SMC complexes is discussed and compared to the predictions made by the loop extrusion model. How SMC complexes may differentially act on chromatin to generate DNA loops and how they could work to generate the dynamic and functionally appropriate organization of DNA in cells is explored.
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Affiliation(s)
- Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Stephanie A Schalbetter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
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43
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Ali EI, Loidl J, Howard-Till RA. A streamlined cohesin apparatus is sufficient for mitosis and meiosis in the protist Tetrahymena. Chromosoma 2018; 127:421-435. [PMID: 29948142 PMCID: PMC6208729 DOI: 10.1007/s00412-018-0673-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 02/03/2023]
Abstract
In order to understand its diverse functions, we have studied cohesin in the evolutionarily distant ciliate model organism Tetrahymena thermophila. In this binucleate cell, the heritable germline genome is maintained separately from the transcriptionally active somatic genome. In a previous study, we showed that a minimal cohesin complex in Tetrahymena consisted of homologs of Smc1, Smc3, and Rec8, which are present only in the germline nucleus, where they are needed for normal chromosome segregation as well as meiotic DNA repair. In this study, we confirm that a putative homolog of Scc3 is a member of this complex. In the absence of Scc3, Smc1 and Rec8 fail to localize to germline nuclei, Rec8 is hypo-phosphorylated, and cells show phenotypes similar to depletion of Smc1 and Rec8. We also identify a homolog of Scc2, which in other organisms is part of a heterodimeric complex (Scc2/Scc4) that helps load cohesin onto chromatin. In Tetrahymena, Scc2 interacts with Rec8 and Scc3, and its absence causes defects in mitotic and meiotic divisions. Scc2 is not required for chromosomal association of cohesin, but Rec8 is hypo-phosphorylated in its absence. Moreover, we did not identify a homolog of the cohesin loader Scc4, and no evidence was found of auxiliary factors, such as Eco1, Pds5, or WAPL. We propose that in Tetrahymena, a single, minimal cohesin complex performs all necessary functions for germline mitosis and meiosis, but is dispensable for transcription regulation and chromatin organization of the somatic genome.
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Affiliation(s)
- Emine I Ali
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Rachel A Howard-Till
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria.
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44
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Miermans CA, Broedersz CP. Bacterial chromosome organization by collective dynamics of SMC condensins. J R Soc Interface 2018; 15:rsif.2018.0495. [PMID: 30333247 DOI: 10.1098/rsif.2018.0495] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various nucleoid-associated proteins, including the ATPase Structural Maintenance of Chromosomes (SMC) condensin. Although the molecular structure of these ATPases has been mapped in detail, it still remains unclear by which physical mechanisms they collectively generate long-range chromosomal contacts. Here, we develop a computational model that captures the subtle interplay between molecular-scale activity of slip-links and large-scale chromosome organization. We first consider a scenario in which the ATPase activity of slip-links regulates their DNA-recruitment near the origin of replication, while the slip-link dynamics is assumed to be diffusive. We find that such diffusive slip-links can collectively organize the entire chromosome into a state with aligned arms, but not within physiological constraints. However, slip-links that include motor activity are far more effective at organizing the entire chromosome over all length-scales. The persistence of motor slip-links at physiological densities can generate large, nested loops and drive them into the bulk of the DNA. Finally, our model with motor slip-links can quantitatively account for the rapid arm-arm alignment of chromosomal arms observed in vivo.
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Affiliation(s)
- Christiaan A Miermans
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Chase P Broedersz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80333 München, Germany
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Nichols MH, Corces VG. A tethered-inchworm model of SMC DNA translocation. Nat Struct Mol Biol 2018; 25:906-910. [PMID: 30250225 PMCID: PMC6311135 DOI: 10.1038/s41594-018-0135-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/03/2018] [Indexed: 12/17/2022]
Abstract
The DNA loop extrusion model is a provocative new concept explaining the formation of chromatin loops that revolutionizes understanding of genome organization. Central to this model is the structural maintenance of chromosomes (SMC) protein family, which is now thought to function as a DNA motor. In this Perspective, we review and reinterpret the current knowledge of SMC structure and function and propose a novel mechanism for SMC motor activity.
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46
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Wang X, Hughes AC, Brandão HB, Walker B, Lierz C, Cochran JC, Oakley MG, Kruse AC, Rudner DZ. In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex. Mol Cell 2018; 71:841-847.e5. [PMID: 30100265 PMCID: PMC6591583 DOI: 10.1016/j.molcel.2018.07.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 11/16/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes shape the genomes of virtually all organisms, but how they function remains incompletely understood. Recent studies in bacteria and eukaryotes have led to a unifying model in which these ring-shaped ATPases act along contiguous DNA segments, processively enlarging DNA loops. In support of this model, single-molecule imaging experiments indicate that Saccharomyces cerevisiae condensin complexes can extrude DNA loops in an ATP-hydrolysis-dependent manner in vitro. Here, using time-resolved high-throughput chromosome conformation capture (Hi-C), we investigate the interplay between ATPase activity of the Bacillus subtilis SMC complex and loop formation in vivo. We show that point mutants in the SMC nucleotide-binding domain that impair but do not eliminate ATPase activity not only exhibit delays in de novo loop formation but also have reduced rates of processive loop enlargement. These data provide in vivo evidence that SMC complexes function as loop extruders.
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Affiliation(s)
- Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Anna C Hughes
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Walker
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carrie Lierz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Cochran
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Martha G Oakley
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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47
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Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers. BIOPHYSICS REPORTS 2018; 4:222-232. [PMID: 30310859 PMCID: PMC6153500 DOI: 10.1007/s41048-018-0064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022] Open
Abstract
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.
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48
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van Ruiten MS, Rowland BD. SMC Complexes: Universal DNA Looping Machines with Distinct Regulators. Trends Genet 2018; 34:477-487. [PMID: 29606284 DOI: 10.1016/j.tig.2018.03.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/30/2018] [Accepted: 03/09/2018] [Indexed: 11/24/2022]
Abstract
What drives the formation of chromatin loops has been a long-standing question in chromosome biology. Recent work provides major insight into the basic principles behind loop formation. Structural maintenance of chromosomes (SMC) complexes, that are conserved from bacteria to humans, are key to this process. The SMC family includes condensin and cohesin, which structure chromosomes to enable mitosis and long-range gene regulation. We discuss novel insights into the mechanism of loop formation and the implications for how these complexes ultimately shape chromosomes. A picture is emerging in which these complexes form small loops that they then processively enlarge. It appears that SMC complexes act by family-wide basic principles, with complex-specific levels of control.
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Affiliation(s)
- Marjon S van Ruiten
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging Evidence of Chromosome Folding by Loop Extrusion. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 82:45-55. [PMID: 29728444 PMCID: PMC6512960 DOI: 10.1101/sqb.2017.82.034710] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chromosome organization poses a remarkable physical problem with many biological consequences: How can molecular interactions between proteins at the nanometer scale organize micron-long chromatinized DNA molecules, insulating or facilitating interactions between specific genomic elements? The mechanism of active loop extrusion holds great promise for explaining interphase and mitotic chromosome folding, yet remains difficult to assay directly. We discuss predictions from our polymer models of loop extrusion with barrier elements and review recent experimental studies that provide strong support for loop extrusion, focusing on perturbations to CTCF and cohesin assayed via Hi-C in interphase. Finally, we discuss a likely molecular mechanism of loop extrusion by structural maintenance of chromosomes complexes.
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Affiliation(s)
- Geoffrey Fudenberg
- Gladstone Institute of Data Science and Technology, University of California, San Francisco, California 94158
| | - Nezar Abdennur
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Maxim Imakaev
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Anton Goloborodko
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Leonid A Mirny
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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50
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Ganji M, Shaltiel IA, Bisht S, Kim E, Kalichava A, Haering CH, Dekker C. Real-time imaging of DNA loop extrusion by condensin. Science 2018; 360:102-105. [PMID: 29472443 DOI: 10.1126/science.aar7831] [Citation(s) in RCA: 443] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
Abstract
It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.
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Affiliation(s)
- Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Indra A Shaltiel
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Ana Kalichava
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
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