1
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Beliveau BJ, Akilesh S. A guide to studying 3D genome structure and dynamics in the kidney. Nat Rev Nephrol 2024:10.1038/s41581-024-00894-2. [PMID: 39406927 DOI: 10.1038/s41581-024-00894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2024] [Indexed: 10/19/2024]
Abstract
The human genome is tightly packed into the 3D environment of the cell nucleus. Rapidly evolving and sophisticated methods of mapping 3D genome architecture have shed light on fundamental principles of genome organization and gene regulation. The genome is physically organized on different scales, from individual genes to entire chromosomes. Nuclear landmarks such as the nuclear envelope and nucleoli have important roles in compartmentalizing the genome within the nucleus. Genome activity (for example, gene transcription) is also functionally partitioned within this 3D organization. Rather than being static, the 3D organization of the genome is tightly regulated over various time scales. These dynamic changes in genome structure over time represent the fourth dimension of the genome. Innovative methods have been used to map the dynamic regulation of genome structure during important cellular processes including organism development, responses to stimuli, cell division and senescence. Furthermore, disruptions to the 4D genome have been linked to various diseases, including of the kidney. As tools and approaches to studying the 4D genome become more readily available, future studies that apply these methods to study kidney biology will provide insights into kidney function in health and disease.
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Affiliation(s)
- Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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2
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Chang LH, Noordermeer D. Permeable TAD boundaries and their impact on genome-associated functions. Bioessays 2024; 46:e2400137. [PMID: 39093600 DOI: 10.1002/bies.202400137] [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: 06/05/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.
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Affiliation(s)
- Li-Hsin Chang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Blood and Transplant Research Unit in Precision Cellular Therapeutics, National Institute of Health Research, Oxford, UK
| | - Daan Noordermeer
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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3
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Olaya I, Burgess SM, Rog O. Formation and resolution of meiotic chromosome entanglements and interlocks. J Cell Sci 2024; 137:jcs262004. [PMID: 38985540 PMCID: PMC11267460 DOI: 10.1242/jcs.262004] [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] [Indexed: 07/12/2024] Open
Abstract
Interactions between parental chromosomes during the formation of gametes can lead to entanglements, entrapments and interlocks between unrelated chromosomes. If unresolved, these topological constraints can lead to misregulation of exchanges between chromosomes and to chromosome mis-segregation. Interestingly, these configurations are largely resolved by the time parental chromosomes are aligned during pachytene. In this Review, we highlight the inevitability of topologically complex configurations and discuss possible mechanisms to resolve them. We focus on the dynamic nature of a conserved chromosomal interface - the synaptonemal complex - and the chromosome movements that accompany meiosis as potential mechanisms to resolve topological constraints. We highlight the advantages of the nematode Caenorhabditis elegans for understanding biophysical features of the chromosome axis and synaptonemal complex that could contribute to mechanisms underlying interlock resolution. In addition, we highlight advantages of using the zebrafish, Danio rerio, as a model to understand how entanglements and interlocks are avoided and resolved.
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Affiliation(s)
- Iván Olaya
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Sean M. Burgess
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA
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4
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Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [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: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
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Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
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5
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression. Proc Natl Acad Sci U S A 2024; 121:e2401494121. [PMID: 38753513 PMCID: PMC11127048 DOI: 10.1073/pnas.2401494121] [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: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension [Formula: see text] is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ([Formula: see text]) longer than tens of minutes to be proportional to [Formula: see text]. We validate our results with hybrid molecular dynamics-Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- World Premier International Research Center Initiative–Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
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6
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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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7
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Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell 2024; 84:1422-1441.e14. [PMID: 38521067 DOI: 10.1016/j.molcel.2024.02.025] [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: 10/17/2022] [Revised: 10/23/2023] [Accepted: 02/24/2024] [Indexed: 03/25/2024]
Abstract
The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations, and multi-contact 3C and find that, by contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a topoisomerase-II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias topoisomerase II activity toward decatenation. At the second stage, the loops are released, and the formation of new entanglements is prevented by lower topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed in experiments and models, a normal interphase state cannot be acquired.
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Affiliation(s)
- Erica M Hildebrand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Bastiaan Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yu Liu
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Temple Health, Philadelphia, PA 19111, USA
| | - Denis L Lafontaine
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - A Nicole Fox
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ying Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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8
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Baxter J. Entangling and disentangling mitotic chromosomes. Mol Cell 2024; 84:1398-1400. [PMID: 38640891 DOI: 10.1016/j.molcel.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
The DNA topological challenges generated by cellular manipulation of extremely long DNA fibers remain poorly understood. In this issue of Molecular Cell, Hildebrand et al.1 describe how mitotic chromosomes are self entangled and that disentanglement requires TOP2 activity in late mitosis.
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Affiliation(s)
- Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK.
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9
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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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10
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Belan S, Parfenyev V. Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model. J Chem Phys 2024; 160:124901. [PMID: 38516975 DOI: 10.1063/5.0199573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.
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Affiliation(s)
- Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Av., 142432 Chernogolovka, Russia
- 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
- National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
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11
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576729. [PMID: 38328091 PMCID: PMC10849557 DOI: 10.1101/2024.01.22.576729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross over between two and four at contour lengths on the order of 30 kilo-base pairs (kbp). The anomalously high fractal dimension D = 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ( Δ t ) longer than tens of minutes to be proportional to Δ t 1 / 3 . We validate our results with hybrid molecular dynamics - Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, United States
- Department of Physics, Duke University, Durham, North Carolina, 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, United States
- World Premier International Research Center Initiative — Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, 001-0021, Japan
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12
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Xie Y, Ruan F, Li Y, Luo M, Zhang C, Chen Z, Xie Z, Weng Z, Chen W, Chen W, Fang Y, Sun Y, Guo M, Wang J, Xu S, Wang H, Tang C. Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers. eLife 2024; 12:RP87868. [PMID: 38236718 PMCID: PMC10945591 DOI: 10.7554/elife.87868] [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] [Indexed: 01/23/2024] Open
Abstract
As the genome is organized into a three-dimensional structure in intracellular space, epigenomic information also has a complex spatial arrangement. However, most epigenetic studies describe locations of methylation marks, chromatin accessibility regions, and histone modifications in the horizontal dimension. Proper spatial epigenomic information has rarely been obtained. In this study, we designed spatial chromatin accessibility sequencing (SCA-seq) to resolve the genome conformation by capturing the epigenetic information in single-molecular resolution while simultaneously resolving the genome conformation. Using SCA-seq, we are able to examine the spatial interaction of chromatin accessibility (e.g. enhancer-promoter contacts), CpG island methylation, and spatial insulating functions of the CCCTC-binding factor. We demonstrate that SCA-seq paves the way to explore the mechanism of epigenetic interactions and extends our knowledge in 3D packaging of DNA in the nucleus.
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Affiliation(s)
| | | | - Yaning Li
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | - Meng Luo
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | | | - Zhichao Chen
- BGI Genomics, BGI-ShenzhenShenzhenChina
- College of Life Sciences, University of Chinese Academy of SciencesBeijingChina
| | - Zhe Xie
- College of Life Sciences, University of Chinese Academy of SciencesBeijingChina
- Department of Biology, Cell Biology and Physiology, University of CopenhagenCopenhagenDenmark
| | - Zhe Weng
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | - Weitian Chen
- BGI Genomics, BGI-ShenzhenShenzhenChina
- College of Life Sciences, University of Chinese Academy of SciencesBeijingChina
| | | | | | - Yuxin Sun
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | - Mei Guo
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | - Juan Wang
- BGI Genomics, BGI-ShenzhenShenzhenChina
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbinChina
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13
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Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Nat Commun 2023; 14:5615. [PMID: 37699887 PMCID: PMC10497529 DOI: 10.1038/s41467-023-41265-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
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Affiliation(s)
- Li-Hsin Chang
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, and National Institute of Health Research, Blood and Transplant Research Unit in Precision Cellular Therapeutics, OX3 9DS, Oxford, UK
| | - Sourav Ghosh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Pathology and Laboratory Medicine, Western University, N6A3K7, London, ON, Canada
| | - Andrea Papale
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
| | - Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Vincent Piras
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Joanne Edouard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mallory Poncelet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nathan Lecouvreur
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sébastien Bloyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Holcman
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
- Churchill College, University of Cambridge, CB3 0DS, Cambridge, UK
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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14
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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15
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Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell 2023; 83:2624-2640. [PMID: 37419111 PMCID: PMC10528254 DOI: 10.1016/j.molcel.2023.06.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Chan Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Frank Alber
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Bo Huang
- University of California, San Francisco, San Francisco, CA, USA
| | - Danwei Huangfu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Reza Kalhor
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Wenbo Li
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yun Li
- University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | | | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Bing Ren
- University of California, San Diego, La Jolla, CA, USA
| | - Yijun Ruan
- Zhejiang University, Hangzhou, Zhejiang, China
| | | | - Yin Shen
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Xiaokun Shu
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Sheng Zhong
- University of California, San Diego, La Jolla, CA, USA.
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16
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Mirny LA. Chromosome and protein folding: In search for unified principles. Curr Opin Struct Biol 2023; 81:102610. [PMID: 37327690 DOI: 10.1016/j.sbi.2023.102610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/18/2023]
Abstract
Structural biology has traditionally focused on the structures of proteins, short nucleic acids, small molecules, and their complexes. However, it is now widely recognized that the 3D organization of chromosomes should also be included in this list, despite significant differences in scale and complexity of organization. Here we highlight some notable similarities between the folding processes that shape proteins and chromosomes. Both biomolecules are folded by two types of processes: the affinity-mediated interactions, and by active (ATP-dependent) processes. Both chromosome and proteins in vivo can have partially unstructured and non-equilibrium ensembles with yet to be understood functional roles. By analyzing these biological systems in parallel, we can uncover universal principles of biomolecular organization that transcend specific biopolymers.
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Affiliation(s)
- Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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17
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Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev 2023; 81:102064. [PMID: 37390583 PMCID: PMC10547022 DOI: 10.1016/j.gde.2023.102064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/02/2023]
Abstract
3D genome folding enables the physical storage of chromosomes into the compact volume of a cell's nucleus, allows for the accurate segregation of chromatin to daughter cells, and has been shown to be tightly coupled to the way in which genetic information is converted into transcriptional programs [1-3]. Importantly, this link between chromatin architecture and gene regulation is a selectable feature in which modifications to chromatin organization accompany, or perhaps even drive the establishment of new regulatory strategies with enduring impacts on animal body plan complexity. Here, we discuss the nature of different 3D genome folding systems found across the tree of life, with particular emphasis on metazoans, and the relative influence of these systems on gene regulation. We suggest how the properties of these folding systems have influenced regulatory strategies employed by different lineages and may have catalyzed the partitioning and specialization of genetic programs that enabled multicellularity and organ-grade body plan complexity.
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Affiliation(s)
- Jenks Hehmeyer
- Department of Organismal Biology and Anatomy, The University of Chicago, USA
| | - François Spitz
- Department of Human Genetics, The University of Chicago, USA
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, USA.
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18
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Chan B, Rubinstein M. Theory of chromatin organization maintained by active loop extrusion. Proc Natl Acad Sci U S A 2023; 120:e2222078120. [PMID: 37253009 PMCID: PMC10266055 DOI: 10.1073/pnas.2222078120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/13/2023] [Indexed: 06/01/2023] Open
Abstract
The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active loop extrusion which predicts that loop formation probability is a nonmonotonic function of loop length and describes chromatin contact probabilities. We validate our model with Monte Carlo and hybrid Molecular Dynamics-Monte Carlo simulations and demonstrate that our theory recapitulates experimental chromatin conformation capture data. Our results support active loop extrusion as a mechanism for chromatin organization and provide an analytical description of chromatin organization that may be used to specifically modify chromatin contact probabilities.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Institute for Chemical Reaction Design and Discovery (World Premier International Research Center Initiative-ICReDD), Hokkaido University, Sapporo001-0021, Japan
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19
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Pickard J, Chen C, Salman R, Stansbury C, Kim S, Surana A, Bloch A, Rajapakse I. HAT: Hypergraph analysis toolbox. PLoS Comput Biol 2023; 19:e1011190. [PMID: 37276238 DOI: 10.1371/journal.pcbi.1011190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized to precisely represent and analyze multi-way interactions. Here we present the Hypergraph Analysis Toolbox (HAT), a software package for visualization and analysis of multi-way interactions in complex systems.
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Affiliation(s)
- Joshua Pickard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- iReprogram, Inc., Ann Arbor, Michigan, United States of America
| | - Can Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rahmy Salman
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cooper Stansbury
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sion Kim
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amit Surana
- Raytheon Technologies Research Center, East Hartford, Connecticut, United States of America
| | - Anthony Bloch
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- iReprogram, Inc., Ann Arbor, Michigan, United States of America
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
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20
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Akbari E, Park EJ, Singh AK, Vinayak V, Virk RKA, Wereszczynksi J, Musselman CA. Multiscale genome organization symposium - annual biophysical society meeting 2023. Biophys Rev 2023; 15:313-315. [PMID: 37396443 PMCID: PMC10310627 DOI: 10.1007/s12551-023-01063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/17/2023] [Indexed: 07/04/2023] Open
Affiliation(s)
- Ehsan Akbari
- Department of Physics, The Ohio State University, Columbus, OH 43210 USA
| | - Eui-Jin Park
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Ajit K. Singh
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405 USA
| | - Vinayak Vinayak
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ranya K. A. Virk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Jeff Wereszczynksi
- Departments of Physics and Biology, Illinois Institute of Technology, Chicago, IL 60616 USA
| | - Catherine A. Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
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21
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Zhong JY, Niu L, Lin ZB, Bai X, Chen Y, Luo F, Hou C, Xiao CL. High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding. Nat Commun 2023; 14:1250. [PMID: 36878904 PMCID: PMC9988853 DOI: 10.1038/s41467-023-36899-x] [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: 06/17/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.
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Affiliation(s)
- Jia-Yong Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Longjian Niu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.,School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhuo-Bin Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xin Bai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, 29634-0974, USA
| | - Chunhui Hou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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22
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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: 26] [Impact Index Per Article: 26.0] [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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23
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Roy AL, Conroy RS, Taylor VG, Mietz J, Fingerman IM, Pazin MJ, Smith P, Hutter CM, Singer DS, Wilder EL. Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program. Mol Cell 2023; 83:335-342. [PMID: 36640770 PMCID: PMC9898192 DOI: 10.1016/j.molcel.2022.12.025] [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: 10/07/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Genomic architecture appears to play crucial roles in health and a variety of diseases. How nuclear structures reorganize over different timescales is elusive, partly because the tools needed to probe and perturb them are not as advanced as needed by the field. To fill this gap, the National Institutes of Health Common Fund started a program in 2015, called the 4D Nucleome (4DN), with the goal of developing and ultimately applying technologies to interrogate the structure and function of nuclear organization in space and time.
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Affiliation(s)
- Ananda L Roy
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA; Division of Program Coordination, Planning, and Strategic Initiative, National Institutes of Health, Bethesda, MD 20892, USA; Office of the National Institutes of Health Director, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Richard S Conroy
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA; Division of Program Coordination, Planning, and Strategic Initiative, National Institutes of Health, Bethesda, MD 20892, USA; Office of the National Institutes of Health Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica G Taylor
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA; Division of Program Coordination, Planning, and Strategic Initiative, National Institutes of Health, Bethesda, MD 20892, USA; Office of the National Institutes of Health Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judy Mietz
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian M Fingerman
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael J Pazin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phillip Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Carolyn M Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dinah S Singer
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth L Wilder
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA; Division of Program Coordination, Planning, and Strategic Initiative, National Institutes of Health, Bethesda, MD 20892, USA; Office of the National Institutes of Health Director, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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25
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Xia C, Huang L, Huang J, Zhang H, Huang Y, Benhamed M, Wang M, Chen X, Zhang M, Liu T, Chen W. Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens. Microbiol Spectr 2022; 10:e0260822. [PMID: 36250889 PMCID: PMC9769607 DOI: 10.1128/spectrum.02608-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 01/07/2023] Open
Abstract
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. tritici, a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. tritici indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. IMPORTANCE Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. tritici, a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.
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Affiliation(s)
- Chongjing Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Liang Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Jie Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Huang
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Moussa Benhamed
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington, USA
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
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26
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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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27
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Gridina M, Taskina A, Lagunov T, Nurislamov A, Kulikova T, Krasikova A, Fishman V. Comparison and critical assessment of single-cell Hi-C protocols. Heliyon 2022; 8:e11023. [PMID: 36281413 PMCID: PMC9587272 DOI: 10.1016/j.heliyon.2022.e11023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/13/2022] [Accepted: 10/06/2022] [Indexed: 01/24/2023] Open
Abstract
Advances in single-cell sequencing technologies make it possible to study the genome architecture in single cells. The rapid growth of the field has been fueled by the development of innovative single-cell Hi-C protocols. However, the protocols vary considerably in their efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. Here, we compare the two most commonly used single-cell Hi-C protocols. We use long-read sequencing to analyze molecular products of the Hi-C assay and show that whole-genome amplification step results in increased number of artifacts, larger coverage biases, and increased amount of noise compared to PCR-based amplification. Our comparison provides guidance for researchers studying chromatin architecture in individual cells.
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28
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Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol 2022; 14:a040147. [PMID: 34518339 PMCID: PMC9248823 DOI: 10.1101/cshperspect.a040147] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Microscopy and genomic approaches provide detailed descriptions of the three-dimensional folding of chromosomes and nuclear organization. The fundamental question is how activity of molecules at the nanometer scale can lead to complex and orchestrated spatial organization at the scale of chromosomes and the whole nucleus. At least three key mechanisms can bridge across scales: (1) tethering of specific loci to nuclear landmarks leads to massive reorganization of the nucleus; (2) spatial compartmentalization of chromatin, which is driven by molecular affinities, results in spatial isolation of active and inactive chromatin; and (3) loop extrusion activity of SMC (structural maintenance of chromosome) complexes can explain many features of interphase chromatin folding and underlies key phenomena during mitosis. Interestingly, many features of chromosome organization ultimately result from collective action and the interplay between these mechanisms, and are further modulated by transcription and topological constraints. Finally, we highlight some outstanding questions that are critical for our understanding of nuclear organization and function. We believe many of these questions can be answered in the coming years.
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Affiliation(s)
- Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, MIT, Cambridge, Massachusetts 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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29
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Brahmachari S, Contessoto V, Di Pierro M, Onuchic J. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
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Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
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30
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Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun 2022; 13:2365. [PMID: 35501320 PMCID: PMC9061818 DOI: 10.1038/s41467-022-29697-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/28/2022] [Indexed: 01/03/2023] Open
Abstract
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.
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Affiliation(s)
- Sarah B Reiff
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew J Schroeder
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Koray Kırlı
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrea Cosolo
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Clara Bakker
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Luisa Mercado
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander D Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander K Balashov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Carl Vitzthum
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kent M Pitman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jeremy Johnson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Shannon R Ehmsen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter Kerpedjiev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Uğur Çamoğlu
- Karya SMD Software Solutions, İzmir, 35040, Turkey
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
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31
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:1368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
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32
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Lorber D, Volk T. Evaluation of chromatin mesoscale organization. APL Bioeng 2022; 6:010902. [PMID: 35071965 PMCID: PMC8758204 DOI: 10.1063/5.0069286] [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: 08/30/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Chromatin organization in the nucleus represents an important aspect of transcription regulation. Most of the studies so far focused on the chromatin structure in cultured cells or in fixed tissue preparations. Here, we discuss the various approaches for deciphering chromatin 3D organization with an emphasis on the advantages of live imaging approaches.
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Affiliation(s)
- Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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33
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SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Nat Protoc 2022; 17:36-75. [PMID: 35013617 DOI: 10.1038/s41596-021-00633-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/13/2021] [Indexed: 12/23/2022]
Abstract
A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus of each cell. We recently developed Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables mapping of higher-order interactions within the nucleus. SPRITE works by cross-linking interacting DNA, RNA and protein molecules and then mapping DNA-DNA spatial arrangements through an iterative split-and-pool barcoding method. All DNA molecules within a cross-linked complex are barcoded by repeatedly splitting complexes across a 96-well plate, ligating molecules with a unique tag sequence, and pooling all complexes into a single well before repeating the tagging. Because all molecules in a cross-linked complex are covalently attached, they will sort together throughout each round of split-and-pool and will obtain the same series of SPRITE tags, which we refer to as a barcode. The DNA fragments and their associated barcodes are sequenced, and all reads sharing identical barcodes are matched to reconstruct interactions. SPRITE accurately maps pairwise DNA interactions within the nucleus and measures higher-order spatial contacts occurring among up to thousands of simultaneously interacting molecules. Here, we provide a detailed protocol for the experimental steps of SPRITE, including a video ( https://youtu.be/6SdWkBxQGlg ). Furthermore, we provide an automated computational pipeline available on GitHub that allows experimenters to seamlessly generate SPRITE interaction matrices starting with raw fastq files. The protocol takes ~5 d from cell cross-linking to high-throughput sequencing for the experimental steps and 1 d for data processing.
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34
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The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations. Methods Mol Biol 2022; 2301:235-258. [PMID: 34415539 DOI: 10.1007/978-1-0716-1390-0_12] [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: 01/12/2023]
Abstract
Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.
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35
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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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36
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Galitsyna AA, Gelfand MS. Single-cell Hi-C data analysis: safety in numbers. Brief Bioinform 2021; 22:bbab316. [PMID: 34406348 PMCID: PMC8575028 DOI: 10.1093/bib/bbab316] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, genome-wide assays for chromatin interactions in single cells have enabled the study of individual nuclei at unprecedented resolution and throughput. Current chromosome conformation capture techniques survey contacts for up to tens of thousands of individual cells, improving our understanding of genome function in 3D. However, these methods recover a small fraction of all contacts in single cells, requiring specialised processing of sparse interactome data. In this review, we highlight recent advances in methods for the interpretation of single-cell genomic contacts. After discussing the strengths and limitations of these methods, we outline frontiers for future development in this rapidly moving field.
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Affiliation(s)
- Aleksandra A Galitsyna
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute for Information Transmission Problems, RAS, Moscow, Russia
- Institute of Gene Biology, RAS, Moscow, Russia
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute for Information Transmission Problems, RAS, Moscow, Russia
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37
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Beel AJ, Azubel M, Matteï PJ, Kornberg RD. Structure of mitotic chromosomes. Mol Cell 2021; 81:4369-4376.e3. [PMID: 34520722 DOI: 10.1016/j.molcel.2021.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/28/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022]
Abstract
Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers.
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Affiliation(s)
- Andrew J Beel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Maia Azubel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
| | - Pierre-Jean Matteï
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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38
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Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods 2021; 18:1046-1055. [PMID: 34480151 PMCID: PMC8446342 DOI: 10.1038/s41592-021-01248-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/18/2021] [Indexed: 01/05/2023]
Abstract
Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project. This analysis systematically evaluates cross-linking chemistry and chromatin fragmentation strategies commonly used in 3C assays and introduces an improved Hi-C protocol for detecting loops and compartments.
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Affiliation(s)
- Betul Akgol Oksuz
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Liyan Yang
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sameer Abraham
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sergey V Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Marlies E Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ankita Nand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hui Mao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rene Maehr
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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39
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Krebs AR. Studying transcription factor function in the genome at molecular resolution. Trends Genet 2021; 37:798-806. [DOI: 10.1016/j.tig.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022]
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40
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Choppakatla P, Dekker B, Cutts EE, Vannini A, Dekker J, Funabiki H. Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. eLife 2021; 10:e68918. [PMID: 34406118 PMCID: PMC8416026 DOI: 10.7554/elife.68918] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic chromosome organization. In vitro chromatin reconstitution experiments demonstrate that H1.8 inhibits binding of condensins and topo II to nucleosome arrays. Accordingly, H1.8 depletion in Xenopus egg extracts increased condensins and topo II levels on mitotic chromatin. Chromosome morphology and Hi-C analyses suggest that H1.8 depletion makes chromosomes thinner and longer through shortening the average loop size and reducing the DNA amount in each layer of mitotic loops. Furthermore, excess loading of condensins and topo II to chromosomes by H1.8 depletion causes hyper-chromosome individualization and dispersion. We propose that condensins and topo II are essential for chromosome individualization, but their functions are tuned by the linker histone to keep chromosomes together until anaphase.
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Affiliation(s)
- Pavan Choppakatla
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Bastiaan Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
- Fondazione Human Technopole, Structural Biology Research Centre, 20157MilanItaly
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
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41
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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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42
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Daban JR. Soft-matter properties of multilayer chromosomes. Phys Biol 2021; 18. [PMID: 34126606 DOI: 10.1088/1478-3975/ac0aff] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/14/2021] [Indexed: 12/17/2022]
Abstract
This perspective aims to identify the relationships between the structural and dynamic properties of chromosomes and the fundamental properties of soft-matter systems. Chromatin is condensed into metaphase chromosomes during mitosis. The resulting structures are elongated cylinders having micrometer-scale dimensions. Our previous studies, using transmission electron microscopy, atomic force microscopy, and cryo-electron tomography, suggested that metaphase chromosomes have a multilayered structure, in which each individual layer has the width corresponding to a mononucleosome sheet. The self-assembly of multilayer chromatin plates from small chromatin fragments suggests that metaphase chromosomes are self-organized hydrogels (in which a single DNA molecule crosslinks the whole structure) with an internal liquid-crystal order produced by the stacking of chromatin layers along the chromosome axis. This organization of chromatin was unexpected, but the spontaneous assembly of large structures has been studied in different soft-matter systems and, according to these studies, the self-organization of chromosomes could be justified by the interplay between weak interactions of repetitive nucleosome building blocks and thermal fluctuations. The low energy of interaction between relatively large building blocks also justifies the easy deformation and structural fluctuations of soft-matter structures and the changes of phase caused by diverse external factors. Consistent with these properties of soft matter, different experimental results show that metaphase chromosomes are easily deformable. Furthermore, at the end of mitosis, condensed chromosomes undergo a phase transition into a more fluid structure, which can be correlated to the decrease in the Mg2+concentration and to the dissociation of condensins from chromosomes. Presumably, the unstacking of layers and chromatin fluctuations driven by thermal energy facilitate gene expression during interphase.
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Affiliation(s)
- Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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43
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Liu S, Zhao K. The Toolbox for Untangling Chromosome Architecture in Immune Cells. Front Immunol 2021; 12:670884. [PMID: 33995409 PMCID: PMC8120992 DOI: 10.3389/fimmu.2021.670884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
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44
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Di Stefano M, Nützmann HW, Marti-Renom M, Jost D. Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana. Nucleic Acids Res 2021; 49:1840-1858. [PMID: 33444439 PMCID: PMC7913674 DOI: 10.1093/nar/gkaa1275] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/16/2020] [Accepted: 01/13/2021] [Indexed: 01/10/2023] Open
Abstract
The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Marc A Marti-Renom
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
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45
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Astakhov AM, Avetisov VA, Nechaev SK, Polovnikov KE. Fractal Dimension Meets Topology: Statistical and Topological Properties of Globular Macromolecules with Volume Interactions. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c01717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexey M. Astakhov
- Physics Department of the Lomonosov Moscow State University, Moscow 119991, Russia
- N.N. Semenov Institute of Chemical Physics RAS, Moscow 119991, Russia
| | | | - Sergei K. Nechaev
- Interdisciplinary Scientific Center Poncelet (CNRS UMI 2615), Moscow 119002, Russia
- P.N. Lebedev Physical Institute RAS, Moscow 119991, Russia
| | - Kirill E. Polovnikov
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
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46
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Belokopytova P, Fishman V. Predicting Genome Architecture: Challenges and Solutions. Front Genet 2021; 11:617202. [PMID: 33552135 PMCID: PMC7862721 DOI: 10.3389/fgene.2020.617202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
Genome architecture plays a pivotal role in gene regulation. The use of high-throughput methods for chromatin profiling and 3-D interaction mapping provide rich experimental data sets describing genome organization and dynamics. These data challenge development of new models and algorithms connecting genome architecture with epigenetic marks. In this review, we describe how chromatin architecture could be reconstructed from epigenetic data using biophysical or statistical approaches. We discuss the applicability and limitations of these methods for understanding the mechanisms of chromatin organization. We also highlight the emergence of new predictive approaches for scoring effects of structural variations in human cells.
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Affiliation(s)
- Polina Belokopytova
- Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Veniamin Fishman
- Natural Sciences Department, Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
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47
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Strickfaden H. Reflections on the organization and the physical state of chromatin in eukaryotic cells. Genome 2020; 64:311-325. [PMID: 33306433 DOI: 10.1139/gen-2020-0132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In recent years, our perception of chromatin structure and organization in the cell nucleus has changed in fundamental ways. The 30 nm chromatin fiber has lost its status as an essential in vivo structure. Hi-C and related biochemical methods, advanced electron and super-resolved fluorescence microscopy, together with concepts from soft matter physics, have revolutionized the field. A comprehensive understanding of the structural and functional interactions that regulate cell cycle and cell type specific nuclear functions appears within reach, but it requires the integration of top-down and bottom-up approachs. In this review, I present an update on nuclear architecture studies with an emphasis on organization and the controversy regarding the physical state of chromatin in cells.
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Affiliation(s)
- Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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48
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Tjalsma SJ, de Laat W. Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture. Curr Opin Genet Dev 2020; 67:10-17. [PMID: 33220512 DOI: 10.1016/j.gde.2020.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022]
Abstract
Recent years have seen a vast expansion of knowledge on three-dimensional (3D) genome organization. The majority of studies on chromosome topology consists of pairwise interaction data of bulk populations of cells and therefore conceals heterogenic and more complex folding patterns. Here, we discuss novel methodologies to study the variation in genome topologies between different cells and techniques that allow analysis of complex, multi-way interactions. These technologies will aid the interpretation of genome-wide chromosome conformation data and provide strategies to further dissect the interplay between genome architecture and transcription regulation.
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Affiliation(s)
- Sjoerd Jd Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
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