1
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Rashid F, Kabbo SA, Wang N. Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force. Cell Rep 2024; 43:114462. [PMID: 39002538 PMCID: PMC11289711 DOI: 10.1016/j.celrep.2024.114462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 07/15/2024] Open
Abstract
Increasing evidence suggests that the mechanics of chromatin and nucleoplasm regulate gene transcription and nuclear function. However, how the chromatin and nucleoplasm sense and respond to forces remains elusive. Here, we employed a strategy of applying forces directly to the chromatin of a cell via a microinjected 200-nm anti-H2B-antibody-coated ferromagnetic nanoparticle (FMNP) and an anti-immunoglobulin G (IgG)-antibody-coated or an uncoated FMNP. The chromatin behaved as a viscoelastic gel-like structure and the nucleoplasm was a softer viscoelastic structure at loading frequencies of 0.1-5 Hz. Protein diffusivity of the chromatin, nucleoplasm, and RNA polymerase II (RNA Pol II) and RNA Pol II activity were upregulated in a chromatin-stretching-dependent manner and stayed upregulated for tens of minutes after force cessation. Chromatin stiffness increased, but the mechanomemory duration of chromatin diffusivity decreased, with substrate stiffness. These findings may provide a mechanomemory mechanism of transcription upregulation and have implications on cell and nuclear functions.
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Affiliation(s)
- Fazlur Rashid
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA; Department of Mechanical Science and Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sadia Amin Kabbo
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA
| | - Ning Wang
- The Institute for Mechanobiology, Northeastern University, Boston, MA 02115, USA; Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA 02115, USA.
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2
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Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. PLoS One 2024; 19:e0301000. [PMID: 38805476 PMCID: PMC11132451 DOI: 10.1371/journal.pone.0301000] [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: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 05/30/2024] Open
Abstract
As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.
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Affiliation(s)
- Anne R. Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Emily M. Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Tiffany Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - I. Chae Ye
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Joshua A. Pritchard
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Cody L. Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Paola Carrillo Gonzalez
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicholas M. Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, United States of America
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
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3
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Banerjee DS, Chigumira T, Lackner RM, Kratz JC, Chenoweth DM, Banerjee S, Zhang H. Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593010. [PMID: 38766065 PMCID: PMC11100695 DOI: 10.1101/2024.05.07.593010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Biomolecular condensates play pivotal roles in many cellular processes, yet predicting condensate growth dynamics within the complex intracellular environment is challenging. While chromatin mechanics are known to influence condensate coarsening in the nucleus, the effect of condensate properties remains unclear. Our study demonstrates that the interplay between condensate properties and chromatin mechanics dictates condensate growth dynamics. Through chemical dimerization, we induced condensates of various properties in the cell nuclei, revealing distinct growth mechanisms: diffusion-driven or ripening-dominated. To explain experimental observations, we developed a quantitative theory that uncovers the role of chromatin in modulating condensate growth via size-dependent pressure. We find that surface tension is a critical factor in determining whether condensates undergo elastic or Ostwald ripening. Our model predicts that different condensates are affected differently by chromatin heterogeneity, validated by experimentally perturbing chromatin organization. Taken together, our work elucidates how condensate surface tension and chromatin heterogeneity govern nuclear condensate ripening.
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Affiliation(s)
- Deb Sankar Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Present address: James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Tafadzwa Chigumira
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rachel M Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Josiah C Kratz
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Present address: Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Huaiying Zhang
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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4
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Eshghi I, Zidovska A, Grosberg AY. Activity-Driven Phase Transition Causes Coherent Flows of Chromatin. PHYSICAL REVIEW LETTERS 2023; 131:048401. [PMID: 37566839 DOI: 10.1103/physrevlett.131.048401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 08/13/2023]
Abstract
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular motors tethered to chromatin. Cooperation occurs if each motor acts simultaneously on the polymer and the surrounding solvent, exerting on them equal and opposite forces. This drives the flow of solvent past the polymer, which in turn affects the orientation of nearby motors and, if the drive is strong enough, an active polar ("ferromagnetic") phase of motors can spontaneously form. Depending on boundary conditions, either transverse flows or sustained longitudinal oscillations and waves are possible. Predicted length scales are consistent with experiments. We now have in hand a coarse-grained description of chromatin dynamics which reproduces the directed coherent flows of chromatin seen in experiments. This field-theoretic description can be analytically coupled to other features of the nuclear environment such as fluctuating or porous boundaries, local heterogeneities in the distribution of chromatin or its activity, leading to insights on the effects of activity on the cell nucleus and its contents.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
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5
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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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6
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Attar S, Browning VE, Liu Y, Nichols EK, Tsue AF, Shechner DM, Shendure J, Lieberman JA, Akilesh S, Beliveau BJ. Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526264. [PMID: 36778496 PMCID: PMC9915481 DOI: 10.1101/2023.01.30.526264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In situ hybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed 'pSABER', for the amplification of ISH signals in cell and tissue systems. pSABER decorates the in situ target with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.
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7
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Eshghi I, Zidovska A, Grosberg AY. Symmetry-based classification of forces driving chromatin dynamics. SOFT MATTER 2022; 18:8134-8146. [PMID: 36239271 DOI: 10.1039/d2sm00840h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chromatin - the functional form of DNA in the cell - exists in the form of a polymer immersed in a nucleoplasmic fluid inside the cell nucleus. Both chromatin and nucleoplasm are subject to active forces resulting from local biological processes. This activity leads to non-equilibrium phenomena, affecting chromatin organization and dynamics, yet the underlying physics is far from understood. Here, we expand upon a previously developed two-fluid model of chromatin and nucleoplasm by considering three types of activity in the form of force dipoles - two with both forces of the dipole acting on the same fluid (either polymer or nucleoplasm) and a third, with two forces pushing chromatin and solvent in opposite directions. We find that this latter type results in the most significant flows, dominating over most length scales of interest. Due to the friction between the fluids and their viscosity, we observe emergent screening length scales in the active flows of this system. We predict that the presence of different activity types and their relative strengths can be inferred from observing the power spectra of hydrodynamic fluctuations in the chromatin and the nucleoplasm.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
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8
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Peng A, Peng W, Wang R, Zhao H, Yu X, Sun Y. Regulation of 3D Organization and Its Role in Cancer Biology. Front Cell Dev Biol 2022; 10:879465. [PMID: 35757006 PMCID: PMC9213882 DOI: 10.3389/fcell.2022.879465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Three-dimensional (3D) genomics is the frontier field in the post-genomics era, its foremost content is the relationship between chromatin spatial conformation and regulation of gene transcription. Cancer biology is a complex system resulting from genetic alterations in key tumor oncogenes and suppressor genes for cell proliferation, DNA replication, cell differentiation, and homeostatic functions. Although scientific research in recent decades has revealed how the genome sequence is mutated in many cancers, high-order chromosomal structures involved in the development and fate of cancer cells represent a crucial but rarely explored aspect of cancer genomics. Hence, dissection of the 3D genome conformation of cancer helps understand the unique epigenetic patterns and gene regulation processes that distinguish cancer biology from normal physiological states. In recent years, research in tumor 3D genomics has grown quickly. With the rapid progress of 3D genomics technology, we can now better determine the relationship between cancer pathogenesis and the chromatin structure of cancer cells. It is becoming increasingly explicit that changes in 3D chromatin structure play a vital role in controlling oncogene transcription. This review focuses on the relationships between tumor gene expression regulation, tumor 3D chromatin structure, and cancer phenotypic plasticity. Furthermore, based on the functional consequences of spatial disorganization in the cancer genome, we look forward to the clinical application prospects of 3D genomic biomarkers.
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Affiliation(s)
- Anghui Peng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Wang Peng
- Department of Oncology, Liuzhou People's Hospital, Liuzhou, China
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Hao Zhao
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xinyang Yu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yihao Sun
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
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9
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Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao-Ortiz M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022; 121:977-990. [PMID: 35150617 PMCID: PMC8943813 DOI: 10.1016/j.bpj.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.
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Affiliation(s)
- Katharina Brandstetter
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tobias Ragoczy
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Steinek
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Toby Barnes
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gabriela Stumberger
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Schwach
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.
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10
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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11
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Lindsly S, Jia W, Chen H, Liu S, Ronquist S, Chen C, Wen X, Stansbury C, Dotson GA, Ryan C, Rehemtulla A, Omenn GS, Wicha M, Li SC, Muir L, Rajapakse I. Functional organization of the maternal and paternal human 4D Nucleome. iScience 2021; 24:103452. [PMID: 34877507 PMCID: PMC8633971 DOI: 10.1016/j.isci.2021.103452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/16/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022] Open
Abstract
Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data from a B lymphoblastoid cell line, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.
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Affiliation(s)
- Stephen Lindsly
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenlong Jia
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Haiming Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sijia Liu
- MIT-IBM Watson AI Lab, IBM Research, Cambridge, MA 02142, USA
| | - Scott Ronquist
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Can Chen
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xingzhao Wen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Cooper Stansbury
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabrielle A. Dotson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles Ryan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max Wicha
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Lindsey Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
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12
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Zhang X, Wang T. Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years. PLANT & CELL PHYSIOLOGY 2021; 62:1648-1661. [PMID: 34486654 PMCID: PMC8664644 DOI: 10.1093/pcp/pcab134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 05/05/2023]
Abstract
Over the past few decades, eukaryotic linear genomes and epigenomes have been widely and extensively studied for understanding gene expression regulation. More recently, the three-dimensional (3D) chromatin organization was found to be important for determining genome functionality, finely tuning physiological processes for appropriate cellular responses. With the development of visualization techniques and chromatin conformation capture (3C)-based techniques, increasing evidence indicates that chromosomal architecture characteristics and chromatin domains with different epigenetic modifications in the nucleus are correlated with transcriptional activities. Subsequent studies have further explored the intricate interplay between 3D genome organization and the function of interacting regions. In this review, we summarize spatial distribution patterns of chromatin, including chromatin positioning, configurations and domains, with a particular focus on the effect of a unique form of interaction between varieties of factors that shape the 3D genome conformation in plants. We further discuss the methods, advantages and limitations of various 3C-based techniques, highlighting the applications of these technologies in plants to identify chromatin domains, and address their dynamic changes and functional implications in evolution, and adaptation to development and changing environmental conditions. Moreover, the future implications and emerging research directions of 3D genome organization are discussed.
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Affiliation(s)
- Xinxin Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, P. R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100093, P. R. China
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13
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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14
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Mohanta TK, Mishra AK, Al-Harrasi A. The 3D Genome: From Structure to Function. Int J Mol Sci 2021; 22:11585. [PMID: 34769016 PMCID: PMC8584255 DOI: 10.3390/ijms222111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/09/2023] Open
Abstract
The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Korea; or
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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15
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Giannuzzi G, Logsdon GA, Chatron N, Miller DE, Reversat J, Munson KM, Hoekzema K, Bonnet-Dupeyron MN, Rollat-Farnier PA, Baker CA, Sanlaville D, Eichler EE, Schluth-Bolard C, Reymond A. Alpha satellite insertion close to an ancestral centromeric region. Mol Biol Evol 2021; 38:5576-5587. [PMID: 34464971 PMCID: PMC8662618 DOI: 10.1093/molbev/msab244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example, during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by fluorescent in situ hybridization a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by the lack of constriction and the absence of CENP-A binding. The insertion was associated with a 2.8-kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats and located ∼10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20–25 million years ago. Long-read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name “alpha satellite insertion.” It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.
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Affiliation(s)
- Giuliana Giannuzzi
- Department of Biosciences, University of Milan, Milan, Italy.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nicolas Chatron
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Service de génétique, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Julie Reversat
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Pierre-Antoine Rollat-Farnier
- Service de génétique, Hospices Civils de Lyon, Lyon, France.,Cellule Bioinformatique, Hospices Civils de Lyon, Lyon, France
| | - Carl A Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Damien Sanlaville
- Service de génétique, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Caroline Schluth-Bolard
- Service de génétique, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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16
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Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K, Rubtsov N. New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis. Cells 2021; 10:cells10071819. [PMID: 34359988 PMCID: PMC8305704 DOI: 10.3390/cells10071819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.
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Affiliation(s)
- Tatyana Karamysheva
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1332)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
| | | | - Marija Rajičić
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Alexey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Jelena Blagojević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Mladen Vujošević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Konstantin Orishchenko
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay Rubtsov
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
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17
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Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021; 17:e9653. [PMID: 34232558 PMCID: PMC8262488 DOI: 10.15252/msb.20209653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
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Affiliation(s)
- Liangqi Xie
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - Zhe Liu
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
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18
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Kudryavtseva N, Ermolaev A, Karlov G, Kirov I, Shigyo M, Sato S, Khrustaleva L. A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps. Int J Mol Sci 2021; 22:5860. [PMID: 34070753 PMCID: PMC8215642 DOI: 10.3390/ijms22115860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.
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Affiliation(s)
- Natalya Kudryavtseva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Kurchatov Genomics Center of ARRIAB, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Masayoshi Shigyo
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan;
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Miyagi 980-8577, Japan;
| | - Ludmila Khrustaleva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
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19
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Hao X, Parmar JJ, Lelandais B, Aristov A, Ouyang W, Weber C, Zimmer C. Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures. Genome Biol 2021; 22:150. [PMID: 33975635 PMCID: PMC8111965 DOI: 10.1186/s13059-021-02343-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller "topologically associated" domains. These domains are often associated with chromatin loops, which largely disappear upon removal of cohesin. Because most Hi-C implementations average contact frequencies over millions of cells and do not provide direct spatial information, it remains unclear whether and how frequently chromatin domains and loops exist in single cells. RESULTS We combine 3D single-molecule localization microscopy with a low-cost fluorescence labeling strategy that does not denature the DNA, to visualize large portions of single human chromosomes in situ at high resolution. In parallel, we develop multi-scale, whole nucleus polymer simulations, that predict chromatin structures at scales ranging from 5 kb up to entire chromosomes. We image chromosomes in G1 and M phase and examine the effect of cohesin on interphase chromatin structure. Depletion of cohesin leads to increased prevalence of loose chromatin stretches, increased gyration radii, and reduced smoothness of imaged chromatin regions. By comparison to model predictions, we estimate that 6-25 or more purely cohesin-dependent chromatin loops coexist per megabase of DNA in single cells, suggesting that the vast majority of the genome is enclosed in loops. CONCLUSION Our results provide new constraints on chromatin structure and showcase an affordable non-invasive approach to study genome organization in single cells.
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Affiliation(s)
- Xian Hao
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
- School of Public Health & Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, 330006, China
| | - Jyotsana J Parmar
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
- Simons Center for the Study of Living Machines, National Center for Biological Sciences (TIFR), Bangalore, Karnataka, 560065, India
| | - Benoît Lelandais
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
| | - Andrey Aristov
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
| | - Wei Ouyang
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
- Université de Paris, F-75013, Paris, France
| | - Christian Weber
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France.
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20
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Hovenga V, Oluwadare O. CBCR: A Curriculum Based Strategy For Chromosome Reconstruction. Int J Mol Sci 2021; 22:ijms22084140. [PMID: 33923653 PMCID: PMC8073114 DOI: 10.3390/ijms22084140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
In this paper, we introduce a novel algorithm that aims to estimate chromosomes’ structure from their Hi-C contact data, called Curriculum Based Chromosome Reconstruction (CBCR). Specifically, our method performs this three dimensional reconstruction using cis-chromosomal interactions from Hi-C data. CBCR takes intra-chromosomal Hi-C interaction frequencies as an input and outputs a set of xyz coordinates that estimate the chromosome’s three dimensional structure in the form of a .pdb file. The algorithm relies on progressively training a distance-restraint-based algorithm with a strategy we refer to as curriculum learning. Curriculum learning divides the Hi-C data into classes based on contact frequency and progressively re-trains the distance-restraint algorithm based on the assumed importance of each curriculum in predicting the underlying chromosome structure. The distance-restraint algorithm relies on a modification of a Gaussian maximum likelihood function that scales probabilities based on the importance of features. We evaluate the performance of CBCR on both simulated and actual Hi-C data and perform validation on FISH, HiChIP, and ChIA-PET data as well. We also compare the performance of CBCR to several current methods. Our analysis shows that the use of curricula affects the rate of convergence of the optimization while decreasing the computational cost of our distance-restraint algorithm. Also, CBCR is more robust to increases in data resolution and therefore yields superior reconstruction accuracy of higher resolution data than all other methods in our comparison.
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Affiliation(s)
- Van Hovenga
- Department of Mathematics, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA;
| | - Oluwatosin Oluwadare
- Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
- Correspondence:
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21
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Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 2021; 16:1647-1713. [PMID: 33619390 PMCID: PMC8525907 DOI: 10.1038/s41596-020-00478-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.
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22
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Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science 2021; 371:eaay3446. [PMID: 33384301 PMCID: PMC7962746 DOI: 10.1126/science.aay3446] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/17/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.
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Affiliation(s)
- Andrew C Payne
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Zachary D Chiang
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paul L Reginato
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Evan M Murray
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | | | - Andrew S Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ajay S Labade
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
- Department of Biology, MIT, Cambridge, MA 02139, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Edward S Boyden
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute, MIT, Cambridge, MA 02139, USA
- Koch Institute, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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23
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Zawalski B, Tuszyńska I, Wilczyński B. QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models. Methods 2020; 181-182:80-85. [PMID: 31445092 DOI: 10.1016/j.ymeth.2019.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/13/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022] Open
Abstract
Recent years have brought us great wealth of new types of experimental data on different aspects of chromatin state, from chromosome conformation assays, through super-resolution microscopic imaging to epigenetic modifications and lamina interaction assays. This rapid increase in data availability have motivated many novel approaches to 3D modeling of chromosomes, their conformations and dynamic behavior. Even though there are many tools already developed for molecular visualization in the field of structural bioinformatics, they are usually optimized for visualization of smaller molecules (like proteins) and much shorter trajectories. We have developed a novel approach to visualization of long trajectories of large polymers, typical in the field of chromatin modeling. Our software, called QChromosomeVisualizer (QCV), allows for quick visualization of long simulations containing thousands or even millions of frames and generating good looking still images and animations including spherical 360 videos that can be viewed in VR headsets. We believe that this kind of tools will be helpful for the broader community of researchers interested in modeling by allowing them to create new and clearer ways to communicate their results.
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Affiliation(s)
- Bartłomiej Zawalski
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Irina Tuszyńska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Bartek Wilczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
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24
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Preparing Map of Chromosome Territory Distribution Frequency. Methods Mol Biol 2020. [PMID: 32820406 DOI: 10.1007/978-1-0716-0664-3_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]
Abstract
The chromosomes in mammalian interphase nuclei are organized into domains called chromosome territories that play a major role in nuclear organization. Here we propose a methodology that combines the use of micro-patterning of adhesive molecules to impose single-cell geometry, with visualization of chromosome territories. This allows obtaining a representative statistical map of the absolute positions of chromosome territories relative to the geometry imposed to the cell population by combining the signal from each cell.
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25
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Liu M, Lu Y, Yang B, Chen Y, Radda JSD, Hu M, Katz SG, Wang S. Multiplexed imaging of nucleome architectures in single cells of mammalian tissue. Nat Commun 2020; 11:2907. [PMID: 32518300 PMCID: PMC7283333 DOI: 10.1038/s41467-020-16732-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/19/2020] [Indexed: 01/13/2023] Open
Abstract
The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged in the same cell and how they are mutually correlated in different cell types in mammalian tissue are largely unknown. Here, we develop Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We apply this method in mouse fetal liver, and identify de novo cell-type-specific chromatin architectures associated with gene expression, as well as cell-type-independent principles of chromatin organization. Polymer simulation shows that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our results illustrate a multi-faceted picture and physical principles of chromatin organization. The three-dimensional architecture of the genome affects genomic functions. Here, the authors developed Multiplexed Imaging of Nucleome Architectures to measure multiscale chromatin folding, RNA profiles, and associations of numerous genomic regions with nuclear lamina and nucleoli in the same, single cells in heterogeneous tissue.
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Affiliation(s)
- Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Yanfang Lu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Bing Yang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Yanbo Chen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Jonathan S D Radda
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Mengwei Hu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Samuel G Katz
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA. .,Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, 06510, USA.
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26
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Role of the nuclear membrane protein Emerin in front-rear polarity of the nucleus. Nat Commun 2020; 11:2122. [PMID: 32358486 PMCID: PMC7195445 DOI: 10.1038/s41467-020-15910-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 04/02/2020] [Indexed: 12/03/2022] Open
Abstract
Cell polarity refers to the intrinsic asymmetry of cells, including the orientation of the cytoskeleton. It affects cell shape and structure as well as the distribution of proteins and organelles. In migratory cells, front-rear polarity is essential and dictates movement direction. While the link between the cytoskeleton and nucleus is well-studied, we aim to investigate if front-rear polarity can be transmitted to the nucleus. We show that the knock-down of emerin, an integral protein of the nuclear envelope, abolishes preferential localization of several nuclear proteins. We propose that the frontally biased localization of the endoplasmic reticulum, through which emerin reaches the nuclear envelope, is sufficient to generate its observed bias. In primary emerin-deficient myoblasts, its expression partially rescues the polarity of the nucleus. Our results demonstrate that front-rear cell polarity is transmitted to the nucleus and that emerin is an important determinant of nuclear polarity. During cell migration, cells are polarized with distinct front vs. rear regions but whether and how polarity is transmitted to the nucleus is unclear. Here the authors show that frontally-biased endoplasmic reticulum and the nuclear membrane protein Emerin contribute to front-rear nuclear cell polarity.
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27
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Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM. Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. Nat Commun 2020; 11:2120. [PMID: 32358536 PMCID: PMC7195386 DOI: 10.1038/s41467-020-15987-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.
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Affiliation(s)
- Paweł Trzaskoma
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA
| | - Katarzyna K Pels
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Katarzyna Krawczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Grzegorz Bokota
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Andrzej A Szczepankiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Jesse Aaron
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA
| | - Agnieszka Walczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 6 Uniwersytetu Poznanskiego St, 61-614, Poznan, Poland
| | - Małgorzata A Śliwińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Michal Kadlof
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Artur Wolny
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Zofia Parteka
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Sebastian Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Magdalena Kiss-Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Dariusz Plewczyński
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
- Mathematics and Information Science, Warsaw Technical University, 75 Koszykowa St, 00-662, Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA.
| | - Grzegorz M Wilczyński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland.
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28
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Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet 2020; 36:273-287. [PMID: 32007290 PMCID: PMC7197267 DOI: 10.1016/j.tig.2019.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.
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Affiliation(s)
- Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Sedona Murphy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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29
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Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2019; 21:207-226. [PMID: 31848476 DOI: 10.1038/s41576-019-0195-2] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.
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Affiliation(s)
- Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
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30
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Di Filippo L, Righelli D, Gagliardi M, Matarazzo MR, Angelini C. HiCeekR: A Novel Shiny App for Hi-C Data Analysis. Front Genet 2019; 10:1079. [PMID: 31749839 PMCID: PMC6844183 DOI: 10.3389/fgene.2019.01079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023] Open
Abstract
The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale. Although such a technique is quite recent, many tools are already available for pre-processing and analyzing Hi-C data, allowing to identify chromatin loops, topological associating domains and A/B compartments. However, only a few of them provide an exhaustive analysis pipeline or allow to easily integrate and visualize other omic layers. Moreover, most of the available tools are designed for expert users, who have great confidence with command-line applications. In this paper, we present HiCeekR (https://github.com/lucidif/HiCeekR), a novel R Graphical User Interface (GUI) that allows researchers to easily perform a complete Hi-C data analysis. With the aid of the Shiny libraries, it integrates several R/Bioconductor packages for Hi-C data analysis and visualization, guiding the user during the entire process. Here, we describe its architecture and functionalities, then illustrate its capabilities using a publicly available dataset.
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Affiliation(s)
- Lucio Di Filippo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Dario Righelli
- Istituto per le Applicazioni del Calcolo "Mauro Picone," Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Miriam Gagliardi
- Max Planck Institute for Psychiatry, Munich, Germany.,Institute of Genetics and Biophysics "A. Buzzati A. Traverso," Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Maria Rosaria Matarazzo
- Institute of Genetics and Biophysics "A. Buzzati A. Traverso," Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo "Mauro Picone," Consiglio Nazionale delle Ricerche, Napoli, Italy
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31
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The Role of RNA Polymerase II Contiguity and Long-Range Interactions in the Regulation of Gene Expression in Human Pluripotent Stem Cells. Stem Cells Int 2019; 2019:1375807. [PMID: 30863449 PMCID: PMC6378007 DOI: 10.1155/2019/1375807] [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: 08/06/2018] [Revised: 12/05/2018] [Accepted: 12/24/2018] [Indexed: 12/02/2022] Open
Abstract
The eukaryotic nucleus is a highly complex structure that carries out multiple functions primarily needed for gene expression, and among them, transcription seems to be the most fundamental. Diverse approaches have demonstrated that transcription takes place at discrete sites known as transcription factories, wherein RNA polymerase II (RNAP II) is attached to the factory and immobilized while transcribing DNA. It has been proposed that transcription factories promote chromatin loop formation, creating long-range interactions in which relatively distant genes can be transcribed simultaneously. In this study, we examined long-range interactions between the POU5F1 gene and genes previously identified as being POU5F1 enhancer-interacting, namely, CDYL, TLE2, RARG, and MSX1 (all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene, RUNX1 was used, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions between POU5F1 and the selected genes change with the onset of differentiation and upon RNAP II inhibition, we performed three-dimensional fluorescence in situ hybridization (3D-FISH) followed by computational simulation analysis. Our analysis showed that the numbers of long-range interactions between specific genes decrease during differentiation, suggesting that the transcription of monitored genes is associated with pluripotency. In addition, we showed that upon inhibition of RNAP II, long-range associations do not disintegrate and remain constant. We also analyzed the distance distributions of these genes in the context of their positions in the nucleus and revealed that they tend to have similar patterns resembling normal distribution. Furthermore, we compared data created in vitro and in silico to assess the biological relevance of our results.
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32
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Walen KH. Genomic Instability in Cancer II: 4N-Skewed (90°) Reductive Division via Fragile Sites to Fitness Increase for Solid and Hematological Cancer Beginnings. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/jct.2019.107045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet 2018; 14:e1007872. [PMID: 30586358 PMCID: PMC6324821 DOI: 10.1371/journal.pgen.1007872] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
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MESH Headings
- Cells, Cultured
- Chromosome Painting/methods
- Chromosome Structures/chemistry
- Chromosome Structures/genetics
- Chromosome Structures/ultrastructure
- Chromosome Walking/methods
- Chromosomes, Human, Pair 19/chemistry
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/ultrastructure
- Female
- Fluorescent Dyes
- Humans
- Imaging, Three-Dimensional
- In Situ Hybridization, Fluorescence/methods
- Male
- Models, Genetic
- Oligonucleotide Probes
- Pedigree
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Affiliation(s)
- Guy Nir
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cynthia Pérez Estrada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Carl G. Ebeling
- Bruker Nano Inc., Salt Lake City, Utah, United States of America
| | - Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Hiroshi M. Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nuno M. C. Martins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huy Q. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sheikh Russell
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Neva C. Durand
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Suhas S. P. Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paula Soler-Vila
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | | | | | - Jeff A. Stuckey
- Bruker Nano Inc., Middleton, Wisconsin, United States of America
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
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Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 2018; 362:eaau1783. [PMID: 30361340 PMCID: PMC6535145 DOI: 10.1126/science.aau1783] [Citation(s) in RCA: 532] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/04/2018] [Indexed: 12/15/2022]
Abstract
The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.
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Affiliation(s)
- Bogdan Bintu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Leslie J Mateo
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Jun-Han Su
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | | | - Mirae Parker
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Seon Kinrot
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Kei Yamaya
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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35
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Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nat Commun 2018; 9:3849. [PMID: 30242161 PMCID: PMC6155075 DOI: 10.1038/s41467-018-06248-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/24/2018] [Indexed: 11/08/2022] Open
Abstract
Self-interacting chromatin domains encompass genes and their cis-regulatory elements; however, the three-dimensional form a domain takes, whether this relies on enhancer-promoter interactions, and the processes necessary to mediate the formation and maintenance of such domains, remain unclear. To examine these questions, here we use a combination of high-resolution chromosome conformation capture, a non-denaturing form of fluorescence in situ hybridisation and super-resolution imaging to study a 70 kb domain encompassing the mouse α-globin regulatory locus. We show that this region forms an erythroid-specific, decompacted, self-interacting domain, delimited by frequently apposed CTCF/cohesin binding sites early in terminal erythroid differentiation, and does not require transcriptional elongation for maintenance of the domain structure. Formation of this domain does not rely on interactions between the α-globin genes and their major enhancers, suggesting a transcription-independent mechanism for establishment of the domain. However, absence of the major enhancers does alter internal domain interactions. Formation of a loop domain therefore appears to be a mechanistic process that occurs irrespective of the specific interactions within.
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Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Nigel A Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Izabela Szczerbal
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK.
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Tian X, Wang Y, Liu Y, Yin J, Chen D, Ke X, Ma W. Comparison of spatial chromosomal organization between bone marrow and peripheral blood in acute myeloid leukemia. Oncol Lett 2018; 16:4656-4662. [PMID: 30214600 DOI: 10.3892/ol.2018.9228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 07/20/2017] [Indexed: 11/05/2022] Open
Abstract
Acute myeloid leukemia associated with t(8;21)(q22;q22)/runt related transcription factor (RUNX)1-RUNX1 translocation partner 1 has been reported to exhibit a favorable outcome. The quantitative polymerase chain reaction is a reliable method for assessing minimal residual disease persistence, and peripheral blood (PB) samples are as informative as bone marrow (BM) samples during follow-up monitoring. However, few studies have compared the spatial organization of leukemia-specific chromosomes between BM and PB. In the present study, paired BM and PB samples were extracted from 6 patients with acute myeloid leukaemia-M2 and compared using three-dimensional fluorescence in situ hybridization. Cells were classified into three types: Normal, proximal and malignant. Comparisons of proportions (% of all cells) of different cell types revealed no significant difference between BM and PB samples. The relative radial positions (RRPs; d/R) of chromosomes 8 and 21 were consistent for 2/3 of BM and PB samples. The RRPs of chromosomes in proximal pairs were more interior in nuclei compared with chromosomes in normal pairs for BM and PB samples. The consistency of the spatial organization of chromosomes between BM and PB suggests that PB may be an alternative to BM for research and clinical diagnosis.
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Affiliation(s)
- Xueli Tian
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, P.R. China
| | - Yanfang Wang
- Department of Hematology, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Yu Liu
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, P.R. China
| | - Jun Yin
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, P.R. China
| | - Dieyan Chen
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, P.R. China
| | - Xiaoyan Ke
- Department of Hematology, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Wanyun Ma
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, P.R. China.,Collaborative Innovation Centre of Quantum Matter, Beijing 100084, P.R. China
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37
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Doğan ES, Liu C. Three-dimensional chromatin packing and positioning of plant genomes. NATURE PLANTS 2018; 4:521-529. [PMID: 30061747 DOI: 10.1038/s41477-018-0199-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Information and function of a genome are not only decorated with epigenetic marks in the linear DNA sequence but also in their non-random spatial organization in the nucleus. Recent research has revealed that three-dimensional (3D) chromatin organization is highly correlated with the functionality of the genome, contributing to many cellular processes. Driven by the improvements in chromatin conformation capture methods and visualization techniques, the past decade has been an exciting period for the study of plants' 3D genome structures, and our knowledge in this area has been substantially advanced. This Review describes our current understanding of plant chromatin organization and positioning beyond the nucleosomal level, and discusses future directions.
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Affiliation(s)
- Ezgi Süheyla Doğan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
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38
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Balajee AS, Sanders JT, Golloshi R, Shuryak I, McCord RP, Dainiak N. Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure. HEALTH PHYSICS 2018; 115:77-89. [PMID: 29787433 DOI: 10.1097/hp.0000000000000840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Higher-order organization of the human genome is well established with chromosomes occupying distinct domains or territories in the interphase nucleus. Spatial organization of chromosome territories in the interphase nucleus occurs in a cell-type-specific manner. Since both stable and unstable aberrations induced by ionizing radiation involve the exchange of material between two or more chromosomes, this study investigated the role of spatial organization of chromosome domains in ionizing-radiation-induced chromosome translocation events. Using multicolor fluorescence in situ hybridization, the study characterized the positioning of each human chromosome relative to its neighborhood territories in the interphase nucleus of lymphocytes and B-lymphoblastoid cells before ionizing radiation and compared this interphase positioning with the spectrum of exchanges observed after ionizing radiation in the metaphase chromosomes. In addition to multicolor fluorescence in situ hybridization, the genome-wide chromosome conformation capture technique (Hi-C) was also performed in mock and x-ray-irradiated human B-lymphoblastoid and fibroblast cells to characterize the interactions among chromosomes and to assess the genome reorganization changes, if any, after ionizing radiation exposure. On average, 35-50% of the total translocations induced by x rays and neutrons correlated with proximity of chromosome territories detected by multicolor fluorescence in situ hybridization in both lymphocytes and lymphoblastoid cells. The translocation rate observed in proximally positioned chromosome territories was consistently higher than distally located territories and was found to be statistically significant (p = 0.01) in human lymphoblastoid cells after x rays. The interchromosome interaction frequencies detected by Hi-C correlate fairly well with ionizing-radiation-induced translocations detected by multicolor fluorescence in situ hybridization, suggesting the importance of chromosome proximity effects in ionizing-radiation-induced chromosomal translocation events.
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Affiliation(s)
- Adayabalam S Balajee
- Radiation Emergency Assistance Center and Training Site, Cytogenetics Biodosimetry Laboratory, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37830
| | - Jacob T Sanders
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Rosela Golloshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Igor Shuryak
- Center for Radiological Research, Department of Radiation Oncology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Nicholas Dainiak
- Radiation Emergency Assistance Center and Training Site, Cytogenetics Biodosimetry Laboratory, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37830
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39
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Lomiento M, Mammoli F, Mazza EMC, Bicciato S, Ferrari S. Chromosome positioning in interphase nuclei of hematopoietic stem cell and myeloid precursor. Hematol Rep 2018; 10:7515. [PMID: 29721254 PMCID: PMC5907646 DOI: 10.4081/hr.2018.7515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
Human myelopoiesis is an intriguing biological process during which multipotent stem cells limit their differentiation potential generating precursors that evolve into terminally differentiated cells. The differentiation process is correlated with differential gene expression and changes in nuclear architecture. In interphase, chromosomes are distinct entities known as chromosome territories and they show a radial localization that could result in a constrain of inter-homologous distance. This element plays a role in genome stability and gene expression. Here, we provide the first experimental evidence of 3D chromosomal arrangement considering two steps of human normal myelopoiesis. Specifically, multicolor 3D-FISH and 3D image analysis revealed that, in both normal human hematopoietic stem cells and myelod precursors CD14-, chromosomal position is correlated with gene density. However, we observed that inter-homologue distances are totally different during differentiation. This could be associated with differential gene expression that we found comparing the two cell types. Our results disclose an unprecedented framework relevant for deciphering the genomic mechanisms at the base of normal human myelopoiesis.
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Affiliation(s)
- Mariana Lomiento
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabiana Mammoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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40
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Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc Natl Acad Sci U S A 2018; 115:E2183-E2192. [PMID: 29463736 PMCID: PMC5877937 DOI: 10.1073/pnas.1714530115] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications.
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Affiliation(s)
- Brian J Beliveau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115;
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Jocelyn Y Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115;
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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41
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Abstract
DNA fluorescence in situ hybridization (DNA FISH) has emerged as a powerful microscopy technique that allows a unique view into the composition and arrangement of the genetic material in its natural context-be it the cell nucleus in interphase, or chromosomes in metaphase spreads. The core principle of DNA FISH is the ability of fluorescently labeled DNA probes (either double- or single-stranded DNA fragments) to bind to their complementary sequences in situ in cells or tissues, revealing the location of their target as fluorescence signals detectable with a fluorescence microscope. Numerous variants and improvements of the original DNA FISH method as well as a vast repertoire of applications have been described since its inception more than 4 decades ago. In recent years, the development of many new fluorescent dyes together with drastic advancements in methods for probe generation (Boyle et al., Chromosome Res 19:901-909, 2011; Beliveau et al., Proc Natl Acad Sci U S A 109:21301-21306, 2012; Bienko et al., Nat Methods 10:122-124, 2012), as well as improvements in the resolution of microscopy technologies, have boosted the number of DNA FISH applications, particularly in the field of genome architecture (Markaki et al., Bioessays 34:412-426, 2012; Beliveau et al., Nat Commun 6:7147, 2015). However, despite these remarkable steps forward, choosing which type of DNA FISH sample preparation protocol, probe design, hybridization procedure, and detection method is best suited for a given application remains still challenging for many research labs, preventing a more widespread use of this powerful technology. Here, we present a comprehensive platform to help researchers choose which DNA FISH protocol is most suitable for their particular application. In addition, we describe computational pipelines that can be implemented for efficient DNA FISH probe design and for signal quantification. Our goal is to make DNA FISH a versatile and streamlined technique that can be easily implemented by both research and diagnostic labs.
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42
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Gudla PR, Nakayama K, Pegoraro G, Misteli T. SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:57-70. [PMID: 29183987 PMCID: PMC6350914 DOI: 10.1101/sqb.2017.82.033761] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA fluorescence in situ hybridization (FISH) is the technique of choice to map the position of genomic loci in three-dimensional (3D) space at the single allele level in the cell nucleus. High-throughput DNA FISH methods have recently been developed using complex libraries of fluorescently labeled synthetic oligonucleotides and automated fluorescence microscopy, enabling large-scale interrogation of genomic organization. Although the FISH signals generated by high-throughput methods can, in principle, be analyzed by traditional spot-detection algorithms, these approaches require user intervention to optimize each interrogated genomic locus, making analysis of tens or hundreds of genomic loci in a single experiment prohibitive. We report here the design and testing of two separate machine learning-based workflows for FISH signal detection in a high-throughput format. The two methods rely on random forest (RF) classification or convolutional neural networks (CNNs), respectively. Both workflows detect DNA FISH signals with high accuracy in three separate fluorescence microscopy channels for tens of independent genomic loci, without the need for manual parameter value setting on a per locus basis. In particular, the CNN workflow, which we named SpotLearn, is highly efficient and accurate in the detection of DNA FISH signals with low signal-to-noise ratio (SNR). We suggest that SpotLearn will be useful to accurately and robustly detect diverse DNA FISH signals in a high-throughput fashion, enabling the visualization and positioning of hundreds of genomic loci in a single experiment.
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Affiliation(s)
- Prabhakar R Gudla
- High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Koh Nakayama
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan 1138510
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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43
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Garcia A, Huang D, Righolt A, Righolt C, Kalaw MC, Mathur S, McAvoy E, Anderson J, Luedke A, Itorralba J, Mai S. Super-resolution structure of DNA significantly differs in buccal cells of controls and Alzheimer's patients. J Cell Physiol 2017; 232:2387-2395. [PMID: 27996096 PMCID: PMC5485033 DOI: 10.1002/jcp.25751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/01/2023]
Abstract
The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) versus age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM). Quantitation of the super-resolution DNA structure revealed that the nuclear super-resolution DNA structure of individuals with AD significantly differs from that of their controls (p < 0.05) with an overall increase in the measured DNA-free/poor spaces. This represents a significant increase in the interchromatin compartment. We also find that the DNA structure of AD significantly differs in mild, moderate, and severe disease with respect to the DNA-containing and DNA-free/poor spaces. We conclude that whole genome remodeling is a feature of buccal cells in AD.
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Affiliation(s)
- Angeles Garcia
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - David Huang
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Amanda Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Christiaan Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Maria Carmela Kalaw
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Shubha Mathur
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Elizabeth McAvoy
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - James Anderson
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Angela Luedke
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Justine Itorralba
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Sabine Mai
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
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44
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Karamysheva TV, Torgasheva AA, Yefremov YR, Bogomolov AG, Liehr T, Borodin PM, Rubtsov NB. Spatial organization of fibroblast and spermatocyte nuclei with different B-chromosome content in Korean field mouse, Apodemus peninsulae (Rodentia, Muridae). Genome 2017; 60:815-824. [PMID: 28732174 DOI: 10.1139/gen-2017-0029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Korean field mouse (Apodemus peninsulae) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying a different number of B chromosomes using laser scanning microscopy and 3D fluorescence in situ hybridization. We detected a co-localization of the B chromosomes with constitutive heterochromatin of the chromosomes of the basic set. We showed a non-random distribution of B chromosomes in the spermatocyte nuclei. Unpaired B chromosomes showed a tendency to occur in the compartment formed by the unpaired part of the XY bivalent.
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Affiliation(s)
- Tatyana V Karamysheva
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anna A Torgasheva
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yaroslav R Yefremov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G Bogomolov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Thomas Liehr
- c Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Pavel M Borodin
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay B Rubtsov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
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45
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Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates. Chromosome Res 2017; 25:261-276. [PMID: 28717965 DOI: 10.1007/s10577-017-9560-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 10/19/2022]
Abstract
Chromosomal rearrangements in humans are largely related to pathological conditions, and phenotypic effects are also linked to alterations in the expression profile following nuclear relocation of genes between functionally different compartments, generally occupying the periphery or the inner part of the cell nuclei. On the other hand, during evolution, chromosomal rearrangements may occur apparently without damaging phenotypic effects and are visible in currently phylogenetically related species. To increase our insight into chromosomal reorganisation in the cell nucleus, we analysed 18 chromosomal regions endowed with different genomic properties in cell lines derived from eight primate species covering the entire evolutionary tree. We show that homologous loci, in spite of their evolutionary relocation along the chromosomes, generally remain localised to the same functional compartment of the cell nuclei. We conclude that evolutionarily successful chromosomal rearrangements are those that leave the nuclear position of the regions involved unchanged. On the contrary, in pathological situations, the effect typically observed is on gene structure alteration or gene nuclear reposition. Moreover, our data indicate that new centromere formation could potentially occur everywhere in the chromosomes, but only those emerging in very GC-poor/gene-poor regions, generally located in the nuclear periphery, have a high probability of being retained through evolution. This suggests that, in the cell nucleus of related species, evolutionary chromosomal reshufflings or new centromere formation does not alter the functionality of the regions involved or the interactions between different loci, thus preserving the expression pattern of orthologous genes.
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46
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Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. eLife 2017; 6. [PMID: 28485713 PMCID: PMC5433842 DOI: 10.7554/elife.21660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/24/2017] [Indexed: 12/17/2022] Open
Abstract
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI:http://dx.doi.org/10.7554/eLife.21660.001
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Affiliation(s)
- Yanxiang Ni
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Bo Cao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tszshan Ma
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Gang Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,LemonData Biotech, Shenzhen, China.,Phil Rivers Technology, Beijing, China
| | - Yingdong Huo
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Danni Chen
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yi Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Bin Yu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Michael Q Zhang
- MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Dallas, United States
| | - Hanben Niu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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47
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Le Dily F, Serra F, Marti-Renom MA. 3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1308] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- François Le Dily
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Dr. Aiguader 88; Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
| | - François Serra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Dr. Aiguader 88; Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
- Structural Genomic Group, CNAG-CRG, Centre for Genomic Regulation (CRG); The Barcelona Institute of Science and Technology, Baldiri Reixac 4; Barcelona Spain
| | - Marc A. Marti-Renom
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Dr. Aiguader 88; Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
- Structural Genomic Group, CNAG-CRG, Centre for Genomic Regulation (CRG); The Barcelona Institute of Science and Technology, Baldiri Reixac 4; Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23; Barcelona Spain
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48
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Abstract
Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architecture. Although DNA FISH is commonly used for confirming 3C-based findings, the two techniques are conceptually and technically different and comparing their results is not trivial. Here, we discuss both 3C-based techniques and DNA FISH approaches to highlight their similarities and differences. We then describe the technical biases that affect each approach, and review the available reports that address their compatibility. Finally, we propose an experimental scheme for comparison of 3C and DNA FISH results.
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Affiliation(s)
- Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.
| | - Edith Heard
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex 05, France. .,Collège de France, Paris, 75005, France.
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49
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Kuzyk A, Gartner J, Mai S. Identification of Neuroblastoma Subgroups Based on Three-Dimensional Telomere Organization. Transl Oncol 2016; 9:348-56. [PMID: 27567959 PMCID: PMC5006808 DOI: 10.1016/j.tranon.2016.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022] Open
Abstract
Using 3D telomere quantitative fluorescence in situ hybridization, we determined the 3D telomere organization of 74 neuroblastoma tissue samples. Hierarchical cluster analysis of the measured telomere parameters identified three subgroups from our patient cohort. These subgroups have unique telomere profiles based on telomere length and nuclear architecture. Subgroups with higher levels of telomere dysfunction were comprised of tumors with greater numbers of telomeres, telomeric aggregates, and short telomeres (P<.0001). Tumors with greater telomere dysfunction were associated with unfavorable tumor characteristics (greater age at diagnosis, unfavorable histology, higher stage of disease, MYCN amplification, and higher MYCN expression) and poor prognostic risk (P<.001). Subgroups with greater telomere dysfunction also had higher intratumor heterogeneity. MYCN overexpression in two neuroblastoma cell lines with constitutively low MYCN expression induced changes in their telomere profile that were consistent with increased telomere dysfunction; this illustrates a functional relationship between MYCN and 3D telomere organization. This study demonstrates the ability to classify neuroblastomas based on the level of telomere dysfunction, which is a novel approach for this cancer.
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Affiliation(s)
- Alexandra Kuzyk
- Manitoba Institute of Cell Biology/The Research Institute of Oncology and Hematology, Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John Gartner
- Departments of Pathology and Immunology, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sabine Mai
- Manitoba Institute of Cell Biology/The Research Institute of Oncology and Hematology, Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
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50
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Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X. Spatial organization of chromatin domains and compartments in single chromosomes. Science 2016; 353:598-602. [PMID: 27445307 DOI: 10.1126/science.aaf8084] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 07/12/2016] [Indexed: 12/13/2022]
Abstract
The spatial organization of chromatin critically affects genome function. Recent chromosome-conformation-capture studies have revealed topologically associating domains (TADs) as a conserved feature of chromatin organization, but how TADs are spatially organized in individual chromosomes remains unknown. Here, we developed an imaging method for mapping the spatial positions of numerous genomic regions along individual chromosomes and traced the positions of TADs in human interphase autosomes and X chromosomes. We observed that chromosome folding deviates from the ideal fractal-globule model at large length scales and that TADs are largely organized into two compartments spatially arranged in a polarized manner in individual chromosomes. Active and inactive X chromosomes adopt different folding and compartmentalization configurations. These results suggest that the spatial organization of chromatin domains can change in response to regulation.
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Affiliation(s)
- Siyuan Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jun-Han Su
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Brian J Beliveau
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bogdan Bintu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey R Moffitt
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chao-ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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