1
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Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [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: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
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Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
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2
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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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3
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Fleming M, Nelson F, Wallace I, Eskiw CH. Genome Tectonics: Linking Dynamic Genome Organization with Cellular Nutrients. Lifestyle Genom 2022; 16:21-34. [PMID: 36446341 DOI: 10.1159/000528011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/06/2022] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Our daily intake of food provides nutrients for the maintenance of health, growth, and development. The field of nutrigenomics aims to link dietary intake/nutrients to changes in epigenetic status and gene expression. SUMMARY Although the relationship between our diet and our genes in under intense investigation, there is still a significant aspect of our genome that has received little attention with regard to this. In the past 15 years, the importance of genome organization has become increasingly evident, with research identifying small-scale local changes to large segments of the genome dynamically repositioning within the nucleus in response to/or mediating change in gene expression. The discovery of these dynamic processes and organization maybe as significant as dynamic plate tectonics is to geology, there is little information tying genome organization to specific nutrients or dietary intake. KEY MESSAGES Here, we detail key principles of genome organization and structure, with emphasis on genome folding and organization, and link how these contribute to our future understand of nutrigenomics.
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Affiliation(s)
- Morgan Fleming
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fina Nelson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- 21st Street Brewery Inc., Saskatoon, Saskatchewan, Canada
| | - Iain Wallace
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Proxima Research and Development, Saskatoon, Saskatchewan, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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4
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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5
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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6
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de Castro IJ, Toner B, Xie SQ, Swingland J, Hodges A, Tabrizi SJ, Turkheimer F, Pombo A, Khalil A. Altered nuclear architecture in blood cells from Huntington's disease patients. Neurol Sci 2021; 43:379-385. [PMID: 33974169 DOI: 10.1007/s10072-021-05289-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.
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Affiliation(s)
- Inês J de Castro
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK. .,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany. .,Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, Im Neuenheimer Feld 344, Heidelberg, 69120, Germany.
| | - Brian Toner
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Sheila Q Xie
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Chromatin and Development Group, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - James Swingland
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,GRIP AI, London, EC2A 3AZ, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Sarah J Tabrizi
- UCL Institute of Neurology, Box 104, National Hospital for Neurology and Neurosurgery Queen Square, University College London, London, WC1N 3BG, UK
| | - Federico Turkheimer
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Huntington's Disease Centre, Department of Neurodegenerative Disease, University College London (UCL) Queen Square Institute of Neurology and the UK Dementia Research Institute, UCL, London, UK
| | - Ana Pombo
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - André Khalil
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA.
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7
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Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Nat Struct Mol Biol 2020; 27:1105-1114. [PMID: 32929283 PMCID: PMC7718335 DOI: 10.1038/s41594-020-0506-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/13/2020] [Indexed: 11/08/2022]
Abstract
During interphase the eukaryotic genome is organized into chromosome territories that are spatially segregated into compartment domains. The extent to which interacting domains or chromosomes are entangled is not known. We analyze series of co-occurring chromatin interactions using multi-contact 3C (MC-3C) in human cells to provide insights into the topological entanglement of chromatin. Multi-contact interactions represent percolation paths (C-walks) through 3D chromatin space. We find that the order of interactions within C-walks that occur across interfaces where chromosomes or compartment domains interact is not random. Polymer simulations show that such C-walks are consistent with distal domains being topologically insulated, i.e. not catenated. Simulations show that even low levels of random strand passage, e.g. by topoisomerase II, would result in entanglements, increased mixing at domain interfaces and an order of interactions within C-walks not consistent with experimental MC-3C data. Our results indicate that during interphase entanglements between chromosomes and chromosomal domains are rare.
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8
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Chiang M, Michieletto D, Brackley CA, Rattanavirotkul N, Mohammed H, Marenduzzo D, Chandra T. Polymer Modeling Predicts Chromosome Reorganization in Senescence. Cell Rep 2020; 28:3212-3223.e6. [PMID: 31533042 PMCID: PMC6859504 DOI: 10.1016/j.celrep.2019.08.045] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/10/2019] [Accepted: 08/13/2019] [Indexed: 12/13/2022] Open
Abstract
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy, and mass spectrometry to dissect the roles played by heterochromatin- and lamina-mediated interactions in nuclear organization. Our model explains the conventional organization of heterochromatin and euchromatin in growing cells and the pathological organization found in oncogene-induced senescence and progeria. We show that the experimentally observed changes in the locality of contacts in senescent and progeroid cells can be explained as arising due to phase transitions in the system. Within our simulations, LADs are highly stochastic, as in experiments. Our model suggests that, once established, the senescent phenotype should be metastable even if lamina-mediated interactions were reinstated. Overall, our simulations uncover a generic physical mechanism that can regulate heterochromatin segregation and LAD formation in a wide range of mammalian nuclei.
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Affiliation(s)
- Michael Chiang
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Centre for Mathematical Biology, and Department of Mathematical Sciences, University of Bath, North Road, Bath BA2 7AY, UK
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Nattaphong Rattanavirotkul
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Tamir Chandra
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK.
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9
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Crosetto N, Bienko M. Radial Organization in the Mammalian Nucleus. Front Genet 2020; 11:33. [PMID: 32117447 PMCID: PMC7028756 DOI: 10.3389/fgene.2020.00033] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, most of the genetic material is contained within a highly specialized organelle-the nucleus. A large body of evidence indicates that, within the nucleus, chromatinized DNA is spatially organized at multiple length scales. The higher-order organization of chromatin is crucial for proper execution of multiple genome functions, including DNA replication and transcription. Here, we review our current knowledge on the spatial organization of chromatin in the nucleus of mammalian cells, focusing in particular on how chromatin is radially arranged with respect to the nuclear lamina. We then discuss the possible mechanisms by which the radial organization of chromatin in the cell nucleus is established. Lastly, we propose a unifying model of nuclear spatial organization, and suggest novel approaches to test it.
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Affiliation(s)
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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10
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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: 297] [Impact Index Per Article: 59.4] [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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11
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Belak ZR, Pickering JA, Gillespie ZE, Audette G, Eramian M, Mitchell JA, Bridger JM, Kusalik A, Eskiw CH. Genes responsive to rapamycin and serum deprivation are clustered on chromosomes and undergo reorganization within local chromatin environments. Biochem Cell Biol 2019; 98:178-190. [PMID: 31479623 DOI: 10.1139/bcb-2019-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We previously demonstrated that genome reorganization, through chromosome territory repositioning, occurs concurrently with significant changes in gene expression in normal primary human fibroblasts treated with the drug rapamycin, or stimulated into quiescence. Although these events occurred concomitantly, it is unclear how specific changes in gene expression relate to reorganization of the genome at higher resolution. We used computational analyses, genome organization assays, and microscopy, to investigate the relationship between chromosome territory positioning and gene expression. We determined that despite relocation of chromosome territories, there was no substantial bias in the proportion of genes changing expression on any one chromosome, including chromosomes 10 and 18. Computational analyses identified that clusters of serum deprivation and rapamycin-responsive genes along the linear extent of chromosomes. Chromosome conformation capture (3C) analysis demonstrated the strengthening or loss of specific long-range chromatin interactions in response to rapamycin and quiescence induction, including a cluster of genes containing Interleukin-8 and several chemokine genes on chromosome 4. We further observed that the LIF gene, which is highly induced upon rapamycin treatment, strengthened interactions with up- and down-stream intergenic regions. Our findings indicate that the repositioning of chromosome territories in response to cell stimuli, this does not reflect gene expression changes occurring within physically clustered groups of genes.
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Affiliation(s)
- Zachery R Belak
- Department of Food and Bioproduct Sciences, University of Saskatchewan, SK S7N 5A8, Canada
| | - Joshua A Pickering
- Department of Biochemistry, University of Saskatchewan, SK S7N 5E5, Canada
| | - Zoe E Gillespie
- Department of Biochemistry, University of Saskatchewan, SK S7N 5E5, Canada
| | - Gerald Audette
- Department of Chemistry, York University, ON M3J 1P3, Canada
| | - Mark Eramian
- Department of Computer Science, University of Saskatchewan, SK S7N 5C9, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3G5, Canada
| | - Joanna M Bridger
- Department of Life Sciences, Brunel University, Uxbridge, UB8 3PH, UK
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, SK S7N 5C9, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, SK S7N 5A8, Canada.,Department of Biochemistry, University of Saskatchewan, SK S7N 5E5, Canada
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12
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Szczepińska T, Rusek AM, Plewczynski D. Intermingling of chromosome territories. Genes Chromosomes Cancer 2019; 58:500-506. [DOI: 10.1002/gcc.22736] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 02/01/2023] Open
Affiliation(s)
| | - Anna Maria Rusek
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Clinical Molecular Biology DepartmentMedical University of Bialystok Bialystok Poland
| | - Dariusz Plewczynski
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Faculty of Mathematics and Information ScienceWarsaw University of Technology Warsaw Poland
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13
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Tan L, Xing D, Chang CH, Li H, Xie XS. Three-dimensional genome structures of single diploid human cells. Science 2018; 361:924-928. [PMID: 30166492 DOI: 10.1126/science.aat5641] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
Abstract
Three-dimensional genome structures play a key role in gene regulation and cell functions. Characterization of genome structures necessitates single-cell measurements. This has been achieved for haploid cells but has remained a challenge for diploid cells. We developed a single-cell chromatin conformation capture method, termed Dip-C, that combines a transposon-based whole-genome amplification method to detect many chromatin contacts, called META (multiplex end-tagging amplification), and an algorithm to impute the two chromosome haplotypes linked by each contact. We reconstructed the genome structures of single diploid human cells from a lymphoblastoid cell line and from primary blood cells with high spatial resolution, locating specific single-nucleotide and copy number variations in the nucleus. The two alleles of imprinted loci and the two X chromosomes were structurally different. Cells of different types displayed statistically distinct genome structures. Such structural cell typing is crucial for understanding cell functions.
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Affiliation(s)
- Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. .,Systems Biology Ph.D. Program, Harvard Medical School, Boston, MA 02115, USA
| | - Dong Xing
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Chi-Han Chang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. .,Innovation Center for Genomics, Peking University, Beijing 100871, China.,Biodynamic and Optical Imaging Center, Peking University, Beijing 100871, China
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14
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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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Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM). Nature 2017; 543:519-524. [PMID: 28273065 PMCID: PMC5366070 DOI: 10.1038/nature21411] [Citation(s) in RCA: 450] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. We developed a novel genome-wide method, Genome Architecture Mapping (GAM), for measuring chromatin contacts, and other features of three-dimensional chromatin topology, based on sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify an enrichment for specific interactions between active genes and enhancers across very large genomic distances, using a mathematical model ‘SLICE’ (Statistical Inference of Co-segregation). GAM also reveals an abundance of three-way contacts genome-wide, especially between regions that are highly transcribed or contain super-enhancers, highlighting a previously inaccessible complexity in genome architecture and a major role for gene-expression specific contacts in organizing the genome in mammalian nuclei.
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16
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Understanding Spatial Genome Organization: Methods and Insights. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:7-20. [PMID: 26876719 PMCID: PMC4792841 DOI: 10.1016/j.gpb.2016.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/20/2022]
Abstract
The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs) appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.
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17
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Ioannou D, Kandukuri L, Simpson JL, Tempest HG. Chromosome territory repositioning induced by PHA-activation of lymphocytes: A 2D and 3D appraisal. Mol Cytogenet 2015; 8:47. [PMID: 26146516 PMCID: PMC4490598 DOI: 10.1186/s13039-015-0146-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022] Open
Abstract
Background Genomes and by extension chromosome territories (CTs) in a variety of organisms exhibit nonrandom organization within interphase nuclei. CTs are susceptible to movement upon induction by a variety of stimuli, including: cell differentiation, growth factors, genotoxic agents, proliferating status, and stimulants that induce novel transcription profiles. These findings suggest nuclear architecture can undergo reorganization, providing support for a functional significance of CT organization. The effect of the initiation of transcription on global scale chromatin architecture has been underexplored. This study investigates the organization of all 24 human chromosomes in lymphocytes from two individuals in resting and phytohaemagglutinin activated lymphocytes using 2D and 3D approaches. Results The radial organization of CTs in lymphocytes in both resting and activated lymphocytes follows a gene-density pattern. However, CT organization in activated nuclei appears less constrained exhibiting a more random organization. We report differences in the spatial relationship between homologous and heterologous CTs in activated nuclei. In addition, a reproducible radial hierarchy of CTs was identified and evidence of a CT repositioning was observed in activated nuclei using both 2D and 3D approaches. Conclusions Alterations between resting and activated lymphocytes could be adaptation of CTs to the new transcription profile and possibly the formation of new neighborhoods of interest or interaction of CTs with nuclear landmarks. The increased distances between homologous and heterologous CTs in activated lymphocytes could be a reflection of a defensive mechanism to reduce potential interaction to prevent any structural chromosome abnormalities (e.g. translocations) as a result of DNA damage that increases during lymphocyte activation.
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Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Lakshmi Kandukuri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Present address Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR) Uppal Road, Hyderabad, 500 007 India
| | - Joe Leigh Simpson
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Helen Ghislaine Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199 USA
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18
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Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
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19
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Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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20
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Harewood L, Fraser P. The impact of chromosomal rearrangements on regulation of gene expression. Hum Mol Genet 2014; 23:R76-82. [PMID: 24907073 DOI: 10.1093/hmg/ddu278] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The effects that coding region single-nucleotide polymorphisms or mutations have on gene expression have been well documented, predominantly owing to their association with disease. The effects of structural chromosomal rearrangements are also receiving increasing attention with the development of new techniques that allow accurate, high-resolution data, whether genomic interaction or transcriptome data, to be generated right down to the single-cell level. Over the past 18 months, these advances in experimental techniques have been used to further confirm and delineate the substantial effects that chromosome rearrangements can have on the regulation of gene expression and provide evidence of direct links between the two.
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Affiliation(s)
- Louise Harewood
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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21
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Wood AM, Garza-Gongora AG, Kosak ST. A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:178-90. [PMID: 24412853 PMCID: PMC3954575 DOI: 10.1016/j.bbagrm.2014.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 01/14/2023]
Abstract
The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Ashley M Wood
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arturo G Garza-Gongora
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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22
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Moindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A. 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res 2012; 40:9470-81. [PMID: 22879376 PMCID: PMC3479194 DOI: 10.1093/nar/gks736] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts.
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Affiliation(s)
- Benoit Moindrot
- Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, CNRS, F-69007 Lyon, France
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23
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Gehlen LR, Gruenert G, Jones MB, Rodley CD, Langowski J, O'Sullivan JM. Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions. Nucleus 2012; 3:370-83. [PMID: 22688649 DOI: 10.4161/nucl.20971] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In recent years there has been considerable and growing interest in the 3-dimensional organization of genomes. In this manuscript we present an integrated computational-molecular study that produces an ensemble of high-resolution 3-dimensional conformations of the budding yeast genome. The compaction, folding and spatial organization of the chromosomes was based on empirical data determined using proximity-based ligation. Our models incorporate external constraints that allow the separation of gross organizational effects from those due to local interactions. Our models show that yeast chromosomes have preferred yet non-exclusive positions. They also identify interaction dependent clustering of tRNAs, early firing origins of replication, and Gal4 protein binding sites, yet the cluster composition is dynamic. Our results support a link between structure and transcription that occurs within the context of a flexible genome organization.
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Affiliation(s)
- Lutz R Gehlen
- Institute of Natural Sciences, Massey University, Auckland, New Zealand
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24
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25
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Innate structure of DNA foci restricts the mixing of DNA from different chromosome territories. PLoS One 2011; 6:e27527. [PMID: 22205925 PMCID: PMC3244381 DOI: 10.1371/journal.pone.0027527] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 10/19/2011] [Indexed: 01/15/2023] Open
Abstract
The distribution of chromatin within the mammalian nucleus is constrained by its organization into chromosome territories (CTs). However, recent studies have suggested that promiscuous intra- and inter-chromosomal interactions play fundamental roles in regulating chromatin function and so might define the spatial integrity of CTs. In order to test the extent of DNA mixing between CTs, DNA foci of individual CTs were labeled in living cells following incorporation of Alexa-488 and Cy-3 conjugated replication precursor analogues during consecutive cell cycles. Uniquely labeled chromatin domains, resolved following random mitotic segregation, were visualized as discrete structures with defined borders. At the level of resolution analysed, evidence for mixing of chromatin from adjacent domains was only apparent within the surface volumes where neighboring CTs touched. However, while less than 1% of the nuclear volume represented domains of inter-chromosomal mixing, the dynamic plasticity of DNA foci within individual CTs allows continual transformation of CT structure so that different domains of chromatin mixing evolve over time. Notably, chromatin mixing at the boundaries of adjacent CTs had little impact on the innate structural properties of DNA foci. However, when TSA was used to alter the extent of histone acetylation changes in chromatin correlated with increased chromatin mixing. We propose that DNA foci maintain a structural integrity that restricts widespread mixing of DNA and discuss how the potential to dynamically remodel genome organization might alter during cell differentiation.
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26
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Abstract
The visualization of cellular structures and components has become an invaluable tool in biological and medical sciences. Imaging subcellular compartments and single molecules within a cell has prompted the development of a wide range of sample preparation techniques as well as various microscope devices to obtain images with increased spatial resolution. Here, we present cryoFISH, a method for fluorescence in situ hybridization (FISH) on thin ( approximately 150 nm thick) cryosections from sucrose-embedded fixed cells or tissues. CryoFISH can be used in combination with immunodetection (IF) of other cellular components. The main advantages of cryoFISH and cryoIF over whole-cell labeling methods are increased spatial resolution with confocal microscopy, greater sensitivity of detection due to increased probe accessibility, and better image contrast. CryoFISH and cryoIF methods typically used on samples fixed in conditions that preserve ultrastructure, are compatible with the labeling of cells in their tissue context and are ideal for correlative studies that compare fluorescence with electron microscopy.
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27
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Knight M, Ittiprasert W, Odoemelam EC, Adema CM, Miller A, Raghavan N, Bridger JM. Non-random organization of the Biomphalaria glabrata genome in interphase Bge cells and the spatial repositioning of activated genes in cells co-cultured with Schistosoma mansoni. Int J Parasitol 2010; 41:61-70. [PMID: 20849859 DOI: 10.1016/j.ijpara.2010.07.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 11/29/2022]
Abstract
Biomphalaria glabrata is a major intermediate host for the parasitic trematode Schistosoma mansoni, a causative agent of human schistosomiasis. To decipher the molecular basis of this host-parasite interaction, the Bge embryonic cell line provides a unique in vitro model system to assess whether interactions between the snail and parasite affect the cell and genome biology in either organism. The organization of the B. glabrata genome in Bge cells was studied using image analysis through positioning territories of differently sized chromosomes within cell nuclei. The snail chromosome territories are similar in morphology as well as in non-random radial positioning as those found in other derived protostome and deuterostome organisms. Specific monitoring of four gene loci, piwi, BgPrx, actin and ferritin, revealed non-random radial positioning of the genome. This indicates that specific parts of the snail genome reside in reproducible nuclear addresses. To determine whether exposure to parasite is reflected in genome organization, the interphase spatial positioning of genes was assessed after co-culturing Bge cells with either normal or irradiation attenuated miracidia for 30 min to 24 h. The loci of actin and ferritin, genes that are up-regulated in the snail when subjected to infection, were visualized by fluorescence in situ hybridisation (FISH) and their radial nuclear positions i.e. their position in the interphase nucleus with respect to the nuclear edge/envelope, mapped. Interestingly, large scale gene repositioning correlated to temporal kinetics of gene expression levels in Bge cells co-cultured with normal miracidia while irradiated parasites failed to elicit similar gene expression or gene loci repositioning as demonstrated using the ferritin gene. This indicates that normal but not attenuated schistosomes provide stimuli that evoke host responses that are reflected in the host's nuclear architecture. We believe that this is not only the first time that gene-repositioning studies have been attempted in a mollusc but also demonstrates a parasite influencing the interphase genome organization of its host.
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Affiliation(s)
- Matty Knight
- Biomedical Research Institute, 12111 Parklawn Dr. Rockville, MD 20852, USA.
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28
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Abstract
Eukaryotic gene expression is an intricate multistep process, regulated within the cell nucleus through the activation or repression of RNA synthesis, processing, cytoplasmic export, and translation into protein. The major regulators of gene expression are chromatin remodeling and transcription machineries that are locally recruited to genes. However, enzymatic activities that act on genes are not ubiquitously distributed throughout the nucleoplasm, but limited to specific and spatially defined foci that promote preferred higher-order chromatin arrangements. The positioning of genes within the nuclear landscape relative to specific functional landmarks plays an important role in gene regulation and disease.
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Affiliation(s)
- Carmelo Ferrai
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London, United Kingdom
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29
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Laster K, Kosak ST. Genomic Pangea: coordinate gene regulation and cell-specific chromosomal topologies. Curr Opin Cell Biol 2010; 22:314-9. [PMID: 20547047 DOI: 10.1016/j.ceb.2010.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/22/2010] [Accepted: 04/23/2010] [Indexed: 01/09/2023]
Abstract
The eukaryotic nucleus is functionally organized. Gene loci, for example, often reveal altered localization patterns according to their developmental regulation. Whole chromosomes also demonstrate non-random nuclear positions, correlated with inherent characteristics such as gene density or size. Given that hundreds to thousands of genes are coordinately regulated in any given cell type, interest has grown in whether chromosomes may be specifically localized according to gene regulation. A synthesis of the evidence for preferential chromosomal organization suggests that, beyond basic characteristics, chromosomes can assume positions functionally related to gene expression. Moreover, analysis of total chromosome organization during cellular differentiation indicates that unique chromosome topologies, albeit probabilistic, in effect define a cell lineage. Future work with new techniques, including the advanced forms of the chromosome conformation capture (3C), and the development of next-generation whole-genome imaging approaches, will help to refine our view of chromosomal organization. We suggest that genomic organization during cellular differentiation should be viewed as a dynamic process, with gene expression patterns leading to chromosome associations that feed back on themselves, leading to the self-organization of the genome according to coordinate gene regulation.
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Affiliation(s)
- Kyle Laster
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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30
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Smith ZJ, Wang JCE, Quataert SA, Berger AJ. Integrated Raman and angular scattering microscopy reveals chemical and morphological differences between activated and nonactivated CD8+ T lymphocytes. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:036021. [PMID: 20615023 PMCID: PMC2903831 DOI: 10.1117/1.3443794] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 02/22/2010] [Accepted: 04/21/2010] [Indexed: 05/29/2023]
Abstract
Integrated Raman and angular-scattering microscopy (IRAM) is a multimodal platform capable of noninvasively probing both the chemistry and morphology of a single cell without prior labeling. Using this system, we are able to detect activation-dependent changes in the Raman and elastic-scattering signals from CD8+ T cells stimulated with either Staphylococcal enterotoxin B (SEB) or phorbol myristate acetate (PMA). In both cases, results obtained from the IRAM instrument correlate well with results obtained from traditional fluorescence-based flow cytometry for paired samples. SEB-mediated activation was distinguished from resting state in CD8+ T cells by an increase in the number and mean size of small ( approximately 500-nm) elastic scatterers as well as a decrease in Raman bands, indicating changes in nuclear content. PMA-mediated activation induced a different profile in CD8+ T cells from SEB, showing a similar increase in small elastic scatterers but a different Raman change, with elevation of cellular protein and lipid bands. These results suggest the potential of this multimodal, label-free optical technique for studying processes in single cells.
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Affiliation(s)
- Zachary J Smith
- University of Rochester, The Institute of Optics, 275 Hutchison Road, Rochester, New York 14627, USA
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31
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Pathak R, Ramakumar A, Subramanian U, Prasanna PGS. Differential radio-sensitivities of human chromosomes 1 and 2 in one donor in interphase- and metaphase-spreads after 60Co gamma-irradiation. BMC MEDICAL PHYSICS 2009; 9:6. [PMID: 19531236 PMCID: PMC2704179 DOI: 10.1186/1756-6649-9-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 06/16/2009] [Indexed: 11/19/2022]
Abstract
Background Radiation-induced chromosome aberrations lead to a plethora of detrimental effects at cellular level. Chromosome aberrations provide broad spectrum of information ranging from probability of malignant transformation to assessment of absorbed dose. Studies mapping differences in radiation sensitivities between human chromosomes are seldom undertaken. Consequently, health risk assessment based on radio-sensitivities of individual chromosomes may be erroneous. Our efforts in this article, attempt to demonstrate differences in radio-sensitivities of human chromosome-1 and/or -2, both in interphase and metaphase spreads. Methods Upon blood collection, dosimetry and irradiation were performed. Lymphocytes were isolated after whole-blood irradiation with 60Co γ-rays in the dose range of 0–5 Gy for both interphase, and metaphase aberration studies. Induction of premature chromosome condensation in interphase cells was accomplished using a phosphatase inhibitor, calyculin-A. Metaphase spreads were harvested from short-term peripheral blood lymphocyte cultures following colcemid arrest and using an automated metaphase harvester and spreader. Aberration analysis in both interphase and metaphase spreads were done using FISH. Results In interphase, aberrant cell and aberration frequency involving chromosome 1 and/or 2 increased linearly with radiation dose. In metaphase, aberrations increased in a linear-quadratic manner with dose. Our studies ascertain that chromosome-2 is more radio-sensitive than chromosome-1 in both interphase and metaphase stages, albeit the DNA content of chromosome-2 is lesser than chromosome-1 by almost 10 million base pairs. Conclusion Differences in radio-sensitivities of chromosomes have implications in genetic damage, chromosome organization, and chromosome function. Designing research experiments based on our vital findings may bring benefit to radiation-induced risk assessment, therapeutics and development of chromosome specific biomarkers.
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Affiliation(s)
- Rupak Pathak
- Armed Forces Radiobiology Research Institute, Uniformed Services University of Health Sciences, 8901 Wisconsin Avenue, Bethesda, MD 20889-5603, USA.
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32
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Transcriptional competence of the integrated HIV-1 provirus at the nuclear periphery. EMBO J 2009; 28:2231-43. [PMID: 19478796 DOI: 10.1038/emboj.2009.141] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 04/29/2009] [Indexed: 11/08/2022] Open
Abstract
Spatial distribution of genes within the nucleus contributes to transcriptional control, allowing optimal gene expression as well as constitutive or regulated gene repression. Human immunodeficiency virus type 1 (HIV-1) integrates into host chromatin to transcribe and replicate its genome. Lymphocytes harbouring a quiescent but inducible provirus are a challenge to viral eradication in infected patients undergoing antiviral therapy. Therefore, our understanding of the contribution of sub-nuclear positioning to viral transcription may also have far-reaching implications in the pathology of the infection. To gain an insight into the conformation of chromatin at the site of HIV-1 integration, we investigated lymphocytes carrying a single latent provirus. In the silenced state, the provirus was consistently found at the nuclear periphery, associated in trans with a pericentromeric region of chromosome 12 in a significant number of quiescent cells. After induction of the transcription, this association was lost, although the location of the transcribing provirus remained peripheral. These results, extended to several other cell clones, unveil a novel mechanism of transcriptional silencing involved in HIV-1 post-transcriptional latency and reinforce the notion that gene transcription may also occur at the nuclear periphery.
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Babu MM, Janga SC, de Santiago I, Pombo A. Eukaryotic gene regulation in three dimensions and its impact on genome evolution. Curr Opin Genet Dev 2008; 18:571-82. [PMID: 19007886 DOI: 10.1016/j.gde.2008.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 10/07/2008] [Accepted: 10/09/2008] [Indexed: 12/11/2022]
Abstract
Recent advances in molecular techniques and high-resolution imaging are beginning to provide exciting insights into the higher order chromatin organization within the cell nucleus and its influence on eukaryotic gene regulation. This improved understanding of gene regulation also raises fundamental questions about how spatial features might have constrained the organization of genes on eukaryotic chromosomes and how mutations that affect these processes might contribute to disease conditions. In this review, we discuss recent studies that highlight the role of spatial components in gene regulation and their impact on genome evolution. We then address implications for human diseases and outline new directions for future research.
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Affiliation(s)
- M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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