51
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Carelli FN, Sharma G, Ahringer J. Broad Chromatin Domains: An Important Facet of Genome Regulation. Bioessays 2017; 39. [PMID: 29058338 DOI: 10.1002/bies.201700124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/09/2017] [Indexed: 12/19/2022]
Abstract
Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans.
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Affiliation(s)
- Francesco N Carelli
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Garima Sharma
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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52
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Zanon C, Tonini GP. Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains. Mol Oncol 2017; 11:1646-1658. [PMID: 28941026 PMCID: PMC5664000 DOI: 10.1002/1878-0261.12139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022] Open
Abstract
Chromosome instability has a pivotal role among the hallmarks of cancer, but its transcriptional counterpart is rarely considered a relevant factor in cell destabilization. To examine transcription instability (TIN), we first devised a metric we named TIN index and used it to evaluate TIN on a dataset containing more than 500 neuroblastoma samples. We found that metastatic tumors from high-risk (HR) patients are characterized by significantly different TIN index values compared to low/intermediate-risk patients. Our results indicate that the TIN index is a good predictor of neuroblastoma patient's outcome, and a related TIN index gene signature (TIN-signature) is also able to predict the neuroblastoma patient's outcome with high confidence. Interestingly, we find that TIN-signature genes have a strong positional association with superenhancers in neuroblastoma tumors. Finally, we show that TIN is linked to chromatin structural domains and interferes with their integrity in HR neuroblastoma patients. This novel approach to gene expression analysis broadens the perspective of genome instability investigations to include functional aspects.
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Affiliation(s)
- Carlo Zanon
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
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53
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Razin SV, Ulianov SV. Gene functioning and storage within a folded genome. Cell Mol Biol Lett 2017; 22:18. [PMID: 28861108 PMCID: PMC5575855 DOI: 10.1186/s11658-017-0050-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/24/2017] [Indexed: 01/28/2023] Open
Abstract
In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome. This article was specially invited by the editors and represents work by leading researchers.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
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54
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Darbellay F, Duboule D. Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci. Curr Top Dev Biol 2017; 116:299-314. [PMID: 26970625 DOI: 10.1016/bs.ctdb.2015.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was due to the accumulation of long-range regulations flanking Hox loci, a phenomenon made possible by the successive genome duplications that occurred at the root of the vertebrate lineage, similar to gene neofunctionalization but applied to a coordinated multigenic system. Here, we propose that the emergence of such large vertebrate regulatory landscapes containing a range of global enhancers was greatly facilitated by the presence of topologically associating domains (TADs). These chromatin domains, mostly constitutive, may have been used as genomic niches where novel regulations could evolve due to both the preexistence of a structural backbone poised to integrate novel regulatory inputs, and a highly adaptive transcriptional readout. We propose a scenario for the coevolution of such TADs and the emergence of pleiotropy at ancestral vertebrate Hox loci.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland; Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
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55
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Chechetkin VR, Lobzin VV. Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique. J Theor Biol 2017; 426:162-179. [PMID: 28552553 DOI: 10.1016/j.jtbi.2017.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/23/2017] [Accepted: 05/23/2017] [Indexed: 12/15/2022]
Abstract
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. coli K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization.
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Affiliation(s)
- V R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilov str., 32, Moscow 119334, Russia; Theoretical Department of Division for Perspective Investigations, Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Moscow, Troitsk District 108840, Russia.
| | - V V Lobzin
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia.
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56
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Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 2017; 33:364-377. [PMID: 28065669 PMCID: PMC5410391 DOI: 10.1016/j.pt.2016.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022]
Abstract
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined. Finally, we address the use of epigenetic processes as targets for novel antimalarial therapies. Collectively, these topics highlight the unique biology of P. falciparum, and contribute to our understanding of mechanisms regulating gene expression in this deadly parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M Lu
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
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Kovina AP, Petrova NV, Gushchanskaya ES, Dolgushin KV, Gerasimov ES, Galitsyna AA, Penin AA, Flyamer IM, Ioudinkova ES, Gavrilov AA, Vassetzky YS, Ulianov SV, Iarovaia OV, Razin SV. Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters. Mol Biol Evol 2017; 34:1492-1504. [DOI: 10.1093/molbev/msx100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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58
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Acemel RD, Maeso I, Gómez-Skarmeta JL. Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [DOI: 10.1002/wdev.265] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/15/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo (CABD); Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide; Seville Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD); Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide; Seville Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD); Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide; Seville Spain
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59
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Tschopp P, Tabin CJ. Deep homology in the age of next-generation sequencing. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150475. [PMID: 27994118 PMCID: PMC5182409 DOI: 10.1098/rstb.2015.0475] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2016] [Indexed: 12/14/2022] Open
Abstract
The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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60
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Barutcu AR, Lian JB, Stein JL, Stein GS, Imbalzano AN. The connection between BRG1, CTCF and topoisomerases at TAD boundaries. Nucleus 2017; 8:150-155. [PMID: 28060558 PMCID: PMC5403164 DOI: 10.1080/19491034.2016.1276145] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries. In this review, we elaborate on our findings and speculate that BRG1 may contribute to the regulation of the structural and functional properties of chromatin at TAD boundaries by affecting the function or the recruitment of CTCF and DNA topoisomerase complexes.
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Affiliation(s)
- A Rasim Barutcu
- a Department of Cell and Developmental Biology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Jane B Lian
- b Department of Biochemistry , University of Vermont College of Medicine , Burlington , VT , USA
| | - Janet L Stein
- b Department of Biochemistry , University of Vermont College of Medicine , Burlington , VT , USA
| | - Gary S Stein
- b Department of Biochemistry , University of Vermont College of Medicine , Burlington , VT , USA
| | - Anthony N Imbalzano
- a Department of Cell and Developmental Biology , University of Massachusetts Medical School , Worcester , MA , USA
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61
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Rana V, Bosco G. Condensin Regulation of Genome Architecture. J Cell Physiol 2017; 232:1617-1625. [PMID: 27888504 DOI: 10.1002/jcp.25702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
Condensin complexes exist across all domains of life and are central to the structure and organization of chromatin. As architectural proteins, condensins control chromatin compaction during interphase and mitosis. Condensin activity has been well studied in mitosis but have recently emerged as important regulators of genome organization and gene expression during interphase. Here, we focus our discussion on recent findings on the molecular mechanism and how condensins are used to shape chromosomes during interphase. These findings suggest condensin activity during interphase is required for proper chromosome organization. J. Cell. Physiol. 232: 1617-1625, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vibhuti Rana
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Giovanni Bosco
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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62
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Galupa R, Heard E. Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:267-278. [DOI: 10.1101/sqb.2017.82.035030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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63
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Wachsmuth M, Knoch TA, Rippe K. Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 2016; 9:57. [PMID: 28035241 PMCID: PMC5192577 DOI: 10.1186/s13072-016-0093-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
Background Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. Results Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells. We identify topologically and dynamically independent chromatin domains of ~1 Mb in size that are best described by a loop-cluster polymer model. Hydrodynamic relaxation times and gyration radii of domains are larger for open (161 ± 15 ms, 297 ± 9 nm) than for dense chromatin (88 ± 7 ms, 243 ± 6 nm) and increase globally upon chromatin hyperacetylation or ATP depletion. Conclusions Based on the domain structure and dynamics measurements, we propose a loop-cluster model for chromatin domains. It suggests that the regulation of chromatin accessibility for soluble factors displays a significantly stronger dependence on factor concentration than search processes within a static network. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0093-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tobias A Knoch
- Biophysical Genomics Group, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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64
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Abstract
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough understanding of nuclear architecture is fundamental to the study of nuclear processes in eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Here, we review experimental and computational methodologies for 3D genome analysis, with special focus on recent advances in high-throughput chromatin conformation capture (3C) techniques and data analysis.
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Affiliation(s)
- Anthony D Schmitt
- Ludwig Institute for Cancer Research and the University of California, San Diego (UCSD) Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ming Hu
- Department of Population Health, Division of Biostatistics, New York University School of Medicine, 650 First Avenue, Room 540, New York, New York 10016, USA
- Present address: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego (UCSD) School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
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65
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Maeso I, Acemel RD, Gómez-Skarmeta JL. Cis-regulatory landscapes in development and evolution. Curr Opin Genet Dev 2016; 43:17-22. [PMID: 27842294 DOI: 10.1016/j.gde.2016.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
The recent advances in our understanding of the 3D organization of the chromatin together with an almost unlimited ability to detect cis-regulatory elements genome-wide using different biochemical signatures has provided us with an unprecedented power to study gene regulation. It is now possible to profile the complete regulatory apparatus controlling the spatio-temporal expression of any given gene, the so-called gene Regulatory Landscapes (RLs). Here we review several studies over the last two years demonstrating the functional consequences of altering RL structure in development, disease and evolution. These works clearly show that a deep understanding of transcriptional regulation is no longer conceivable without considering the 3D modular organization of animal genomes.
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Affiliation(s)
- Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain.
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Carretera de Utrera Km1, Seville, Spain.
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66
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Barutcu AR, Hong D, Lajoie BR, McCord RP, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1389-1397. [PMID: 27514584 PMCID: PMC5071180 DOI: 10.1016/j.bbagrm.2016.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023]
Abstract
RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organization. We characterized genome-wide RUNX1 localization and performed RNA-seq and Hi-C in RUNX1-depleted and control MCF-7 breast cancer cells. RNA-seq analysis showed that RUNX1 depletion led to up-regulation of genes associated with chromatin structure and down-regulation of genes related to extracellular matrix biology, as well as NEAT1 and MALAT1 lncRNAs. Our ChIP-Seq analysis supports a prominent role for RUNX1 in transcriptional activation. About 30% of all RUNX1 binding sites were intergenic, indicating diverse roles in promoter and enhancer regulation and suggesting additional functions for RUNX1. Hi-C analysis of RUNX1-depleted cells demonstrated that overall three-dimensional genome organization is largely intact, but indicated enhanced association of RUNX1 near Topologically Associating Domain (TAD) boundaries and alterations in long-range interactions. These results suggest an architectural role for RUNX1 in fine-tuning local interactions rather than in global organization. Our results provide novel insight into RUNX1-mediated perturbations of higher-order genome organization that are functionally linked with RUNX1-dependent compromised gene expression in breast cancer cells.
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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
| | - Deli Hong
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Bryan R Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Rachel Patton McCord
- Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Andre J van Wijnen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Jane B Lian
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, 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 Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
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Dumler JS, Sinclair SH, Pappas-Brown V, Shetty AC. Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression. Front Cell Infect Microbiol 2016; 6:97. [PMID: 27703927 PMCID: PMC5028410 DOI: 10.3389/fcimb.2016.00097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils, and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR)-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: (i) intergenic regions predicted to be MARs; (ii) within predicted lamina-associated domains; and (iii) at promoters ≤ 3000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome “re-organizer.” AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.
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Affiliation(s)
- J Stephen Dumler
- Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences Bethesda, MD, USA
| | | | - Valeria Pappas-Brown
- Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences Bethesda, MD, USA
| | - Amol C Shetty
- Informatics Resource Center, Institute for Genome Sciences, University of Maryland Baltimore, MD, USA
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68
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Abstract
Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle. Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination. Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes.
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Affiliation(s)
- Matthias Merkenschlager
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom;
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158;
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69
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Barutcu AR, Lajoie BR, Fritz AJ, McCord RP, Nickerson JA, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Stein GS, Imbalzano AN. SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells. Genome Res 2016; 26:1188-201. [PMID: 27435934 PMCID: PMC5052043 DOI: 10.1101/gr.201624.115] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/08/2016] [Indexed: 01/20/2023]
Abstract
The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Bryan R Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Andrew J Fritz
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
| | - Rachel P McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Andre J van Wijnen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jane B Lian
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
| | - Janet L Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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70
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Single-cell genome-wide studies give new insight into nongenetic cell-to-cell variability in animals. Histochem Cell Biol 2016; 146:239-54. [DOI: 10.1007/s00418-016-1466-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2016] [Indexed: 01/21/2023]
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71
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Vasquez PA, Hult C, Adalsteinsson D, Lawrimore J, Forest MG, Bloom K. Entropy gives rise to topologically associating domains. Nucleic Acids Res 2016; 44:5540-9. [PMID: 27257057 PMCID: PMC4937343 DOI: 10.1093/nar/gkw510] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/06/2016] [Accepted: 05/25/2016] [Indexed: 12/15/2022] Open
Abstract
We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.
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Affiliation(s)
- Paula A Vasquez
- Department of Mathematics, University of South Carolina, Columbia, SC 29808, USA
| | - Caitlin Hult
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark G Forest
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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72
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Liquid-like behavior of chromatin. Curr Opin Genet Dev 2016; 37:36-45. [DOI: 10.1016/j.gde.2015.11.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022]
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73
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Lupiáñez DG, Spielmann M, Mundlos S. Breaking TADs: How Alterations of Chromatin Domains Result in Disease. Trends Genet 2016; 32:225-237. [DOI: 10.1016/j.tig.2016.01.003] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
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74
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Fujioka M, Mistry H, Schedl P, Jaynes JB. Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans. PLoS Genet 2016; 12:e1005889. [PMID: 26910731 PMCID: PMC4765946 DOI: 10.1371/journal.pgen.1005889] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/30/2016] [Indexed: 12/11/2022] Open
Abstract
The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible for both subdividing the chromatin fiber into discrete domains, and determining the topological organization of these domains. Central to the architectural functions of insulators are heterologous and homologous insulator:insulator pairing interactions. In Drosophila, the former defines the topology of individual looped domains in cis, while the latter dictates the process of homolog alignment and pairing in trans. Here we use two insulators from the even skipped locus to elucidate the principles governing these two architectural functions. These principles align with several longstanding observations, and resolve a number of conundrums regarding chromosome topology and function.
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Affiliation(s)
- Miki Fujioka
- Deptartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Hemlata Mistry
- Departments of Biology and Biochemistry, Widener University, Chester, Pennsylvania, United States of America
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (PS); (JBJ)
| | - James B. Jaynes
- Deptartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PS); (JBJ)
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75
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Abstract
'Epigenome' refers to the panoply of chemical modifications borne by DNA and its associated proteins that locally affect genome function. Epigenomic patterns are thought to be determined by external constraints resulting from development, disease and the environment, but DNA sequence is also a potential influence. We propose that domains of relatively uniform DNA base composition may modulate the epigenome through cell type-specific proteins that recognize short, frequent sequence motifs. Differential recruitment of epigenomic modifiers may adjust gene expression in multigene blocks as an alternative to tuning the activity of each gene separately, thus simplifying gene expression programming.
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76
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Visualizing the HoxD Gene Cluster at the Nanoscale Level. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:9-16. [PMID: 26767994 DOI: 10.1101/sqb.2015.80.027177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcription of HoxD cluster genes in limbs is coordinated by two topologically associating domains (TADs), neighboring the cluster and containing various enhancers. Here, we use a combination of microscopy approaches and chromosome conformation capture to assess the structural changes occurring in this global architecture in various functional states. We observed that despite their spatial juxtaposition, the TADs are consistently kept as distinct three-dimensional units. Hox genes located at their boundary can show significant spatial segregation over long distances, suggesting that physical elongation of the HoxD cluster occurs. The use of superresolution imaging (STORM [stochastic optical reconstruction microscopy]) revealed that the gene cluster can be in an either compact or elongated shape. The latter configuration is observed in transcriptionally active tissue and in embryonic stem cells, consistent with chromosome conformation capture results. Such morphological changes at HoxD in developing digits seem to be associated with its position at the boundary between two TADs and support the idea that chromatin dynamics is important in the establishment of transcriptional activity.
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77
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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78
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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79
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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80
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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81
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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82
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Matsunaga S. FISH Is in the Limelight Again As More Than a Cytogenetical Technique for Metaphase Chromosomes. CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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83
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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84
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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85
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Barutcu AR, Fritz AJ, Zaidi SK, vanWijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016; 231:31-5. [PMID: 26059817 PMCID: PMC4586368 DOI: 10.1002/jcp.25062] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
Three-dimensional organization of the chromatin has important roles in transcription, replication, DNA repair, and pathologic events such as translocations. There are two fundamental ways to study higher-order chromatin organization: microscopic and molecular approaches. In this review, we briefly introduce the molecular approaches, focusing on chromosome conformation capture or "3C" technology and its derivatives, which can be used to probe chromatin folding at resolutions beyond that provided by microscopy techniques. We further discuss the different types of data generated by the 3C-based methods and how they can be used to answer distinct biological questions.
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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
| | - Andrew J. Fritz
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology, 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, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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86
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Ferrier DEK. The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal. Brief Funct Genomics 2015; 15:333-41. [PMID: 26637506 DOI: 10.1093/bfgp/elv056] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A key aim in evolutionary biology is to deduce ancestral states to better understand the evolutionary origins of clades of interest and the diversification process(es) that has/have elaborated them. These ancestral deductions can hit difficulties when undetected loss events are misinterpreted as ancestral absences. With the ever-increasing amounts of animal genomic sequence data, we are gaining a much clearer view of the preponderance of differential gene losses across animal lineages. This has become particularly clear with recent progress in our understanding of the origins of the Hox/ParaHox developmental control genes relative to the earliest branching lineages of the animal kingdom: the sponges (Porifera), comb jellies (Ctenophora) and placozoans (Placozoa). These reassessments of the diversity and complexity of developmental control genes in the earliest animal ancestors need to go hand-in-hand with complementary advances in comparative morphology, phylogenetics and palaeontology to clarify our understanding of the complexity of the last common ancestor of all animals. The field is currently undergoing a shift from the traditional consensus of a sponge-like animal ancestor from which morphological and molecular elaboration subsequently evolved, to a scenario of a more complex animal ancestor, with subsequent losses and simplifications in various lineages.
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87
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Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:169-85. [PMID: 26558551 DOI: 10.1002/wdev.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Abstract
During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Hörnblad
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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88
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Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states. Proc Natl Acad Sci U S A 2015; 112:13964-9. [PMID: 26504220 DOI: 10.1073/pnas.1517972112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around the HoxD gene cluster. This reorganization follows a global transition from one set of regulatory contacts to another, between two topologically associating domains (TADs) located on either side of the HoxD locus. Here, we use 3D DNA FISH to assess the spatial organization of chromatin at and around the HoxD gene cluster and report that although the two TADs are tightly associated, they appear as spatially distinct units. We measured the relative position of genes within the cluster and found that they segregate over long distances, suggesting that a physical elongation of the HoxD cluster can occur. We analyzed this possibility by super-resolution imaging (STORM) and found that tissues with distinct transcriptional activity exhibit differing degrees of elongation. We also observed that the morphological change of the HoxD cluster in developing digits is associated with its position at the boundary between the two TADs. Such variations in the fine-scale architecture of the gene cluster suggest causal links among its spatial configuration, transcriptional activation, and the flanking chromatin context.
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89
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Golovnin A, Melnikova L, Shapovalov I, Kostyuchenko M, Georgiev P. EAST Organizes Drosophila Insulator Proteins in the Interchromosomal Nuclear Compartment and Modulates CP190 Binding to Chromatin. PLoS One 2015; 10:e0140991. [PMID: 26489095 PMCID: PMC4638101 DOI: 10.1371/journal.pone.0140991] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/02/2015] [Indexed: 12/02/2022] Open
Abstract
Recent data suggest that insulators organize chromatin architecture in the nucleus. The best studied Drosophila insulator proteins, dCTCF (a homolog of the vertebrate insulator protein CTCF) and Su(Hw), are DNA-binding zinc finger proteins. Different isoforms of the BTB-containing protein Mod(mdg4) interact with Su(Hw) and dCTCF. The CP190 protein is a cofactor for the dCTCF and Su(Hw) insulators. CP190 is required for the functional activity of insulator proteins and is involved in the aggregation of the insulator proteins into specific structures named nuclear speckles. Here, we have shown that the nuclear distribution of CP190 is dependent on the level of EAST protein, an essential component of the interchromatin compartment. EAST interacts with CP190 and Mod(mdg4)-67.2 proteins in vitro and in vivo. Over-expression of EAST in S2 cells leads to an extrusion of the CP190 from the insulator bodies containing Su(Hw), Mod(mdg4)-67.2, and dCTCF. In consistent with the role of the insulator bodies in assembly of protein complexes, EAST over-expression led to a striking decrease of the CP190 binding with the dCTCF and Su(Hw) dependent insulators and promoters. These results suggest that EAST is involved in the regulation of CP190 nuclear localization.
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Affiliation(s)
- Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Igor Shapovalov
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
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90
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Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. Cell Rep 2015; 13:337-49. [PMID: 26411685 PMCID: PMC4617833 DOI: 10.1016/j.celrep.2015.08.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022] Open
Abstract
Expression of Pitx2 on the left side of the embryo patterns left-right (LR) organs including the dorsal mesentery (DM), whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr), are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH), and variations of chromatin conformation capture (3C) demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.
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Affiliation(s)
- Ian C Welsh
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Frances L Chen
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Melissa Werner
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lindsay S Shopland
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Eastern Maine Medical Center Cancer Care, 33 Whiting Hill Road, Brewer, ME 04412, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Min Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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91
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Kelsey AD, Yang C, Leung D, Minks J, Dixon-McDougall T, Baldry SEL, Bogutz AB, Lefebvre L, Brown CJ. Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST. Genome Biol 2015; 16:208. [PMID: 26429547 PMCID: PMC4591629 DOI: 10.1186/s13059-015-0774-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosomes in mammalian females. To understand how the RNA can establish silencing across millions of basepairs of DNA we have modelled the process by inducing expression of XIST from nine different locations in human HT1080 cells. Results Localization of XIST, depletion of Cot-1 RNA, perinuclear localization, and ubiquitination of H2A occurs at all sites examined, while recruitment of H3K9me3 was not observed. Recruitment of the heterochromatic features SMCHD1, macroH2A, H3K27me3, and H4K20me1 occurs independently of each other in an integration site-dependent manner. Silencing of flanking reporter genes occurs at all sites, but the spread of silencing to flanking endogenous human genes is variable in extent of silencing as well as extent of spread, with silencing able to skip regions. The spread of H3K27me3 and loss of H3K27ac correlates with the pre-existing levels of the modifications, and overall the extent of silencing correlates with the ability to recruit additional heterochromatic features. Conclusions The non-coding RNA XIST functions as a cis-acting silencer when expressed from nine different locations throughout the genome. A hierarchy among the features of heterochromatin reveals the importance of interaction with the local chromatin neighborhood for optimal spread of silencing, as well as the independent yet cooperative nature of the establishment of heterochromatin by the non-coding XIST RNA. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0774-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela D Kelsey
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Christine Yang
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Danny Leung
- Ludwig Institute for Cancer Research, University of California at San Diego School of Medicine, La Jolla, CA, USA. .,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Jakub Minks
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Thomas Dixon-McDougall
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Sarah E L Baldry
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Aaron B Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
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92
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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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93
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Akdemir KC, Chin L. HiCPlotter integrates genomic data with interaction matrices. Genome Biol 2015; 16:198. [PMID: 26392354 PMCID: PMC4576377 DOI: 10.1186/s13059-015-0767-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/02/2015] [Indexed: 11/10/2022] Open
Abstract
Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or the presence of architectural proteins have been implicated in regulation and assembly of the chromatin architecture. Therefore, comprehensive visualization of this multi-faceted structure is important to unravel the connections between nuclear architecture and transcriptional regulation. Here, we present an easy-to-use open-source visualization tool, HiCPlotter, to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. https://github.com/kcakdemir/HiCPlotter
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Affiliation(s)
- Kadir Caner Akdemir
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Lynda Chin
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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94
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Bartman CR, Blobel GA. Perturbing Chromatin Structure to Understand Mechanisms of Gene Expression. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:207-12. [PMID: 26370411 DOI: 10.1101/sqb.2015.80.027359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The study of nuclear structure falls between the fields of cell biology and molecular biology and draws on techniques from both fields. In recent years, many exciting advances have been made in these areas, including single-molecule and superresolution imaging and the development of chromosome conformation capture (3C)-based technologies, which have brought the advent of genome-wide analysis of chromatin structure and contacts. However, many questions remain as to the function of nuclear structures, in particular their influence on transcription. Here we describe studies that have directly manipulated nuclear architecture at various levels and thus have clarified the causal influence of structure on transcription. We will also highlight open questions in the field, most notably regarding our understanding of the dynamics and variability in nuclear structure and its influence on gene expression.
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Affiliation(s)
- Caroline R Bartman
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania 19104 Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania 19104 Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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95
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Abstract
The respiratory endoderm develops from a small cluster of cells located on the ventral anterior foregut. This population of progenitors generates the myriad epithelial lineages required for proper lung function in adults through a complex and delicately balanced series of developmental events controlled by many critical signaling and transcription factor pathways. In the past decade, understanding of this process has grown enormously, helped in part by cell lineage fate analysis and deep sequencing of the transcriptomes of various progenitors and differentiated cell types. This review explores how these new techniques, coupled with more traditional approaches, have provided a detailed picture of development of the epithelial lineages in the lung and insight into how aberrant development can lead to lung disease.
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96
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Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. FEBS Lett 2015; 589:2877-84. [PMID: 26348399 DOI: 10.1016/j.febslet.2015.08.044] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization. Here we outline our current understanding of such domains in different organisms and their roles in gene regulation.
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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, MA 01605, USA.
| | - Edith Heard
- Institut Curie, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.
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97
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Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biol 2015; 16:183. [PMID: 26328929 PMCID: PMC4556012 DOI: 10.1186/s13059-015-0745-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/10/2015] [Indexed: 11/10/2022] Open
Abstract
The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome. In particular, with recent trends towards higher-resolution high-throughput chromosome conformation capture (Hi-C) data, the diversity and complexity of biological hypotheses that can be tested necessitates rigorous computational and statistical methods as well as scalable pipelines to interpret these datasets. Here we review computational tools to interpret Hi-C data, including pipelines for mapping, filtering, and normalization, and methods for confidence estimation, domain calling, visualization, and three-dimensional modeling.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Feinberg School of Medicine, Northwestern University, Chicago, 60661, IL, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Department of Computer Science and Engineering, University of Washington, Seattle, 98195, WA, USA.
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98
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Functional Requirements for Fab-7 Boundary Activity in the Bithorax Complex. Mol Cell Biol 2015; 35:3739-52. [PMID: 26303531 DOI: 10.1128/mcb.00456-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/17/2015] [Indexed: 12/23/2022] Open
Abstract
Chromatin boundaries are architectural elements that determine the three-dimensional folding of the chromatin fiber and organize the chromosome into independent units of genetic activity. The Fab-7 boundary from the Drosophila bithorax complex (BX-C) is required for the parasegment-specific expression of the Abd-B gene. We have used a replacement strategy to identify sequences that are necessary and sufficient for Fab-7 boundary function in the BX-C. Fab-7 boundary activity is known to depend on factors that are stage specific, and we describe a novel ∼700-kDa complex, the late boundary complex (LBC), that binds to Fab-7 sequences that have insulator functions in late embryos and adults. We show that the LBC is enriched in nuclear extracts from late, but not early, embryos and that it contains three insulator proteins, GAF, Mod(mdg4), and E(y)2. Its DNA binding properties are unusual in that it requires a minimal sequence of >65 bp; however, other than a GAGA motif, the three Fab-7 LBC recognition elements display few sequence similarities. Finally, we show that mutations which abrogate LBC binding in vitro inactivate the Fab-7 boundary in the BX-C.
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99
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Poot M, Haaf T. Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. Mol Syndromol 2015; 6:110-34. [PMID: 26732513 DOI: 10.1159/000438812] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 01/08/2023] Open
Abstract
Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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100
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Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster. BMC Biol 2015; 13:63. [PMID: 26248466 PMCID: PMC4528719 DOI: 10.1186/s12915-015-0168-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/15/2015] [Indexed: 12/22/2022] Open
Abstract
Background Insulators play a central role in gene regulation, chromosomal architecture and genome function in higher eukaryotes. To learn more about how insulators carry out their diverse functions, we have begun an analysis of the Drosophila CTCF (dCTCF). CTCF is one of the few insulator proteins known to be conserved from flies to man. Results In the studies reported here we have focused on the identification and characterization of two dCTCF protein interaction modules. The first mediates dCTCF multimerization, while the second mediates dCTCF–CP190 interactions. The multimerization domain maps in the N-terminus of the dCTCF protein and likely mediates the formation of tetrameric complexes. The CP190 interaction module encompasses a sequence ~200 amino acids long that spans the C-terminal and mediates interactions with the N-terminal BTB domain of the CP190 protein. Transgene rescue experiments showed that a dCTCF protein lacking sequences critical for CP190 interactions was almost as effective as wild type in rescuing the phenotypic effects of a dCTCF null allele. The mutation did, however, affect CP190 recruitment to specific Drosophila insulator elements and had a modest effect on dCTCF chromatin association. A protein lacking the N-terminal dCTCF multimerization domain incompletely rescued the zygotic and maternal effect lethality of the null and did not rescue the defects in Abd-B regulation evident in surviving adult dCTCF mutant flies. Finally, we show that elimination of maternally contributed dCTCF at the onset of embryogenesis has quite different effects on development and Abd-B regulation than is observed when the homozygous mutant animals develop in the presence of maternally derived dCTCF activity. Conclusions Our results indicate that dCTCF–CP190 interactions are less critical for the in vivo functions of the dCTCF protein than the N-terminal dCTCF–dCTCF interaction domain. We also show that the phenotypic consequences of dCTCF mutations differ depending upon when and how dCTCF activity is lost. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0168-7) contains supplementary material, which is available to authorized users.
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