1
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Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol 2024; 20:e1012067. [PMID: 38709825 PMCID: PMC11098495 DOI: 10.1371/journal.pcbi.1012067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/16/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sameer Abraham
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Betul A. Oksuz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Yao Xiao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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2
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Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: From sequencing data to chromosome contacts. PLoS Comput Biol 2024; 20:e1012164. [PMID: 38809952 PMCID: PMC11164360 DOI: 10.1371/journal.pcbi.1012164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/10/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools-a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
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3
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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4
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Dreyer J, Ricci G, van den Berg J, Bhardwaj V, Funk J, Armstrong C, van Batenburg V, Sine C, VanInsberghe MA, Marsman R, Mandemaker IK, di Sanzo S, Costantini J, Manzo SG, Biran A, Burny C, Völker-Albert M, Groth A, Spencer SL, van Oudenaarden A, Mattiroli F. Acute multi-level response to defective de novo chromatin assembly in S-phase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586291. [PMID: 38585916 PMCID: PMC10996472 DOI: 10.1101/2024.03.22.586291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyperaccessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. As a result, histone variants usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.
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Affiliation(s)
- Jan Dreyer
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Giulia Ricci
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen van den Berg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Janina Funk
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Vincent van Batenburg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Chance Sine
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Michael A. VanInsberghe
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Richard Marsman
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Imke K. Mandemaker
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Simone di Sanzo
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | - Juliette Costantini
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Stefano G. Manzo
- Oncode Institute, The Netherlands
- Division of Gene Regulation, Netherlands Cancer Institute, The Netherlands
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Claire Burny
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | | | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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5
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Liu T, Qiu QT, Hua KJ, Ma BG. Chromosome structure modeling tools and their evaluation in bacteria. Brief Bioinform 2024; 25:bbae044. [PMID: 38385874 PMCID: PMC10883143 DOI: 10.1093/bib/bbae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/31/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.
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Affiliation(s)
- Tong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin-Tian Qiu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kang-Jian Hua
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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6
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Gilbert BR, Luthey-Schulten Z. Replicating Chromosomes in Whole-Cell Models of Bacteria. Methods Mol Biol 2024; 2819:625-653. [PMID: 39028527 DOI: 10.1007/978-1-0716-3930-6_29] [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: 07/20/2024]
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.
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Affiliation(s)
- Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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7
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Poinsignon T, Gallopin M, Grognet P, Malagnac F, Lelandais G, Poulain P. 3D models of fungal chromosomes to enhance visual integration of omics data. NAR Genom Bioinform 2023; 5:lqad104. [PMID: 38058589 PMCID: PMC10696920 DOI: 10.1093/nargab/lqad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in Saccharomyces cerevisiae, the backbones of the cohesin anchor regions, which were aligned all along the chromosomes, (ii) in Schizosaccharomyces pombe, the oscillations of the coiling of chromosome arms throughout the cell cycle and (iii) in Neurospora crassa, the massive relocalization of histone marks in mutants of heterochromatin regulators. 3D modeling of the chromosomes brings new opportunities for visual integration of omics data. This holistic perspective supports intuition and lays the foundation for building new concepts.
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Affiliation(s)
- Thibault Poinsignon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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8
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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9
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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10
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Jia BB, Jussila A, Kern C, Zhu Q, Ren B. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol 2023; 41:1004-1017. [PMID: 36593410 PMCID: PMC10344783 DOI: 10.1038/s41587-022-01568-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
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Affiliation(s)
- Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Adam Jussila
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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11
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Borrie MS, Kraycer PM, Gartenberg MR. Transcription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo. Mol Cell Biol 2023; 43:254-268. [PMID: 37178128 PMCID: PMC10251789 DOI: 10.1080/10985549.2023.2199660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cohesin is a central architectural element of chromosomes that regulates numerous DNA-based events. The complex holds sister chromatids together until anaphase onset and organizes individual chromosomal DNAs into loops and self-associating domains. Purified cohesin diffuses along DNA in an ATP-independent manner but can be propelled by transcribing RNA polymerase. In conjunction with a cofactor, the complex also extrudes DNA loops in an ATP-dependent manner. In this study we examine transcription-driven translocation of cohesin under various conditions in yeast. To this end, obstacles of increasing size were tethered to DNA to act as roadblocks to complexes mobilized by an inducible gene. The obstacles were built from a GFP-lacI core fused to one or more mCherries. A chimera with four mCherries blocked cohesin passage in late G1. During M phase, the threshold barrier depended on the state of cohesion: non-cohesive complexes were also blocked by four mCherries whereas cohesive complexes were blocked by as few as three mCherries. Furthermore cohesive complexes that were stalled at obstacles, in turn, blocked the passage of non-cohesive complexes. That synthetic barriers capture mobilized cohesin demonstrates that transcription-driven complexes translocate processively in vivo. Together, this study reveals unexplored limitations to cohesin movement on chromosomes.
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Affiliation(s)
- Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Paul M. Kraycer
- Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Member of The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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12
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Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: from sequencing data to chromosome contacts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528389. [PMID: 36824968 PMCID: PMC9949071 DOI: 10.1101/2023.02.13.528389] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools - a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. Pairtools provides both crucial core tools as well as auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for multi-way contacts, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, MA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Geoffrey Fudenberg
- Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, CA, USA
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
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13
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Roh S, Lee T, Cheong DY, Kim Y, Oh S, Lee G. Direct observation of surface charge and stiffness of human metaphase chromosomes. NANOSCALE ADVANCES 2023; 5:368-377. [PMID: 36756276 PMCID: PMC9846444 DOI: 10.1039/d2na00620k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (ca. 44.9 ± 16.48 mV) and showed uniform stiffness (ca. 6.23 ± 1.98 MPa). In contrast, after getting rid of the extra materials through treatment with RNase and protease, the chromosomes were strongly negatively charged (ca. -197.4 ± 77.87 mV) and showed relatively non-uniform and augmented stiffness (ca. 36.87 ± 17.56 MPa). The results suggested undulating but compact coordination of condensed chromosomes. Additionally, excessive treatment with RNase and protease could destroy the chromosomal structure, providing an exceptional opportunity for multiscale stiffness mapping of polynucleotides, nucleosomes, chromatin fibers, and chromosomes in a single image. Our approach offers a new horizon in terms of an analytical technique for studying chromosome-related diseases.
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Affiliation(s)
- Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Yeonjin Kim
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University Sejong 30019 Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
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14
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Kariti H, Feld T, Kaplan N. Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments. Nucleic Acids Res 2023; 51:1103-1119. [PMID: 36629266 PMCID: PMC9943678 DOI: 10.1093/nar/gkac1258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
The Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challenge. Genomic compartments are a checkered Hi-C interaction pattern suggested to represent the partitioning of the genome into two self-interacting states associated with active and inactive chromatin. Based on a few elementary mechanistic assumptions, we derive a generative probabilistic model of genomic compartments, called deGeco. Testing our model, we find it can explain observed Hi-C interaction maps in a highly robust manner, allowing accurate inference of interaction probability maps from extremely sparse data without any training of parameters. Taking advantage of the interpretability of the model parameters, we then test hypotheses regarding the nature of genomic compartments. We find clear evidence of multiple states, and that these states self-interact with different affinities. We also find that the interaction rules of chromatin states differ considerably within and between chromosomes. Inspecting the molecular underpinnings of a four-state model, we show that a simple classifier can use histone marks to predict the underlying states with 87% accuracy. Finally, we observe instances of mixed-state loci and analyze these loci in single-cell Hi-C maps, finding that mixing of states occurs mainly at the cell level.
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Affiliation(s)
- Hagai Kariti
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Tal Feld
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel,Viterbi Faculty of Electrical & Computer Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Noam Kaplan
- To whom correspondence should be addressed. Tel: +972 4 8295293;
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15
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Regulation of the mitotic chromosome folding machines. Biochem J 2022; 479:2153-2173. [PMID: 36268993 DOI: 10.1042/bcj20210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
Abstract
Over the last several years enormous progress has been made in identifying the molecular machines, including condensins and topoisomerases that fold mitotic chromosomes. The discovery that condensins generate chromatin loops through loop extrusion has revolutionized, and energized, the field of chromosome folding. To understand how these machines fold chromosomes with the appropriate dimensions, while disentangling sister chromatids, it needs to be determined how they are regulated and deployed. Here, we outline the current understanding of how these machines and factors are regulated through cell cycle dependent expression, chromatin localization, activation and inactivation through post-translational modifications, and through associations with each other, with other factors and with the chromatin template itself. There are still many open questions about how condensins and topoisomerases are regulated but given the pace of progress in the chromosome folding field, it seems likely that many of these will be answered in the years ahead.
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16
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Fleck K, Raj R, Erceg J. The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front Cell Dev Biol 2022; 10:968145. [PMID: 36036013 PMCID: PMC9402908 DOI: 10.3389/fcell.2022.968145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Genome organization includes contacts both within a single chromosome and between distinct chromosomes. Thus, regulatory organization in the nucleus may include interplay of these two types of chromosomal interactions with genome activity. Emerging advances in omics and single-cell imaging technologies have allowed new insights into chromosomal contacts, including those of homologs and sister chromatids, and their significance to genome function. In this review, we highlight recent studies in this field and discuss their impact on understanding the principles of chromosome organization and associated functional implications in diverse cellular processes. Specifically, we describe the contributions of intra-chromosomal, inter-homolog, and inter-sister chromatid contacts to genome organization and gene expression.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Romir Raj
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- *Correspondence: Jelena Erceg,
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17
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Srinivasan D, Shisode T, Shrinet J, Fraser P. Chromosome organization through the cell cycle at a glance. J Cell Sci 2022; 135:275498. [PMID: 35608019 DOI: 10.1242/jcs.244004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome organization and the three-dimensional folding of chromosomes are now seen as major contributors to nearly all nuclear functions including gene regulation, replication and repair. Recent studies have shown that in addition to the dramatic metamorphoses in chromosome conformation associated with entry to, and exit from mitosis, chromosomes undergo continual conformational changes throughout interphase with differential dynamics in loop structure, topological domains, compartments and lamina-associated domains. Understanding and accounting for these cell-cycle-dependent conformational changes is essential for the interpretation of data from a growing array of powerful molecular techniques to investigate genome conformation function, and to identify the molecules and mechanisms that drive chromosome conformational changes. In this Cell Science at a Glance article and the accompanying poster, we review Hi-C and microscopy studies describing cell-cycle-dependent conformational changes in chromosome structure.
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Affiliation(s)
- Divyaa Srinivasan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Tarak Shisode
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
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18
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Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022; 17:1486-1517. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Abstract
Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.
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19
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Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data. PLoS Comput Biol 2021; 17:e1009546. [PMID: 34793453 PMCID: PMC8601426 DOI: 10.1371/journal.pcbi.1009546] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.
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20
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Starkov D, Parfenyev V, Belan S. Conformational statistics of non-equilibrium polymer loops in Rouse model with active loop extrusion. J Chem Phys 2021; 154:164106. [PMID: 33940823 DOI: 10.1063/5.0048942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper, we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is characterized statistically by the mean gyration radius and the pairwise contact probabilities. It turns out that a single dimensionless parameter, which is given by the ratio of the loop relaxation time over the time elapsed since the start of extrusion, controls the crossover between near-equilibrium and highly non-equilibrium asymptotics in the statistics of the extruded loop, regardless of the specific time dependence of the extrusion velocity. In addition, we show that two-sided and one-sided loop extruding motors produce the loops with almost identical properties. Our predictions are based on two rigorous semi-analytical methods accompanied by asymptotic analysis of slow and fast extrusion limits.
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Affiliation(s)
- Dmitry Starkov
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Vladimir Parfenyev
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova av., 142432 Chernogolovka, Russia and National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
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21
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Jerkovic I, Cavalli G. Understanding 3D genome organization by multidisciplinary methods. Nat Rev Mol Cell Biol 2021; 22:511-528. [PMID: 33953379 DOI: 10.1038/s41580-021-00362-w] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 02/03/2023]
Abstract
Understanding how chromatin is folded in the nucleus is fundamental to understanding its function. Although 3D genome organization has been historically difficult to study owing to a lack of relevant methodologies, major technological breakthroughs in genome-wide mapping of chromatin contacts and advances in imaging technologies in the twenty-first century considerably improved our understanding of chromosome conformation and nuclear architecture. In this Review, we discuss methods of 3D genome organization analysis, including sequencing-based techniques, such as Hi-C and its derivatives, Micro-C, DamID and others; microscopy-based techniques, such as super-resolution imaging coupled with fluorescence in situ hybridization (FISH), multiplex FISH, in situ genome sequencing and live microscopy methods; and computational and modelling approaches. We describe the most commonly used techniques and their contribution to our current knowledge of nuclear architecture and, finally, we provide a perspective on up-and-coming methods that open possibilities for future major discoveries.
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Affiliation(s)
- Ivana Jerkovic
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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22
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Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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23
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Gregan J. The Spatial Organization of Sister Chromatids. Trends Biochem Sci 2021; 46:255-257. [PMID: 33593592 DOI: 10.1016/j.tibs.2021.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/19/2022]
Abstract
Understanding how genomes are spatially organized is central to many aspects of cell biology. However, it has been difficult to study the relationships between sister chromatids because sequencing-based techniques such as Hi-C could not distinguish identical sister DNAs. Here, I discuss recent developments that provide insights into sister chromatid organization.
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Affiliation(s)
- Juraj Gregan
- Advanced Microscopy Facility, VBCF, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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24
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Mitter M, Gerlich DW. Mapping Sister Chromatid Conformation in Replicated Chromosomes. Trends Biochem Sci 2020; 46:169-170. [PMID: 33342665 DOI: 10.1016/j.tibs.2020.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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