51
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Ghavi-Helm Y. Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All? J Mol Biol 2019; 432:665-675. [PMID: 31626801 DOI: 10.1016/j.jmb.2019.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 12/14/2022]
Abstract
Chromosomes are folded and organized into topologically associating domains (TADs) which provide a framework for the interaction of enhancers with the promoter of their target gene(s). Structural rearrangements observed during evolution or in disease contexts suggest that changes in genome organization strongly affect gene expression and can have drastic phenotypic effects. In this review, I will discuss how recent genomic engineering experiments reveal a more contrasted picture, suggesting that TADs are important but not always essential for gene expression regulation.
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Affiliation(s)
- Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 Allée D'Italie, F-69364 Lyon, France.
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52
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Shi G, Thirumalai D. Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox. Nat Commun 2019; 10:3894. [PMID: 31467267 PMCID: PMC6715811 DOI: 10.1038/s41467-019-11897-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 08/06/2019] [Indexed: 11/19/2022] Open
Abstract
Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations. Studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci is paradoxically larger compared to another pair with a smaller value of the contact probability. Here the authors use a theory based on a Generalized Rouse Model for Chromosomes to resolve this paradox.
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Affiliation(s)
- Guang Shi
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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53
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Deakin JE, Potter S, O'Neill R, Ruiz-Herrera A, Cioffi MB, Eldridge MDB, Fukui K, Marshall Graves JA, Griffin D, Grutzner F, Kratochvíl L, Miura I, Rovatsos M, Srikulnath K, Wapstra E, Ezaz T. Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes (Basel) 2019; 10:genes10080627. [PMID: 31434289 PMCID: PMC6723020 DOI: 10.3390/genes10080627] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Rachel O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marcelo B Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Kichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871, Osaka, Japan
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
- School of Life Sciences, LaTrobe University, Melbourne, VIC 3168, Australia
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Frank Grutzner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics & Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Erik Wapstra
- School of Natural Sciences, University of Tasmania, Hobart 7000, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
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54
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Yildirim A, Feig M. High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization. Nucleic Acids Res 2019. [PMID: 29529244 PMCID: PMC5934669 DOI: 10.1093/nar/gky141] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C. crescentus cell dimensions. The models allowed a direct mapping of the genomic sequence onto the three-dimensional nucleoid structures. Distinct spatial distributions were found for several genomic elements such as AT-rich sequence elements where nucleoid associated proteins (NAPs) are likely to bind, promoter sites, and some genes with common cellular functions. These findings shed light on the correlation between the spatial organization of the genome and biological functions.
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Affiliation(s)
- Asli Yildirim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, MI 48824, USA
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55
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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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56
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Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annu Rev Cell Dev Biol 2019; 35:357-379. [PMID: 31283382 DOI: 10.1146/annurev-cellbio-100617-062719] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and the use of low-affinity binding sites, which are better able to distinguish between similar TFs. However, because these sites have low affinity, it is challenging to understand how TFs recognize them in vivo. Here, we summarize recent findings and technological advancements that allow for the quantification and mechanistic interpretation of TF recognition across a wide range of affinities. We propose a model that integrates insights from the fields of genetics and cell biology to provide further conceptual understanding of TF binding specificity. We argue that in eukaryotes, target specificity is driven by an inhomogeneous 3D nuclear distribution of TFs and by variation in DNA binding affinity such that locally elevated TF concentration allows low-affinity binding sites to be functional.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA; .,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10031, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
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57
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Qi Y, Zhang B. Predicting three-dimensional genome organization with chromatin states. PLoS Comput Biol 2019; 15:e1007024. [PMID: 31181064 PMCID: PMC6586364 DOI: 10.1371/journal.pcbi.1007024] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/20/2019] [Accepted: 04/13/2019] [Indexed: 11/19/2022] Open
Abstract
We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements. Detailed characterization of the predicted structural ensemble reveals the dynamical flexibility of chromatin loops and the presence of cross-talk among neighboring TADs. Analysis of the model's energy function uncovers distinct mechanisms for chromatin folding at various length scales and suggests a need to go beyond simple A/B compartment types to predict specific contacts between regulatory elements using polymer simulations.
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Affiliation(s)
- Yifeng Qi
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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58
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Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 2019; 8:e41769. [PMID: 31124784 PMCID: PMC6534382 DOI: 10.7554/elife.41769] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.
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Affiliation(s)
- Jeffrey M Alexander
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Juan Guan
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bingkun Li
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Lenka Maliskova
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michael Song
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
| | - Yin Shen
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
- Mortimer B Zuckerman Mind Brain and Behavior InstituteColumbia UniversityNew York CityUnited States
| | - Orion D Weiner
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
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59
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tRNA Genes Affect Chromosome Structure and Function via Local Effects. Mol Cell Biol 2019; 39:MCB.00432-18. [PMID: 30718362 DOI: 10.1128/mcb.00432-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.
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60
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61
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Ma H, Tu LC, Chung YC, Naseri A, Grunwald D, Zhang S, Pederson T. Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. J Cell Biol 2019; 218:1467-1477. [PMID: 30846483 PMCID: PMC6504907 DOI: 10.1083/jcb.201807162] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 02/08/2023] Open
Abstract
In contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics during interphase are less understood. We deployed a CRISPR-based DNA imaging system to track the dynamics of genomic loci situated kilobases to megabases apart on a single chromosome. Two distinct modes of dynamics were resolved: local movements as well as ones that might reflect translational movements of the entire domain within the nucleoplasmic space. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S phase. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle dependence suggest the existence of a hitherto unrecognized compaction-relaxation dynamic of the interphase chromosome fiber, operating concurrently with changes in the extent of overall movements of loci in the 4D genome.
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Affiliation(s)
- Hanhui Ma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Li-Chun Tu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Yu-Chieh Chung
- Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Japan
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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62
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Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell 2019; 176:1502-1515.e10. [PMID: 30799036 DOI: 10.1016/j.cell.2019.01.020] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 10/18/2018] [Accepted: 01/09/2019] [Indexed: 01/16/2023]
Abstract
Several general principles of global 3D genome organization have recently been established, including non-random positioning of chromosomes and genes in the cell nucleus, distinct chromatin compartments, and topologically associating domains (TADs). However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are still poorly characterized. Here, we systematically probe heterogeneity in genome organization. High-throughput optical mapping of several hundred intra-chromosomal interactions in individual human fibroblasts demonstrates low association frequencies, which are determined by genomic distance, higher-order chromatin architecture, and chromatin environment. The structure of TADs is variable between individual cells, and inter-TAD associations are common. Furthermore, single-cell analysis reveals independent behavior of individual alleles in single nuclei. Our observations reveal extensive variability and heterogeneity in genome organization at the level of individual alleles and demonstrate the coexistence of a broad spectrum of genome configurations in a cell population.
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Affiliation(s)
| | - Gianluca Pegoraro
- High-throughput Imaging Facility, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marlies E Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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63
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Altered three-dimensional organization of sperm genome in DPY19L2-deficient globozoospermic patients. J Assist Reprod Genet 2018; 36:69-77. [PMID: 30362053 DOI: 10.1007/s10815-018-1342-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To explore the three-dimensional (3D) organization of sperm genome in DPY19L2-deficient globozoospermic patients speculating a link between DPY19L2 and genome organization of sperm nucleus. METHODS This is a study of chromatin organization in DPY19L2-deficient globozoospermic patients and healthy donors using three-dimensional fluorescence in situ hybridization (3D-FISH) combined with confocal laser scanning microscopy followed by 3D image analysis. The 3D structures of sperm nuclei, chromocenter, telomeric regions and chromosome territories (CTs), were reconstructed using IMARIS software, and the relative radial position for each individual signal was calculated. Statistical analysis used a non-parametric Mann-Whitney test was appropriate with significance at p < 0.05. RESULTS DPY19L2-deficient globozoospermic patients display impaired sperm chromocenter organization resulting in an increased number of chromocenters (5.4 vs 3.5; p < 0.0001). Moreover, radial positions of telomeres are modified with a more central position in globozoospermic nuclei. 3D-FISH analysis of five chromosome territories (CTs) (X, Y, 7, 17, 18) showed that DPY19L2-deficient globozoospermic sperm nuclei display altered spatial organization of CT X, CT 7 and CT 18. CONCLUSIONS Our findings strengthen the hypothesis that DPY19L2 might be considered as a LINC-like protein having a crucial role in the organization of nuclear chromatin in sperm nucleus through its interaction with nuclear lamina. Our results might also explain defective embryonic development after intracytoplasmic sperm injection (ICSI) performed with DPY19L2-deficient globozoospermic sperm.
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64
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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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65
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Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 2018; 50:1352-1358. [PMID: 30262815 DOI: 10.1038/s41588-018-0236-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/19/2018] [Indexed: 11/09/2022]
Abstract
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear genome is folded in ways that may modulate how genes are expressed during the basic functioning of cells. Importantly, it is now possible to build 3D models of how the genome folds within the nucleus and changes over time (4D). Because genome folding influences its function, this opens exciting new possibilities to broaden our understanding of the mechanisms that determine cell fate. However, the rapid evolution of methods and the increasing complexity of data can result in ambiguity and reproducibility challenges, which may hamper the progress of this field. Here, we describe such challenges ahead and provide guidelines to think about strategies for shared standardized validation of experimental 4D nucleome data sets and models.
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66
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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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67
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Doğan ES, Liu C. Three-dimensional chromatin packing and positioning of plant genomes. NATURE PLANTS 2018; 4:521-529. [PMID: 30061747 DOI: 10.1038/s41477-018-0199-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Information and function of a genome are not only decorated with epigenetic marks in the linear DNA sequence but also in their non-random spatial organization in the nucleus. Recent research has revealed that three-dimensional (3D) chromatin organization is highly correlated with the functionality of the genome, contributing to many cellular processes. Driven by the improvements in chromatin conformation capture methods and visualization techniques, the past decade has been an exciting period for the study of plants' 3D genome structures, and our knowledge in this area has been substantially advanced. This Review describes our current understanding of plant chromatin organization and positioning beyond the nucleosomal level, and discusses future directions.
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Affiliation(s)
- Ezgi Süheyla Doğan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
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68
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Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell 2018; 174:744-757.e24. [PMID: 29887377 PMCID: PMC6548320 DOI: 10.1016/j.cell.2018.05.024] [Citation(s) in RCA: 546] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/18/2018] [Accepted: 05/10/2018] [Indexed: 11/22/2022]
Abstract
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.
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Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barbara Tabak
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ali Palla
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jan Marten Schmidt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth Detmar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mason M Lai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Erik Aznauryan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela Russell
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Christine Cheng
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Patrick McDonel
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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69
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Slaughter BD, Hawley RS. The anatomy of a nucleus: As revealed by chromosome painting. PLoS Genet 2018; 14:e1007445. [PMID: 30001330 PMCID: PMC6042688 DOI: 10.1371/journal.pgen.1007445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - R. Scott Hawley
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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70
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Genome organization at different scales: nature, formation and function. Curr Opin Cell Biol 2018; 52:145-153. [DOI: 10.1016/j.ceb.2018.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/23/2018] [Indexed: 02/01/2023]
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71
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Waldispühl J, Zhang E, Butyaev A, Nazarova E, Cyr Y. Storage, visualization, and navigation of 3D genomics data. Methods 2018; 142:74-80. [PMID: 29792917 DOI: 10.1016/j.ymeth.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/27/2023] Open
Abstract
The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art computing technology, as well as the solutions adopted by the platforms currently available.
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Affiliation(s)
| | - Eric Zhang
- School of Computer Science, McGill University, Montréal, Canada
| | | | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, Canada
| | - Yan Cyr
- Beam Me Up Labs, Montréal, Canada
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72
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Developing novel methods to image and visualize 3D genomes. Cell Biol Toxicol 2018; 34:367-380. [PMID: 29577183 PMCID: PMC6133007 DOI: 10.1007/s10565-018-9427-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/11/2018] [Indexed: 02/07/2023]
Abstract
To investigate three-dimensional (3D) genome organization in prokaryotic and eukaryotic cells, three main strategies are employed, namely nuclear proximity ligation-based methods, imaging tools (such as fluorescence in situ hybridization (FISH) and its derivatives), and computational/visualization methods. Proximity ligation-based methods are based on digestion and re-ligation of physically proximal cross-linked chromatin fragments accompanied by massively parallel DNA sequencing to measure the relative spatial proximity between genomic loci. Imaging tools enable direct visualization and quantification of spatial distances between genomic loci, and advanced implementation of (super-resolution) microscopy helps to significantly improve the resolution of images. Computational methods are used to map global 3D genome structures at various scales driven by experimental data, and visualization methods are used to visualize genome 3D structures in virtual 3D space-based on algorithms. In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system. As the fluorescence-capturing capability of a particular microscope is very important for the sensitivity of bioimaging experiments, we also introduce two novel super-resolution microscopy methods, SDOM and low-power super-resolution STED, which have potential for time-lapse super-resolution live-cell imaging of chromatin. Finally, we review some software tools developed recently to visualize proximity ligation-based data. The imaging and visualization methods are complementary to each other, and all three strategies are not mutually exclusive. These methods provide powerful tools to explore the mechanisms of gene regulation and transcription in cell nuclei.
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73
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Qi Y, Zhang B. Predicting three-dimensional genome organization with chromatin states.. [DOI: 10.1101/282095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
ABSTRACTWe introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements. Detailed characterization of the predicted structural ensemble reveals the dynamical flexibility of chromatin loops and the presence of cross-talk among neighboring TADs. Analysis of the model’s energy function uncovers distinct mechanisms for chromatin folding at various length scales.
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74
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Abstract
Imaging (fluorescence in situ hybridization [FISH]) and genome-wide chromosome conformation capture (Hi-C) are two major approaches to the study of higher-order genome organization in the nucleus. Intra-chromosomal and inter-chromosomal interactions (referred to as non-homologous chromosomal contacts [NHCCs]) have been observed by several FISH-based studies, but locus-specific NHCCs have not been detected by Hi-C. Due to crosslinking, neither of these approaches assesses spatiotemporal properties. Toward resolving the discrepancies between imaging and Hi-C, we sought to understand the spatiotemporal properties of NHCCs in living cells by CRISPR/Cas9 live-cell imaging (CLING). In mammalian cells, we find that NHCCs are stable and occur as frequently as intra-chromosomal interactions, but NHCCs occur at farther spatial distance that could explain their lack of detection in Hi-C. By revealing the spatiotemporal properties in living cells, our study provides fundamental insights into the biology of NHCCs.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Catherine L Weiner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
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75
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Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function. Nat Commun 2018; 9:292. [PMID: 29348663 PMCID: PMC5773557 DOI: 10.1038/s41467-017-02113-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022] Open
Abstract
The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark of endothelial homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS expression is modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations of eNOS, particularly through long non-coding RNAs (lncRNAs) and chromatin remodeling, remain to be explored. Here we identify an enhancer-associated lncRNA that enhances eNOS expression (LEENE). Combining RNA-sequencing and chromatin conformation capture methods, we demonstrate that LEENE is co-regulated with eNOS and that its enhancer resides in proximity to eNOS promoter in endothelial cells (ECs). Gain- and Loss-of-function of LEENE differentially regulate eNOS expression and EC function. Mechanistically, LEENE facilitates the recruitment of RNA Pol II to the eNOS promoter to enhance eNOS nascent RNA transcription. Our findings unravel a new layer in eNOS regulation and provide novel insights into cardiovascular regulation involving endothelial function. eNOS expression is dynamically regulated both transcriptionally and post-transcriptionally by various stimuli. Here the authors identify an enhancer-associated lncRNA (LEENE) that is co-regulated with, and enhances eNOS expression.
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76
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Brejc K, Bian Q, Uzawa S, Wheeler BS, Anderson EC, King DS, Kranzusch PJ, Preston CG, Meyer BJ. Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase. Cell 2017; 171:85-102.e23. [PMID: 28867287 PMCID: PMC5678999 DOI: 10.1016/j.cell.2017.07.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/25/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023]
Abstract
Chromatin modification and higher-order chromosome structure play key roles in gene regulation, but their functional interplay in controlling gene expression is elusive. We have discovered the machinery and mechanism underlying the dynamic enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during C. elegans dosage compensation and demonstrated H4K20me1's pivotal role in regulating higher-order chromosome structure and X-chromosome-wide gene expression. The structure and the activity of the dosage compensation complex (DCC) subunit DPY-21 define a Jumonji demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals. Selective inactivation of demethylase activity eliminates H4K20me1 enrichment in somatic cells, elevates X-linked gene expression, reduces X chromosome compaction, and disrupts X chromosome conformation by diminishing the formation of topologically associating domains (TADs). Unexpectedly, DPY-21 also associates with autosomes of germ cells in a DCC-independent manner to enrich H4K20me1 and trigger chromosome compaction. Our findings demonstrate the direct link between chromatin modification and higher-order chromosome structure in long-range regulation of gene expression.
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Affiliation(s)
- Katjuša Brejc
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Qian Bian
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Satoru Uzawa
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Bayly S Wheeler
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Erika C Anderson
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - David S King
- HHMI Mass Spectrometry Laboratory, University of California, Berkeley, Berkeley, California 94720-3204, USA
| | - Philip J Kranzusch
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Christine G Preston
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Barbara J Meyer
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA.
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77
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Fudenberg G, Imakaev M. FISH-ing for captured contacts: towards reconciling FISH and 3C. Nat Methods 2017; 14:673-678. [PMID: 28604723 PMCID: PMC5517086 DOI: 10.1038/nmeth.4329] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/03/2017] [Indexed: 11/20/2022]
Abstract
Chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) are two widely used technologies that provide distinct readouts of 3D chromosome organization. While both technologies can assay locus-specific organization, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. Contact frequency, measured by Hi-C, and spatial distance, measured by FISH, are often assumed to quantify the same phenomena and used interchangeably. Here, however, we demonstrate that contact frequency is distinct from average spatial distance, both in polymer simulations and in experimental data. Performing a systematic analysis of the technologies, we show that this distinction can create a seemingly paradoxical relationship between 3C and FISH, both in minimal polymer models with dynamic looping interactions and in loop-extrusion simulations. Together, our results indicate that cross-validation of Hi-C and FISH should be carefully designed, and that jointly considering contact frequency and spatial distance is crucial for fully understanding chromosome organization.
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Affiliation(s)
- Geoffrey Fudenberg
- Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maxim Imakaev
- Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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78
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Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 2017; 169:930-944.e22. [PMID: 28525758 PMCID: PMC5538188 DOI: 10.1016/j.cell.2017.05.004] [Citation(s) in RCA: 1050] [Impact Index Per Article: 150.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023]
Abstract
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Johan H Gibcus
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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79
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Abstract
The spatial organization of genomes is studied using microscopy- and chromosome conformation capture (3C)-based methods. The two types of methods produce data that are often consistent, but there are cases where they appear discordant. These cases provide opportunities to derive better models of chromatin folding, which can reconcile the datasets.
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Affiliation(s)
- Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605-0103, USA
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80
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Zhan Y, Giorgetti L, Tiana G. Modelling genome-wide topological associating domains in mouse embryonic stem cells. Chromosome Res 2017; 25:5-14. [PMID: 28108933 DOI: 10.1007/s10577-016-9544-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023]
Abstract
Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre. However, coarse-grained polymer models based on 5C data can be used to extract the single-cell conformations of single TADs. Here, we extend this approach to analyse around 2500 TADs in murine embryonic stem cells based on high-resolution Hi-C data. This allowed to predict the cell-to-cell variability in single contacts within genome-wide TADs and correlations between them. Based on these results, we predict that TADs are more similar to ideal chains than to globules in terms of their physical size and three-dimensional shape distribution. Furthermore, we show that their physical size and the degree of structural anisotropy of single TADs are correlated with the level of transcriptional activity of the genes that it harbours. Finally, we show that a large number of multiplets of genomic loci co-localize more often than expected by random, and these loci are particularly enriched in promoters, enhancers and CTCF-bound sites. These results provide the first genome-wide structural reconstruction of TADs using polymeric models obeying the laws of thermodynamics and reveal important universal trends in the correlation between chromosome structure and transcription.
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Affiliation(s)
- Y Zhan
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland
| | - L Giorgetti
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland.
| | - G Tiana
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, I-20133, Milan, Italy.
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