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Raynal F, Sengupta K, Plewczynski D, Aliaga B, Pancaldi V. Global chromatin reorganization and regulation of genes of specific evolutionary age in differentiation and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564438. [PMID: 39149250 PMCID: PMC11326123 DOI: 10.1101/2023.10.30.564438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Oncogenesis is accompanied by chromatin organization alterations and reactivation of unicellular phenotypes at the metabolic and transcriptional level. The mechanisms connecting these two observations are unexplored, despite its relevance in cancer biology. Assigning evolutionary ages to genes in the context of 3D chromatin structure, we characterize the epigenomic landscape, expression regulation and spatial organization of genes according to their evolutionary ages. We describe topological changes across differentiation and find some of the patterns, involving Polycomb repression and RNA Pol II pausing, being reversed during oncogenesis. Going beyond the evidence of non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions of old, intermediate and young genes, mediated by respectively RNA Polymerase II, Polycomb and the lamina. Our results are in line and expand recent findings implicating loss of Polycomb repression and activation of embryonal and early evolutionary programs in cancer.
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Affiliation(s)
- Flavien Raynal
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Benoît Aliaga
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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2
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Min A, Schreiber J, Kundaje A, Noble WS. Predicting chromatin conformation contact maps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589240. [PMID: 38645064 PMCID: PMC11030330 DOI: 10.1101/2024.04.12.589240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin architecture. Accordingly, making sense of the relationship between genome structure and function requires teasing apart two closely related questions: how does chromatin 3D structure change from one cell type to the next, and how do different measurements of that structure differ from one another, even when the two assays are carried out in the same cell type? In this work, we assemble a collection of chromatin 3D datasets-each represented as a 2D contact map- spanning multiple assay types and cell types. We then build a machine learning model that predicts missing contact maps in this collection. We use the model to systematically explore how genome 3D architecture changes, at the level of compartments, domains, and loops, between cell type and between assay types.
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Affiliation(s)
- Alan Min
- Department of Statistics, University of Washington
| | | | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington
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3
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Chen Y, Guo J. Multiplexed Single-Cell in Situ Protein Profiling. ACS MEASUREMENT SCIENCE AU 2022; 2:296-303. [PMID: 35996537 PMCID: PMC9389644 DOI: 10.1021/acsmeasuresciau.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ability to profile a large number of different proteins in individual cells in their native cellular locations is critical to accelerate our understanding of normal cell physiology and disease pathogenesis. Bulk cell protein quantification masks the cell heterogeneity in complex biological systems, while conventional immunofluorescence or immunohistochemistry are limited by their low multiplexing capacity. Recent technological advances in multiplexed protein imaging approaches allow many distinct proteins to be analyzed in single cells in situ. These methods will bring new insights into various biological and biomedical fields, such as cell type and subtype classification, signaling network regulation, tissue architecture, and disease diagnosis and prognosis, along with treatment monitoring. In this Review, we will describe the recent advances of multiplexed single-cell in situ protein profiling technologies, discuss their unique advantages and limitations, highlight their applications in biology and medicine, present the current challenges, and propose potential solutions.
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Segueni J, Noordermeer D. CTCF: a misguided jack-of-all-trades in cancer cells. Comput Struct Biotechnol J 2022; 20:2685-2698. [PMID: 35685367 PMCID: PMC9166472 DOI: 10.1016/j.csbj.2022.05.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/13/2022] Open
Abstract
The emergence and progression of cancers is accompanied by a dysregulation of transcriptional programs. The three-dimensional (3D) organization of the human genome has emerged as an important multi-level mediator of gene transcription and regulation. In cancer cells, this organization can be restructured, providing a framework for the deregulation of gene activity. The CTCF protein, initially identified as the product from a tumor suppressor gene, is a jack-of-all-trades for the formation of 3D genome organization in normal cells. Here, we summarize how CTCF is involved in the multi-level organization of the human genome and we discuss emerging insights into how perturbed CTCF function and DNA binding causes the activation of oncogenes in cancer cells, mostly through a process of enhancer hijacking. Moreover, we highlight non-canonical functions of CTCF that can be relevant for the emergence of cancers as well. Finally, we provide guidelines for the computational identification of perturbed CTCF binding and reorganized 3D genome structure in cancer cells.
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5
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Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell 2022; 33:ar72. [PMID: 35476603 PMCID: PMC9635277 DOI: 10.1091/mbc.e21-11-0593] [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] [Indexed: 12/02/2022] Open
Abstract
Chromosome structure and nuclear organization are important factors in the regulation of gene expression. Transcription of a gene is influenced by local and global chromosome features such as chromatin condensation status. The relationship between the 3D position of a gene in the nucleus and its activity is less clear. Here we used high-throughput imaging to perform a large-scale analysis of the spatial location of nearly 100 hypoxia-responsive genes to determine whether their location and activity state are correlated. Radial distance analysis demonstrated that the majority of Hypoxia-Inducible Factor (HIF)- and CREB-dependent hypoxia-responsive genes are located in the intermediate region of the nucleus, and some of them changed their radial position in hypoxia. Analysis of the relative distances among a subset of HIF target genes revealed that some gene pairs altered their relative location to each other on hypoxic treatment, suggesting higher-order chromatin rearrangements. While these changes in location occurred in response to hypoxic activation of the target genes, they did not correlate with the extent of their activation. These results suggest that induction of the hypoxia-responsive gene expression program is accompanied by spatial alterations of the genome, but that radial and relative gene positions are not directly related to gene activity.
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Affiliation(s)
- Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan.,Department of Pharmacology, School of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Elizabeth H Finn
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Hiroyuki Sato
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akihiro Hirakawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tom Misteli
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
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6
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Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
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Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
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7
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet 2021; 108:269-283. [PMID: 33545030 PMCID: PMC7895846 DOI: 10.1016/j.ajhg.2021.01.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/29/2020] [Indexed: 12/22/2022] Open
Abstract
Topologically associating domains (TADs) are fundamental units of three-dimensional (3D) nuclear organization. The regions bordering TADs-TAD boundaries-contribute to the regulation of gene expression by restricting interactions of cis-regulatory sequences to their target genes. TAD and TAD-boundary disruption have been implicated in rare-disease pathogenesis; however, we have a limited framework for integrating TADs and their variation across cell types into the interpretation of common-trait-associated variants. Here, we investigate an attribute of 3D genome architecture-the stability of TAD boundaries across cell types-and demonstrate its relevance to understanding how genetic variation in TADs contributes to complex disease. By synthesizing TAD maps across 37 diverse cell types with 41 genome-wide association studies (GWASs), we investigate the differences in disease association and evolutionary pressure on variation in TADs versus TAD boundaries. We demonstrate that genetic variation in TAD boundaries contributes more to complex-trait heritability, especially for immunologic, hematologic, and metabolic traits. We also show that TAD boundaries are more evolutionarily constrained than TADs. Next, stratifying boundaries by their stability across cell types, we find substantial variation. Compared to boundaries unique to a specific cell type, boundaries stable across cell types are further enriched for complex-trait heritability, evolutionary constraint, CTCF binding, and housekeeping genes. Thus, considering TAD boundary stability across cell types provides valuable context for understanding the genome's functional landscape and enabling variant interpretation that takes 3D structure into account.
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Affiliation(s)
- Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158; Bakar Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158.
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9
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Kempf N, Moutahir F, Goiffon I, Cantaloube S, Bystricky K, Lavigne AC. Analysis of Cellular EMT States Using Molecular Biology and High Resolution FISH Labeling. Methods Mol Biol 2021; 2179:353-383. [PMID: 32939733 DOI: 10.1007/978-1-0716-0779-4_27] [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] [Indexed: 01/10/2023]
Abstract
Metastasis results from the ability of cancer cells to grow and to spread beyond the primary tumor to distant organs. Epithelial-to-Mesenchymal Transition (EMT), a fundamental developmental process, is reactivated in cancer cells, and causes epithelial properties to evolve into mesenchymal and invasive ones. EMT changes cellular characteristics between two distinct states, yet, the process is not binary but rather reflects a broad spectrum of partial EMT states in which cells exhibit various degrees of intermediate epithelial and mesenchymal phenotypes. EMT is a complex multistep process that involves cellular reprogramming through numerous signaling pathways, alterations in gene expression, and changes in chromatin morphology. Therefore, expression of key proteins, including cadherins, occludin, or vimentin must be precisely regulated. A comprehensive understanding of how changes in nuclear organization, at the level of single genes clusters, correlates with these processes during formation of metastatic cells is still missing and yet may help personalized prognosis and treatment in the clinic. Here, we describe methods to correlate physiological and molecular states of cells undergoing an EMT process with chromatin rearrangements observed via FISH labeling of specific domains.
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Affiliation(s)
- Noémie Kempf
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France
| | - Fatima Moutahir
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France
| | - Isabelle Goiffon
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France
| | - Sylvain Cantaloube
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France
| | - Kerstin Bystricky
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France
| | - Anne-Claire Lavigne
- Center for Integrative Biology (CBI), Laboratoire de Biologie Moléculaire des Eucaryotes (LBME), University of Toulouse, UPS, CNRS, F-31062 Toulouse, France.
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10
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Pham T, Tyagi A, Wang YS, Guo J. Single-cell proteomic analysis. WIREs Mech Dis 2020; 13:e1503. [PMID: 32748522 DOI: 10.1002/wsbm.1503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
The ability to comprehensively profile proteins in every individual cell of complex biological systems is crucial to advance our understanding of normal physiology and disease pathogenesis. Conventional bulk cell experiments mask the cell heterogeneity in the population, while the single-cell imaging methods suffer from the limited multiplexing capacities. Recent advances in microchip-, mass spectrometry-, and reiterative staining-based technologies have enabled comprehensive protein profiling in single cells. These approaches will bring new insights into a variety of biological and biomedical fields, such as signaling network regulation, cell heterogeneity, tissue architecture, disease diagnosis, and treatment monitoring. In this article, we will review the recent advances in the development of single-cell proteomic technologies, describe their advantages, discuss the current limitations and challenges, and propose potential solutions. We will also highlight the wide applications of these technologies in biology and medicine. This article is categorized under: Cancer > Molecular and Cellular Physiology.
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Affiliation(s)
- Thai Pham
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Ankush Tyagi
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Yu-Sheng Wang
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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Pradhan R, Nallappa MJ, Sengupta K. Lamin A/C modulates spatial organization and function of the Hsp70 gene locus via nuclear myosin I. J Cell Sci 2020; 133:jcs236265. [PMID: 31988151 DOI: 10.1242/jcs.236265] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
The structure-function relationship of the nucleus is tightly regulated, especially during heat shock. Typically, heat shock activates molecular chaperones that prevent protein misfolding and preserve genome integrity. However, the molecular mechanisms that regulate nuclear structure-function relationships during heat shock remain unclear. Here, we show that lamin A and C (hereafter lamin A/C; both lamin A and C are encoded by LMNA) are required for heat-shock-mediated transcriptional induction of the Hsp70 gene locus (HSPA genes). Interestingly, lamin A/C regulates redistribution of nuclear myosin I (NM1) into the nucleus upon heat shock, and depletion of either lamin A/C or NM1 abrogates heat-shock-induced repositioning of Hsp70 gene locus away from the nuclear envelope. Lamins and NM1 also regulate spatial positioning of the SC35 (also known as SRSF2) speckles - important nuclear landmarks that modulates Hsp70 gene locus expression upon heat shock. This suggests an intricate crosstalk between nuclear lamins, NM1 and SC35 organization in modulating transcriptional responses of the Hsp70 gene locus during heat shock. Taken together, this study unravels a novel role for lamin A/C in the regulation of the spatial dynamics and function of the Hsp70 gene locus upon heat shock, via the nuclear motor protein NM1.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Roopali Pradhan
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Muhunden Jayakrishnan Nallappa
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Kundan Sengupta
- Biology, Main Building, First Floor, Room B-216, Indian Institute of Science Education and Research (IISER), Pune 411008, India
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12
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Meaburn KJ, Misteli T. Assessment of the Utility of Gene Positioning Biomarkers in the Stratification of Prostate Cancers. Front Genet 2019; 10:1029. [PMID: 31681438 PMCID: PMC6812139 DOI: 10.3389/fgene.2019.01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
There is a pressing need for additional clinical biomarkers to predict the aggressiveness of individual cancers. Here, we examine the potential usefulness of spatial genome organization as a prognostic tool for prostate cancer. Using fluorescence in situ hybridization on formalin-fixed, paraffin embedded human prostate tissue specimens, we compared the nuclear positions of four genes between clinically relevant subgroups of prostate tissues. We find that directional repositioning of SP100 and TGFB3 gene loci stratifies prostate cancers of differing Gleason scores. A more peripheral position of SP100 and TGFB3 in the nucleus, compared to benign tissues, is associated with low Gleason score cancers, whereas more internal positioning correlates with higher Gleason scores. Conversely, LMNA is more internally positioned in many non-metastatic prostate cancers, while its position is indistinguishable from benign tissue in metastatic cancer. The false positive rates were relatively low, whereas, the false negative rates of single or combinations of genes were high, limiting the clinical utility of this assay in its current form. Nevertheless, our findings of subtype-specific gene positioning patterns in prostate cancer provides proof-of-concept for the potential usefulness of spatial gene positioning for prognostic applications, and encourage further exploration of spatial gene positioning patterns to identify novel clinically relevant molecular biomarkers, which may aid treatment decisions for cancer patients.
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Affiliation(s)
- Karen J Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
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13
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Sauerwald N, Singhal A, Kingsford C. Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR Genom Bioinform 2019; 2. [PMID: 31687663 PMCID: PMC6824515 DOI: 10.1093/nargab/lqz008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Akshat Singhal
- Department of Computer Science, Stony Brook University, Stony Brook, NY 11790, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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14
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Wang YXR, Sarkar P, Ursu O, Kundaje A, Bickel PJ. NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA. Ann Appl Stat 2019; 13:1511-1536. [PMID: 32968472 PMCID: PMC7508461 DOI: 10.1214/19-aoas1244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. One specific feature of the 3D organization is known as topologically associating domains (TADs), which are densely interacting, contiguous chromatin regions playing important roles in regulating gene expression. A few algorithms have been proposed to detect TADs. In particular, the structure of Hi-C data naturally inspires application of community detection methods. However, one of the drawbacks of community detection is that most methods take exchangeability of the nodes in the network for granted; whereas the nodes in this case, that is, the positions on the chromosomes, are not exchangeable. We propose a network model for detecting TADs using Hi-C data that takes into account this nonexchangeability. in addition, our model explicitly makes use of cell-type specific CTCF binding sites as biological covariates and can be used to identify conserved TADs across multiple cell types. The model leads to a likelihood objective that can be efficiently optimized via relaxation. We also prove that when suitably initialized, this model finds the underlying TAD structure with high probability. using simulated data, we show the advantages of our method and the caveats of popular community detection methods, such as spectral clustering, in this application. Applying our method to real Hi-C data, we demonstrate the domains identified have desirable epigenetic features and compare them across different cell types.
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15
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Sauerwald N, Kingsford C. Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics 2019; 34:i475-i483. [PMID: 29949963 PMCID: PMC6022623 DOI: 10.1093/bioinformatics/bty265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Motivation Three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi-C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs. Results We present an analysis of 23 human Hi-C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome-level structural similarity, and compare the relative similarity between cancer and non-cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan-cancer genes than normal cells at these same locations. Availability and implementation Software for the methods and analysis can be found at https://github.com/Kingsford-Group/localtadsim
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- To whom correspondence should be addressed.
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16
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Damodaran K, Crestani M, Jokhun DS, Shivashankar GV. Nuclear morphometrics and chromatin condensation patterns as disease biomarkers using a mobile microscope. PLoS One 2019; 14:e0218757. [PMID: 31314779 PMCID: PMC6636717 DOI: 10.1371/journal.pone.0218757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/08/2019] [Indexed: 12/26/2022] Open
Abstract
Current cancer diagnosis involves the use of nuclear morphology and chromatin condensation signatures for accurate advanced stage classification. While such diagnostic approaches rely on high resolution imaging of the cell nucleus using expensive microscopy systems, developing portable mobile microscopes to visualize nuclear and chromatin condensation patterns is desirable at clinical settings with limited infrastructure. In this study, we develop a portable fluorescent mobile microscope capable of acquiring high resolution images of the nucleus and chromatin. Using this we extracted nuclear morphometric and chromatin texture based features and were able to discriminate between normal and cancer cells with similar accuracy as wide-field fluorescence microscopy. We were also able to detect subtle changes in nuclear and chromatin features in cells subjected to compressive forces, cytoskeletal perturbations and cytokine stimulation, thereby highlighting the sensitivity of the portable microscope. Taken together, we present a versatile platform to exploit nuclear morphometrics and chromatin condensation features as physical biomarkers for point-of-care diagnostic solutions.
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Affiliation(s)
- Karthik Damodaran
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Michele Crestani
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Doorgesh Sharma Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - G. V. Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular Oncology, Italian Foundation for Cancer Research, Milan, Italy
- * E-mail:
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17
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Gaillard MC, Broucqsault N, Morere J, Laberthonnière C, Dion C, Badja C, Roche S, Nguyen K, Magdinier F, Robin JD. Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy. Sci Rep 2019; 9:10327. [PMID: 31316120 PMCID: PMC6637155 DOI: 10.1038/s41598-019-46861-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Facio-Scapulo Humeral dystrophy (FSHD) is the third most common myopathy, affecting 1 amongst 10,000 individuals (FSHD1, OMIM #158900). This autosomal dominant pathology is associated in 95% of cases with genetic and epigenetic alterations in the subtelomeric region at the extremity of the long arm of chromosome 4 (q arm). A large proportion of the remaining 5% of cases carry a mutation in the SMCHD1 gene (FSHD2, OMIM #158901). Here, we explored the 3D organization of the 4q35 locus by three-dimensions DNA in situ fluorescent hybridization (3D-FISH) in primary fibroblasts isolated from patients and healthy donors. We found that D4Z4 contractions and/or SMCHD1 mutations impact the spatial organization of the 4q35 region and trigger changes in the expression of different genes. Changes in gene expression were corroborated in muscle biopsies suggesting that the modified chromatin landscape impelled a modulation in the level of expression of a number of genes across the 4q35 locus in FSHD. Using induced pluripotent stem cells (hIPSC), we further examined whether chromatin organization is inherited after reprogramming or acquired during differentiation and showed that folding of the 4q35 region is modified upon differentiation. These results together with previous findings highlight the role of the D4Z4 macrosatellite repeat in the topological organization of chromatin and further indicate that the D4Z4-dependent 3D structure induces transcriptional changes of 4q35 genes expression.
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Affiliation(s)
| | | | - Julia Morere
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | | | - Camille Dion
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Cherif Badja
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | | | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.
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18
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Krumm A, Duan Z. Understanding the 3D genome: Emerging impacts on human disease. Semin Cell Dev Biol 2019; 90:62-77. [PMID: 29990539 PMCID: PMC6329682 DOI: 10.1016/j.semcdb.2018.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
Recent burst of new technologies that allow for quantitatively delineating chromatin structure has greatly expanded our understanding of how the genome is organized in the three-dimensional (3D) space of the nucleus. It is now clear that the hierarchical organization of the eukaryotic genome critically impacts nuclear activities such as transcription, replication, as well as cellular and developmental events such as cell cycle, cell fate decision and embryonic development. In this review, we discuss new insights into how the structural features of the 3D genome hierarchy are established and maintained, how this hierarchy undergoes dynamic rearrangement during normal development and how its perturbation will lead to human disease, highlighting the accumulating evidence that links the diverse 3D genome architecture components to a multitude of human diseases and the emerging mechanisms by which 3D genome derangement causes disease phenotypes.
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Affiliation(s)
- Anton Krumm
- Department of Microbiology, University of Washington, USA.
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
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19
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Federico C, Owoka T, Ragusa D, Sturiale V, Caponnetto D, Leotta CG, Bruno F, Foster HA, Rigamonti S, Giudici G, Cazzaniga G, Bridger JM, Sisu C, Saccone S, Tosi S. Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders. Cancers (Basel) 2019; 11:cancers11040585. [PMID: 31027247 PMCID: PMC6521283 DOI: 10.3390/cancers11040585] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/03/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022] Open
Abstract
The radial spatial positioning of individual gene loci within interphase nuclei has been associated with up- and downregulation of their expression. In cancer, the genome organization may become disturbed due to chromosomal abnormalities, such as translocations or deletions, resulting in the repositioning of genes and alteration of gene expression with oncogenic consequences. In this study, we analyzed the nuclear repositioning of HLXB9 (also called MNX1), mapping at 7q36.3, in patients with hematological disorders carrying interstitial deletions of 7q of various extents, with a distal breakpoint in 7q36. We observed that HLXB9 remains at the nuclear periphery, or is repositioned towards the nuclear interior, depending upon the compositional properties of the chromosomal regions involved in the rearrangement. For instance, a proximal breakpoint leading the guanine-cytosine (GC)-poor band 7q21 near 7q36 would bring HLXB9 to the nuclear periphery, whereas breakpoints that join the GC-rich band 7q22 to 7q36 would bring HLXB9 to the nuclear interior. This nuclear repositioning is associated with transcriptional changes, with HLXB9 in the nuclear interior becoming upregulated. Here we report an in cis rearrangement, involving one single chromosome altering gene behavior. Furthermore, we propose a mechanistic model for chromatin reorganization that affects gene expression via the influences of new chromatin neighborhoods.
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Affiliation(s)
- Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Temitayo Owoka
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Denise Ragusa
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Valentina Sturiale
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Domenica Caponnetto
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Claudia Giovanna Leotta
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Francesca Bruno
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Helen A Foster
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
- College of Health and Life Science, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Silvia Rigamonti
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Giovanni Giudici
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Giovanni Cazzaniga
- Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy.
| | - Joanna M Bridger
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Cristina Sisu
- College of Health and Life Science, Brunel University London, Kingston Lane UB8 3PH, UK.
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy.
| | - Sabrina Tosi
- Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK.
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20
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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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21
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Bikkul MU, Faragher RGA, Worthington G, Meinke P, Kerr ARW, Sammy A, Riyahi K, Horton D, Schirmer EC, Hubank M, Kill IR, Anderson RM, Slijepcevic P, Makarov E, Bridger JM. Telomere elongation through hTERT immortalization leads to chromosome repositioning in control cells and genomic instability in Hutchinson-Gilford progeria syndrome fibroblasts, expressing a novel SUN1 isoform. Genes Chromosomes Cancer 2019; 58:341-356. [PMID: 30474255 PMCID: PMC6590296 DOI: 10.1002/gcc.22711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023] Open
Abstract
Immortalizing primary cells with human telomerase reverse transcriptase (hTERT) has been common practice to enable primary cells to be of extended use in the laboratory because they avoid replicative senescence. Studying exogenously expressed hTERT in cells also affords scientists models of early carcinogenesis and telomere behavior. Control and the premature ageing disease—Hutchinson‐Gilford progeria syndrome (HGPS) primary dermal fibroblasts, with and without the classical G608G mutation have been immortalized with exogenous hTERT. However, hTERT immortalization surprisingly elicits genome reorganization not only in disease cells but also in the normal control cells, such that whole chromosome territories normally located at the nuclear periphery in proliferating fibroblasts become mislocalized in the nuclear interior. This includes chromosome 18 in the control fibroblasts and both chromosomes 18 and X in HGPS cells, which physically express an isoform of the LINC complex protein SUN1 that has previously only been theoretical. Additionally, this HGPS cell line has also become genomically unstable and has a tetraploid karyotype, which could be due to the novel SUN1 isoform. Long‐term treatment with the hTERT inhibitor BIBR1532 enabled the reduction of telomere length in the immortalized cells and resulted that these mislocalized internal chromosomes to be located at the nuclear periphery, as assessed in actively proliferating cells. Taken together, these findings reveal that elongated telomeres lead to dramatic chromosome mislocalization, which can be restored with a drug treatment that results in telomere reshortening and that a novel SUN1 isoform combined with elongated telomeres leads to genomic instability. Thus, care should be taken when interpreting data from genomic studies in hTERT‐immortalized cell lines.
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Affiliation(s)
- Mehmet U. Bikkul
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | | | - Gemma Worthington
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Peter Meinke
- Friedrich‐Baur‐InstitutKlinikum der Universität MünchenMünchenGermany
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Alastair R. W. Kerr
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Aakila Sammy
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Kumars Riyahi
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Daniel Horton
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Michael Hubank
- Centre for Molecular PathologyThe Royal Marsden HospitalLondonEngland
| | - Ian R. Kill
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Rhona M. Anderson
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Predrag Slijepcevic
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Evgeny Makarov
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Joanna M. Bridger
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
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22
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Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol 2019; 218:27-38. [PMID: 30181316 PMCID: PMC6314556 DOI: 10.1083/jcb.201806052] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
Nuclei require a precise three- and four-dimensional organization of DNA to establish cell-specific gene-expression programs. Underscoring the importance of DNA topology, alterations to the nuclear architecture can perturb gene expression and result in disease states. More recently, it has become clear that not only intrachromosomal interactions, but also interchromosomal interactions, a less studied feature of chromosomes, are required for proper physiological gene-expression programs. Here, we review recent studies with emerging insights into where and why cross-chromosomal communication is relevant. Specifically, we discuss how long noncoding RNAs (lncRNAs) and three-dimensional gene positioning are involved in genome organization and how low-throughput (live-cell imaging) and high-throughput (Hi-C and SPRITE) techniques contribute to understand the fundamental properties of interchromosomal interactions.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
- University of Colorado, BioFrontiers, Department of Biochemistry, Boulder, CO
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23
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Szalaj P, Plewczynski D. Three-dimensional organization and dynamics of the genome. Cell Biol Toxicol 2018; 34:381-404. [PMID: 29568981 PMCID: PMC6133016 DOI: 10.1007/s10565-018-9428-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand. In this review, we summarize the current view of the genome architecture on the scales ranging from chromatin loops to the whole genome. We describe cell-to-cell variability, links between genome reorganization and various genomic processes, such as chromosome X inactivation and cell differentiation, and the interplay between different experimental techniques.
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Affiliation(s)
- Przemyslaw Szalaj
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland.
- I-BioStat, Hasselt University, Hasselt, Belgium.
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Dariusz Plewczynski
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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24
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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25
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Jowhar Z, Gudla PR, Shachar S, Wangsa D, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. HiCTMap: Detection and analysis of chromosome territory structure and position by high-throughput imaging. Methods 2018; 142:30-38. [PMID: 29408376 PMCID: PMC5993577 DOI: 10.1016/j.ymeth.2018.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/15/2017] [Accepted: 01/25/2018] [Indexed: 12/23/2022] Open
Abstract
The spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells. HiCTMap is a high-throughput imaging-based chromosome detection method which enables routine analysis of chromosome structure and nuclear position. Using an optimized FISH staining protocol in a 384-well plate format in conjunction with a bespoke automated image analysis workflow, HiCTMap faithfully detects chromosome territories and their position in 2D and 3D in a large population of cells per experimental condition. We apply this novel technique to visualize chromosomes 18, X, and Y in male and female primary human skin fibroblasts, and show accurate detection of the correct number of chromosomes in the respective genotypes. Given the ability to visualize and quantitatively analyze large numbers of nuclei, we use HiCTMap to measure chromosome territory area and volume with high precision and determine the radial position of chromosome territories using either centroid or equidistant-shell analysis. The HiCTMap protocol is also compatible with RNA FISH as demonstrated by simultaneous labeling of X chromosomes and Xist RNA in female cells. We suggest HiCTMap will be a useful tool for routine precision mapping of chromosome territories in a wide range of cell types and tissues.
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MESH Headings
- Animals
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Chromosome Mapping/instrumentation
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 18/metabolism
- Chromosomes, Human, X/genetics
- Chromosomes, Human, X/metabolism
- Chromosomes, Human, Y/genetics
- Chromosomes, Human, Y/metabolism
- Female
- Fibroblasts
- Humans
- Image Processing, Computer-Assisted/instrumentation
- Image Processing, Computer-Assisted/methods
- In Situ Hybridization, Fluorescence/instrumentation
- In Situ Hybridization, Fluorescence/methods
- Male
- Primary Cell Culture/methods
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Skin/cytology
- Staining and Labeling/instrumentation
- Staining and Labeling/methods
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Affiliation(s)
- Ziad Jowhar
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Prabhakar R Gudla
- NCI High-throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Sigal Shachar
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Jill L Russ
- Human Genetics Branch, National Institute of Mental Health, NIH, Bethesda, MD 20892, United States
| | - Gianluca Pegoraro
- NCI High-throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, United States
| | - Armin Raznahan
- Human Genetics Branch, National Institute of Mental Health, NIH, Bethesda, MD 20892, United States
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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26
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Kocanova S, Goiffon I, Bystricky K. 3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines. Methods 2018; 142:3-15. [PMID: 29501423 DOI: 10.1016/j.ymeth.2018.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/19/2017] [Accepted: 02/14/2018] [Indexed: 11/28/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
| | - Isabelle Goiffon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France.
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
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27
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Mondal M, Liao R, Guo J. Highly Multiplexed Single-Cell Protein Analysis. Chemistry 2018; 24:7083-7091. [PMID: 29194810 DOI: 10.1002/chem.201705014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 12/17/2022]
Abstract
Single-cell proteomic analysis is crucial to advance our understanding of normal physiology and disease pathogenesis. The comprehensive protein profiling in individual cells of a heterogeneous sample can provide new insights into many important biological issues, such as the regulation of inter- and intracellular signaling pathways or the varied cellular compositions of normal and diseased tissues. With highly multiplexed molecular imaging of many different protein biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment. In this Minireview, we will describe the recent technological advances of single-cell proteomic assays, discuss their advantages and limitations, highlight their applications in biology and precision medicine, and present the current challenges and potential solutions.
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Affiliation(s)
- Manas Mondal
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Renjie Liao
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
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28
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Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol 2018; 25:176-184. [PMID: 29343869 PMCID: PMC5805655 DOI: 10.1038/s41594-017-0015-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022]
Abstract
Imaging and chromatin capture techniques have shed important insights into our understanding of nuclear organization. A limitation of these techniques is the inability to resolve allele-specific spatiotemporal properties of genomic loci in living cells. Here, we describe an allele-specific CRISPR live-cell DNA imaging technique (SNP-CLING) to provide the first comprehensive insights into allelic positioning across space and time in mouse embryonic stem cells and fibroblasts. In 3D-imaging, we studied alleles on different chromosomes in relation to one another and relative to nuclear substructures such as the nucleolus. We find that alleles maintain similar positions relative to each other and the nucleolus, however loci occupy different unique positions. To monitor spatiotemporal dynamics by SNP-CLING, we performed 4D-imaging, determining that alleles are either stably positioned, or fluctuating during cell state transitions, such as apoptosis. SNP-CLING is a universally applicable technique that enables dissecting allele-specific spatiotemporal genome organization in live cells.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - David M Shechner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Pharmacology, The University of Washington, Seattle, WA, USA
| | - Catherine L Weiner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Marta Melé
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA. .,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA. .,Department of Biochemistry, University of Colorado, BioFrontiers, Boulder, CO, USA.
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29
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Ioannou D, Tempest HG. Does genome organization matter in spermatozoa? A refined hypothesis to awaken the silent vessel. Syst Biol Reprod Med 2018; 64:518-534. [DOI: 10.1080/19396368.2017.1421278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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30
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Abstract
Epigenetic mechanisms that cause maternally and paternally inherited alleles to be expressed differently in offspring have the potential to radically change our understanding of the mechanisms that shape disease susceptibility, phenotypic variation, cell fate, and gene expression. However, the nature and prevalence of these effects
in vivo have been unclear and are debated. Here, I consider major new studies of epigenetic allelic effects in cell lines and primary cells and
in vivo. The emerging picture is that these effects take on diverse forms, and this review attempts to clarify the nature of the different forms that have been uncovered for genomic imprinting and random monoallelic expression (RME). I also discuss apparent discrepancies between
in vitro and
in vivo studies. Importantly, multiple studies suggest that allelic effects are prevalent and can be developmental stage- and cell type-specific. I propose some possible functions and consider roles for allelic effects within the broader context of gene regulatory networks, cellular diversity, and plasticity. Overall, the field is ripe for discovery and is in need of mechanistic and functional studies.
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31
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Abstract
The eukaryotic genome is organized in a manner that allows folding of the genetic material in the confined space of the cell nucleus, while at the same time enabling its physiological function. A major principle of spatial genome organization is the non-random position of genomic loci relative to other loci and to nuclear bodies. The mechanisms that determine the spatial position of a locus, and how position affects function, are just beginning to be characterized. Initial results suggest that there are multiple, gene-specific mechanisms and the involvement of a wide range of cellular machineries. In this Commentary, we review recent findings from candidate approaches and unbiased screening methods that provide initial insight into the cellular mechanisms of positioning and their functional consequences. We highlight several specific mechanisms, including tethering of genome regions to the nuclear periphery, passage through S-phase and histone modifications, that contribute to gene positioning in yeast, plants and mammals.
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Affiliation(s)
- Sigal Shachar
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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32
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The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity. Sci Rep 2016; 6:38063. [PMID: 27905489 PMCID: PMC5131312 DOI: 10.1038/srep38063] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
Mechanical integration of the nucleus with the extracellular matrix (ECM) is established by linkage between the cytoskeleton and the nucleus. This integration is hypothesized to mediate sensing of ECM rigidity, but parsing the function of nucleus-cytoskeleton linkage from other mechanisms has remained a central challenge. Here we took advantage of the fact that the LINC (linker of nucleoskeleton and cytoskeleton) complex is a known molecular linker of the nucleus to the cytoskeleton, and asked how it regulates the sensitivity of genome-wide transcription to substratum rigidity. We show that gene mechanosensitivity is preserved after LINC disruption, but reversed in direction. Combined with myosin inhibition studies, we identify genes that depend on nuclear tension for their regulation. We also show that LINC disruption does not attenuate nuclear shape sensitivity to substrate rigidity. Our results show for the first time that the LINC complex facilitates mechano-regulation of expression across the genome.
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33
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Tordini F, Aldinucci M, Milanesi L, Liò P, Merelli I. The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer. Front Genet 2016; 7:194. [PMID: 27895661 PMCID: PMC5108817 DOI: 10.3389/fgene.2016.00194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level. Using this representation, we can describe how driver and passenger mutations accumulate during the development of diseases providing, for example, a tool able to characterize the evolution of cancer. Indeed, our test case concerns the MCF-7 breast cancer cell line, before and after the stimulation with estrogen, since many datasets are available for this case study. In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic patterns, gene expression, and metabolic pathways in our multi-layer representation will allow a better interpretation of the mechanisms behind a complex disease such as cancer. Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different pathways, such as metabolic processes, that are very important for tumor development. Working on this model, a variance analysis can be implemented to identify normal variations within each omics and to characterize, by contrast, variations that can be accounted to pathological samples compared to normal ones. This integrative model can be used to identify novel biomarkers and to provide innovative omic-based guidelines for treating many diseases, improving the efficacy of decision trees currently used in clinic.
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Affiliation(s)
- Fabio Tordini
- Computer Science Department, University of Torino Torino, Italy
| | - Marco Aldinucci
- Computer Science Department, University of Torino Torino, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge Cambridge, UK
| | - Ivan Merelli
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
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34
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Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells. Sci Rep 2016; 6:30593. [PMID: 27503568 PMCID: PMC4977554 DOI: 10.1038/srep30593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 07/05/2016] [Indexed: 12/16/2022] Open
Abstract
The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.
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Brickner DG, Sood V, Tutucci E, Coukos R, Viets K, Singer RH, Brickner JH. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell 2016; 27:2980-93. [PMID: 27489341 PMCID: PMC5042583 DOI: 10.1091/mbc.e16-03-0174] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/27/2016] [Indexed: 01/10/2023] Open
Abstract
“DNA zip codes” control positioning and interchromosomal clustering of GAL1-10 in yeast. However, these two phenomena have distinct molecular mechanisms, requiring different nuclear pore proteins, and are regulated differently by transcription and the cell cycle. On activation, the GAL genes in yeast are targeted to the nuclear periphery through interaction with the nuclear pore complex. Here we identify two cis-acting “DNA zip codes” from the GAL1-10 promoter that are necessary and sufficient to induce repositioning to the nuclear periphery. One of these zip codes, GRS4, is also necessary and sufficient to promote clustering of GAL1-10 alleles. GRS4, and to a lesser extent GRS5, contribute to stronger expression of GAL1 and GAL10 by increasing the fraction of cells that respond to the inducer. The molecular mechanism controlling targeting to the NPC is distinct from the molecular mechanism controlling interchromosomal clustering. Targeting to the nuclear periphery and interaction with the nuclear pore complex are prerequisites for gene clustering. However, once formed, clustering can be maintained in the nucleoplasm, requires distinct nuclear pore proteins, and is regulated differently through the cell cycle. In addition, whereas targeting of genes to the NPC is independent of transcription, interchromosomal clustering requires transcription. These results argue that zip code–dependent gene positioning at the nuclear periphery and interchromosomal clustering represent interdependent phenomena with distinct molecular mechanisms.
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Affiliation(s)
| | - Varun Sood
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Kayla Viets
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
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36
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Meaburn KJ. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool. Front Genet 2016; 7:134. [PMID: 27507988 PMCID: PMC4961005 DOI: 10.3389/fgene.2016.00134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
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Affiliation(s)
- Karen J. Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
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37
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Shachar S, Voss TC, Pegoraro G, Sciascia N, Misteli T. Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping. Cell 2016; 162:911-23. [PMID: 26276637 DOI: 10.1016/j.cell.2015.07.035] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/08/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022]
Abstract
Genomes are arranged non-randomly in the 3D space of the cell nucleus. Here, we have developed HIPMap, a high-precision, high-throughput, automated fluorescent in situ hybridization imaging pipeline, for mapping of the spatial location of genome regions at large scale. High-throughput imaging position mapping (HIPMap) enabled an unbiased siRNA screen for factors involved in genome organization in human cells. We identify 50 cellular factors required for proper positioning of a set of functionally diverse genomic loci. Positioning factors include chromatin remodelers, histone modifiers, and nuclear envelope and pore proteins. Components of the replication and post-replication chromatin re-assembly machinery are prominently represented among positioning factors, and timely progression of cells through replication, but not mitosis, is required for correct gene positioning. Our results establish a method for the large-scale mapping of genome locations and have led to the identification of a compendium of cellular factors involved in spatial genome organization.
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Affiliation(s)
- Sigal Shachar
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ty C Voss
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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38
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Meaburn KJ, Agunloye O, Devine M, Leshner M, Roloff GW, True LD, Misteli T. Tissue-of-origin-specific gene repositioning in breast and prostate cancer. Histochem Cell Biol 2016; 145:433-46. [PMID: 26791532 DOI: 10.1007/s00418-015-1401-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 01/25/2023]
Abstract
Genes have preferential non-random spatial positions within the cell nucleus. The nuclear position of a subset of genes differ between cell types and some genes undergo repositioning events in disease, including cancer. It is currently unclear whether the propensity of a gene to reposition reflects an intrinsic property of the locus or the tissue. Using quantitative FISH analysis of a set of genes which reposition in cancer, we test here the tissue specificity of gene repositioning in normal and malignant breast or prostate tissues. We find tissue-specific organization of the genome in normal breast and prostate with 40 % of genes occupying differential positions between the two tissue types. While we demonstrate limited overlap between gene sets that repositioned in breast and prostate cancer, we identify two genes that undergo disease-related gene repositioning in both cancer types. Our findings indicate that gene repositioning in cancer is tissue-of-origin specific.
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Affiliation(s)
| | | | | | - Marc Leshner
- National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | | | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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39
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Warford A. In situ hybridisation: Technologies and their application to understanding disease. ACTA ACUST UNITED AC 2015; 50:37-48. [PMID: 26797255 DOI: 10.1016/j.proghi.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
Abstract
In situ hybridisation (ISH) is unique amongst molecular analysis methods in providing for the precise microscopic localisation of genes, mRNA and microRNA in metaphase spreads, cell and tissue preparations. The method is well established as a tool to guide appropriate therapeutic intervention in breast, gastric and lung cancer. With the description of ultrasensitive ISH technologies for low copy mRNA demonstration and the relative ease by which microRNA can be visualised, the applications for research and diagnostic purposes is set to increase dramatically. In this review ISH is considered with emphasis on recent technological developments and surveyed for present and future applications in the context of the demonstration of genes, mRNA and microRNA in health and disease.
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Affiliation(s)
- Anthony Warford
- University of Westminster, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
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40
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Leshner M, Devine M, Roloff GW, True LD, Misteli T, Meaburn KJ. Locus-specific gene repositioning in prostate cancer. Mol Biol Cell 2015; 27:236-46. [PMID: 26564800 PMCID: PMC4713128 DOI: 10.1091/mbc.e15-05-0280] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/05/2015] [Indexed: 01/16/2023] Open
Abstract
The spatial organization of the genome is altered in prostate cancer compared to normal tissue in a gene-specific manner. The repositioning of two genes, FLI1 and MMP9, is specific to cancer, and the positioning patterns of these genes may serve as diagnostic biomarkers. Genes occupy preferred spatial positions within interphase cell nuclei. However, positioning patterns are not an innate feature of a locus, and genes can alter their localization in response to physiological and pathological changes. Here we screen the radial positioning patterns of 40 genes in normal, hyperplasic, and malignant human prostate tissues. We find that the overall spatial organization of the genome in prostate tissue is largely conserved among individuals. We identify three genes whose nuclear positions are robustly altered in neoplastic prostate tissues. FLI1 and MMP9 position differently in prostate cancer than in normal tissue and prostate hyperplasia, whereas MMP2 is repositioned in both prostate cancer and hyperplasia. Our data point to locus-specific reorganization of the genome during prostate disease.
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Affiliation(s)
- Marc Leshner
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michelle Devine
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Gregory W Roloff
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Karen J Meaburn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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41
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Shachar S, Pegoraro G, Misteli T. HIPMap: A High-Throughput Imaging Method for Mapping Spatial Gene Positions. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:73-81. [PMID: 26472748 PMCID: PMC6317989 DOI: 10.1101/sqb.2015.80.027417] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The three-dimensional organization of genes inside the cell nucleus affects their functions including DNA transcription, replication, and repair. A major goal in the field of nuclear architecture is to determine what cellular factors establish and maintain the position of individual genes. Here, we describe HIPMap, a high-throughput imaging and analysis pipeline for the mapping of endogenous gene loci within the 3D space of the nucleus. HIPMap can be used for a variety of applications including screening, mapping translocations, validating chromosome conformation capture data, probing DNA-protein interactions, and interrogation of the relationship of gene expression with localization.
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Affiliation(s)
- Sigal Shachar
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gianluca Pegoraro
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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42
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Tosi S, Mostafa Kamel Y, Owoka T, Federico C, Truong TH, Saccone S. Paediatric acute myeloid leukaemia with the t(7;12)(q36;p13) rearrangement: a review of the biological and clinical management aspects. Biomark Res 2015; 3:21. [PMID: 26605042 PMCID: PMC4657620 DOI: 10.1186/s40364-015-0041-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/25/2015] [Indexed: 12/05/2022] Open
Abstract
The presence of chromosomal abnormalities is one of the most important criteria for leukaemia diagnosis and management. Infant leukaemia is a rare disease that affects children in their first year of life. It has been estimated that approximately one third of infants with acute myeloid leukaemia harbour the t(7;12)(q36;p13) rearrangement in their leukaemic blasts. However, the WHO classification of acute myeloid leukaemia does not yet include the t(7;12) as a separate entity among the different genetic subtypes, although the presence of this chromosomal abnormality has been associated with an extremely poor clinical outcome. Currently, there is no consensus treatment for t(7;12) leukaemia patients. However, with the inferior outcome with the standard induction therapy, stem cell transplantation may offer a better chance for disease control. A better insight into the chromosome biology of this entity might shed some light into the pathogenic mechanisms arising from this chromosomal translocation, that at present are not fully understood. Further work is needed to improve our understanding of the molecular and genetic basis of this disorder. This will hopefully open some grounds for possible tailored treatment for this subset of very young patients with inferior disease outcome. This review aims at highlighting the cytogenetic features that characterise the t(7;12) leukaemias for a better detection of the abnormality in the diagnostic setting. We also review treatment and clinical outcome in the cases reported to date.
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Affiliation(s)
- Sabrina Tosi
- Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University London, Middlesex, UB8 3PH UK
| | - Yasser Mostafa Kamel
- Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University London, Middlesex, UB8 3PH UK
| | - Temitayo Owoka
- Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University London, Middlesex, UB8 3PH UK
| | - Concetta Federico
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Sezione di Biologia Animale, University of Catania, Catania, Italy
| | - Tony H Truong
- Division of Pediatric Oncology, Blood and Marrow Transplant, Alberta Children's Hospital, University of Calgary, Calgary, Canada
| | - Salvatore Saccone
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Sezione di Biologia Animale, University of Catania, Catania, Italy
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43
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Shavit Y, Merelli I, Milanesi L, Lio’ P. How computer science can help in understanding the 3D genome architecture. Brief Bioinform 2015; 17:733-44. [DOI: 10.1093/bib/bbv085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 01/20/2023] Open
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44
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Barutcu AR, Lajoie BR, McCord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol 2015; 16:214. [PMID: 26415882 PMCID: PMC4587679 DOI: 10.1186/s13059-015-0768-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/03/2015] [Indexed: 12/17/2022] Open
Abstract
Background Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. Results Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16–22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16–22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. Conclusions We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0768-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Bryan R Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Rachel P McCord
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Deli Hong
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.,Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Terri L Messier
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Gillian Browne
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andre J van Wijnen
- Department of Biochemistry & Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
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Rafique S, Thomas JS, Sproul D, Bickmore WA. Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer. Genome Biol 2015; 16:145. [PMID: 26235388 PMCID: PMC4536608 DOI: 10.1186/s13059-015-0719-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/06/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers. RESULTS We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen. CONCLUSIONS Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.
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Affiliation(s)
- Sehrish Rafique
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Jeremy S Thomas
- Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity. BIOMED RESEARCH INTERNATIONAL 2015; 2015:213750. [PMID: 26339594 PMCID: PMC4538409 DOI: 10.1155/2015/213750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/16/2015] [Indexed: 01/19/2023]
Abstract
Predicting disease genes for a particular genetic disease is very challenging in bioinformatics. Based on current research studies, this challenge can be tackled via network-based approaches. Furthermore, it has been highlighted that it is necessary to consider disease similarity along with the protein's proximity to disease genes in a protein-protein interaction (PPI) network in order to improve the accuracy of disease gene prioritization. In this study we propose a new algorithm called proximity disease similarity algorithm (ProSim), which takes both of the aforementioned properties into consideration, to prioritize disease genes. To illustrate the proposed algorithm, we have conducted six case studies, namely, prostate cancer, Alzheimer's disease, diabetes mellitus type 2, breast cancer, colorectal cancer, and lung cancer. We employed leave-one-out cross validation, mean enrichment, tenfold cross validation, and ROC curves to evaluate our proposed method and other existing methods. The results show that our proposed method outperforms existing methods such as PRINCE, RWR, and DADA.
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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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Arican-Goktas HD, Ittiprasert W, Bridger JM, Knight M. Differential spatial repositioning of activated genes in Biomphalaria glabrata snails infected with Schistosoma mansoni. PLoS Negl Trop Dis 2014; 8:e3013. [PMID: 25211244 PMCID: PMC4161332 DOI: 10.1371/journal.pntd.0003013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
Schistosomiasis is an infectious disease infecting mammals as the definitive host and fresh water snails as the intermediate host. Understanding the molecular and biochemical relationship between the causative schistosome parasite and its hosts will be key to understanding and ultimately treating and/or eradicating the disease. There is increasing evidence that pathogens that have co-evolved with their hosts can manipulate their hosts' behaviour at various levels to augment an infection. Bacteria, for example, can induce beneficial chromatin remodelling of the host genome. We have previously shown in vitro that Biomphalaria glabrata embryonic cells co-cultured with schistosome miracidia display genes changing their nuclear location and becoming up-regulated. This also happens in vivo in live intact snails, where early exposure to miracidia also elicits non-random repositioning of genes. We reveal differences in the nuclear repositioning between the response of parasite susceptible snails as compared to resistant snails and with normal or live, attenuated parasites. Interestingly, the stress response gene heat shock protein (Hsp) 70 is only repositioned and then up-regulated in susceptible snails with the normal parasite. This movement and change in gene expression seems to be controlled by the parasite. Other differences in the behaviour of genes support the view that some genes are responding to tissue damage, for example the ferritin genes move and are up-regulated whether the snails are either susceptible or resistant and upon exposure to either normal or attenuated parasite. This is the first time host genome reorganisation has been seen in a parasitic host and only the second time for any pathogen. We believe that the parasite elicits a spatio-epigenetic reorganisation of the host genome to induce favourable gene expression for itself and this might represent a fundamental mechanism present in the human host infected with schistosome cercariae as well as in other host-pathogen relationships. Bilharzia is a parasitic disease endemic in many parts of the world. The schistosoma parasite that causes Bilharzia infects humans but uses a fresh water snail as a secondary host. These two organisms have co-evolved together, and as such the parasite will have mechanisms to overcome the host defences. Understanding this delicately balanced relationship is fundamental to controlling or eradicating the disease. We have studied how this parasite can influence how the DNA within the snail behaves. We have shown snail genes have specific locations within the cell nuclei. Further, we have revealed that specific snail genes related to a schistosome infection change to a new non-random nuclear location as they are turned on or up-regulated. We have snail strains that are susceptible or resistant to the infection of parasites and we can also take live parasites and make them unable to complete an infection by irradiating them. In this unique study, we have shown a gene that is involved in stress pathways moves to a new nuclear location and becomes turned on, but only in susceptible snails, infected with fully functional parasite. Our data suggest that this gene is regulated by the parasite, which has control over the host's DNA, so that the gene is moved to an area where it can be actively expressed. We have uncovered a novel mechanism whereby the spatial organization of a host organism is interfered with by a pathogen. This type of control is probably found in other host-pathogen relationships.
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Affiliation(s)
- Halime D. Arican-Goktas
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
| | | | - Joanna M. Bridger
- Lab of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Biosciences, School of Health Sciences and Social Care, Brunel University, London, United Kingdom
- * E-mail: (JMB); (MK)
| | - Matty Knight
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Science, George Washington University, Washington, D.C., United States of America
- * E-mail: (JMB); (MK)
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Abstract
Current anti-cancer therapies have a great deal of undesirable side effects; therefore, there is a need to develop efficient and cancer cell-specific new drugs without strong dose-limiting side effects. In my opinion, mechanisms of nuclear assembly and organization represent a novel platform for drug targets, which might fulfill these criteria. The nuclear stiffness and organization of some cancer types are often compromised, making them more vulnerable for further targeting the mechanisms of nuclear integrity than their normal counterparts. Here I will discuss the nuclear organization of normal cells and cancer cells, the molecular mechanisms that govern nuclear assembly with emphasis on those that, in my view, might be considered as targets for future anti-cancer therapies.
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Affiliation(s)
- Mátyás Gorjánácz
- Bayer Pharma AG; Bayer Healthcare Pharmaceuticals; Global Drug Discovery; Therapeutic Research Group Oncology; Berlin, Germany
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50
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Bridger JM, Arican-Gotkas HD, Foster HA, Godwin LS, Harvey A, Kill IR, Knight M, Mehta IS, Ahmed MH. The Non-random Repositioning of Whole Chromosomes and Individual Gene Loci in Interphase Nuclei and Its Relevance in Disease, Infection, Aging, and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:263-79. [DOI: 10.1007/978-1-4899-8032-8_12] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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