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Cattoni DI, Cardozo Gizzi AM, Georgieva M, Di Stefano M, Valeri A, Chamousset D, Houbron C, Déjardin S, Fiche JB, González I, Chang JM, Sexton T, Marti-Renom MA, Bantignies F, Cavalli G, Nollmann M. Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. Nat Commun 2017; 8:1753. [PMID: 29170434 PMCID: PMC5700980 DOI: 10.1038/s41467-017-01962-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/29/2017] [Indexed: 11/09/2022] Open
Abstract
At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we are able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs are to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small-frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.
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Affiliation(s)
- Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Andrés M Cardozo Gizzi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Mariya Georgieva
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Marco Di Stefano
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08010, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Alessandro Valeri
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Delphine Chamousset
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Christophe Houbron
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Stephanie Déjardin
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Inma González
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015, Paris, France
| | - Jia-Ming Chang
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
- Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan
| | - Thomas Sexton
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
- Institut de génétique et de biologie moléculaire et cellulaire, CNRS UMR 7104 - Inserm U 964, 67404, Illkirch, France
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08010, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Frédéric Bantignies
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Giacomo Cavalli
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France.
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Suciu N, Plaiasu V. A time stamp comparative analysis of frequent chromosomal abnormalities in Romanian patients. J Matern Fetal Neonatal Med 2013; 27:1-6. [DOI: 10.3109/14767058.2013.794215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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3
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Li S, Heermann DW. Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae. Nucleus 2013; 4:216-28. [PMID: 23674068 DOI: 10.4161/nucl.24875] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Among cellular processes gene transcription is central. More and more evidence is mounting that transcription is tightly connected with the spatial organization of the chromosomes. Spatial proximity of genes sharing transcriptional machinery is one of the consequences of this organization. Motivated by information on the physical relationship among genes identified via chromosomal conformation capture methods, we complement the spatial organization with the idea that genes under similar transcription factor control, but possible scattered throughout the genome, might be in physically proximity to facilitate the access of their commonly used transcription factors. Unlike the transcription factory model, "interacting" genes in our "Gene Proximity Model" are not necessarily immediate physical neighbors but are in spatial proximity. Considering the stochastic nature of TF-promoter binding, this local condensation mechanism could serve as a tie to recruit co-regulated genes to guarantee the swiftness of biological reactions. We tested this idea with a simple eukaryotic organism, Saccharomyces cerevisiae. Chromosomal interaction patterns and folding behavior generated by our model re-construct those obtained from experiments. We show that the transcriptional regulatory network has a close linkage with the genome organization in budding yeast, which is fundamental and instrumental to later studies on other more complex eukaryotes.
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Affiliation(s)
- Songling Li
- Institute for Theoretical Physics, University of Heidelberg, Heidelberg, Germany
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Gagniuc P, Ionescu-Tirgoviste C. Gene promoters show chromosome-specificity and reveal chromosome territories in humans. BMC Genomics 2013; 14:278. [PMID: 23617842 PMCID: PMC3668249 DOI: 10.1186/1471-2164-14-278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 02/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background Gene promoters have guided evolution processes for millions of years. It seems that they were the main engine responsible for the integration of different mutations favorable for the environmental conditions. In cooperation with different transcription factors and other biochemical components, these regulatory regions dictate the synthesis frequency of RNA molecules. Predominantly in the last decade, it has become clear that nuclear organization impacts upon gene regulation. To fully understand the connections between Homo sapiens chromosomes and their gene promoters, we analyzed 1200 promoter sequences using our Kappa Index of Coincidence method. Results In order to measure the structural similarity of gene promoters, we used two-dimensional image-based patterns obtained through Kappa Index of Coincidence (Kappa IC) and (C+G)% values. The center of weight of each promoter pattern indicated a structure similarity between promoters of each chromosome. Furthermore, the proximity of chromosomes seems to be in accordance to the structural similarity of their gene promoters. The arrangement of chromosomes according to Kappa IC values of promoters, shows a striking symmetry between the chromosome length and the structure of promoters located on them. High Kappa IC and (C+G)% values of gene promoters were also directly associated with the most frequent genetic diseases. Taking into consideration these observations, a general hypothesis for the evolutionary dynamics of the genome has been proposed. In this hypothesis, heterochromatin and euchromatin domains exchange DNA sequences according to a difference in the rate of Slipped Strand Mispairing and point mutations. Conclusions In this paper we showed that gene promoters appear to be specific to each chromosome. Furthermore, the proximity between chromosomes seems to be in accordance to the structural similarity of their gene promoters. Our findings are based on comprehensive data from Transcriptional Regulatory Element Database and a new computer model whose core is using Kappa index of coincidence.
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Affiliation(s)
- Paul Gagniuc
- Institute of Genetics, University of Bucharest, Bucharest, Romania.
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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Li S, Heermann DW. Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts. DNA Res 2012; 20:45-53. [PMID: 23213109 PMCID: PMC3576657 DOI: 10.1093/dnares/dss032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transcription-induced chimaeric transcripts, the potential post-transcriptional processing products, might reflect the spatial proximity of actively transcribed genes co-localized in transcription factories. A growing number of expression data deposited in databases provide us with the raw material for screening such chimaeric transcripts and using them as the probes to identify interactions between genes in cis or in trans. Based on the high-quality chimaeric transcripts gleaned from human expression sequence tag data with selection criteria, we identified the patterns of inter- and intrachromosomal gene–gene interactions. On top the contact pattern from interchromosomal interactions, we also observed an exponential behaviour of the intrachromosomal interactions within a certain length scale, which is consistent with the independent experimental results from Hi-C screening and with the Random Loop Model. A compatible result is found for mouse. Transcription-induced chimaeric transcripts, most of which might be accidental products with trivial functions, shed light on the spatial organization of chromosomes. These inter- and intrachromosomal interactions might contribute to the compaction of chromosomes, their segregation and formation of the chromosome territories, and their spatial distribution within the nucleus.
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Affiliation(s)
- Songling Li
- Theoretical Biophysics Group, Institute for Theoretical Physics, University of Heidelberg, Heidelberg, Germany
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Belmont AS. Estrogen fueled, nuclear kiss: did it move for you? Nucleus 2012; 1:440-3. [PMID: 21326827 DOI: 10.4161/nucl.1.5.13051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 07/16/2010] [Indexed: 11/19/2022] Open
Abstract
A paper appearing in late 2008,1 attracted considerable attention with its description of a dramatic juxtaposition of two estrogen responsive genes on different chromosomes within 15-60 minutes of adding estradiol. These results challenged a growing consensus of limited chromosome mobility within interphase nuclei, while raising questions of whether a hitherto unknown molecular mechanism might exist to move chromosomes long distances within the nucleus. These results also raised the fascinating question of how two genes on widely separated chromosomes might find each other over such a short time span. Now, a more recent paper reports no such long-range interaction or chromosome movements in the same cell types under what appear to be well replicated conditions, forcing a reexamination of the prior results.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Heterochromatin instability in cancer: from the Barr body to satellites and the nuclear periphery. Semin Cancer Biol 2012; 23:99-108. [PMID: 22722067 DOI: 10.1016/j.semcancer.2012.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/25/2012] [Accepted: 06/11/2012] [Indexed: 12/31/2022]
Abstract
In recent years it has been recognized that the development of cancer involves a series of not only genetic but epigenetic changes across the genome. At the same time, connections between epigenetic regulation, chromatin packaging, and overall nuclear architecture are increasingly appreciated. The cell-type specific organization of heterochromatin, established upon cell differentiation, is responsible for maintaining much of the genome in a repressed state, within a highly compartmentalized nucleus. This review focuses on recent evidence that in cancer the normal packaging and higher organization of heterochromatin is often compromised. Gross changes in nuclear morphology have long been a criterion for pathologic diagnosis of many cancers, but the specific nuclear components impacted, the mechanisms involved, and the implications for cancer progression have barely begun to emerge. We discuss recent findings regarding distinct heterochromatin types, including the inactive X chromosome, constitutive heterochromatin of peri/centric satellites, and the peripheral heterochromatic compartment (PHC). A theme developed here is that the higher-order organization of satellites and the peripheral heterochromatic compartment may be tightly linked, and that compromise of this organization may promote broad epigenomic imbalance in cancer. Recent studies into the potential role(s) of the breast cancer tumor suppressor, BRCA1, in maintaining heterochromatin will be highlighted. Many questions remain about this new area of cancer epigenetics, which is likely more important in cancer development and progression than widely appreciated. We propose that broad, stochastic compromise in heterochromatin maintenance would create a diversity of expression profiles, and thus a rich opportunity for one or more cells to emerge with a selective growth advantage and potential for neoplasia.
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Dorier J, Stasiak A. The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res 2010; 38:7410-21. [PMID: 20675721 PMCID: PMC2995080 DOI: 10.1093/nar/gkq666] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/29/2010] [Accepted: 07/15/2010] [Indexed: 11/14/2022] Open
Abstract
Using numerical simulations, we investigate the underlying physical effects responsible for the overall organization of chromosomal territories in interphase nuclei. In particular, we address the following three questions: (i) why are chromosomal territories with relatively high transcriptional activity on average, closer to the centre of cell's nucleus than those with the lower activity? (ii) Why are actively transcribed genes usually located at the periphery of their chromosomal territories? (iii) Why are pair-wise contacts between active and inactive genes less frequent than those involving only active or only inactive genes? We show that transcription factories-mediated contacts between active genes belonging to different chromosomal territories are instrumental for all these features of nuclear organization to emerge spontaneously due to entropic effects arising when chromatin fibres are highly crowded.
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Affiliation(s)
- Julien Dorier
- Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
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Tchélidzé P, Chatron-Colliet A, Thiry M, Lalun N, Bobichon H, Ploton D. Tomography of the cell nucleus using confocal microscopy and medium voltage electron microscopy. Crit Rev Oncol Hematol 2009; 69:127-43. [DOI: 10.1016/j.critrevonc.2008.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 07/18/2008] [Indexed: 12/18/2022] Open
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Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes. J Mol Evol 2008; 68:56-65. [DOI: 10.1007/s00239-008-9187-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 11/02/2008] [Accepted: 11/17/2008] [Indexed: 11/25/2022]
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12
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Falk M, Lukasova E, Gabrielova B, Ondrej V, Kozubek S. Local changes of higher-order chromatin structure during DSB-repair. ACTA ACUST UNITED AC 2008. [DOI: 10.1088/1742-6596/101/1/012018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Finch KA, Fonseka G, Ioannou D, Hickson N, Barclay Z, Chatzimeletiou K, Mantzouratou A, Handyside A, Delhanty J, Griffin DK. Nuclear organisation in totipotent human nuclei and its relationship to chromosomal abnormality. J Cell Sci 2008; 121:655-63. [DOI: 10.1242/jcs.025205] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Studies of nuclear organisation, most commonly determining the nuclear location of chromosome territories and individual loci, have furthered our understanding of nuclear function, differentiation and disease. In this study, by examining eight loci on different chromosomes, we tested hypotheses that: (1) totipotent human blastomeres adopt a nuclear organisation akin to that of committed cells; (2) nuclear organisation is different in chromosomally abnormal blastomeres; and (3) human blastomeres adopt a `chromocentre' pattern. Analysis of in vitro fertilisation (IVF) conceptuses permits valuable insight into the cell biology of totipotent human nuclei. Here, extrapolations from images of preimplantation genetic screening (PGS) cases were used to make comparisons between totipotent blastomeres and several committed cells, showing some differences and similarities. Comparisons between chromosomally abnormal nuclei and those with no detected abnormality (NDA) suggest that the former display a significant non-random pattern for all autosomal loci, but there is a less distinct, possibly random, pattern in `NDA' nuclei. No evidence was found that the presence of an extra chromosome is accompanied by an altered nuclear location for that chromosome. Centromeric loci on chromosomes 15 and 16 normally seen at the nuclear periphery were mostly centrally located in aneuploid cells, providing some evidence of a `chromocentre'; however, the chromosome-18 centromere was more peripheral, similar to committed cells. Our results provide clues to the nature of totipotency in human cells and might have future applications for preimplantation diagnosis and nuclear transfer.
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Affiliation(s)
- Katie A. Finch
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Gothami Fonseka
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Dimitris Ioannou
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Nicholas Hickson
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Zoe Barclay
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Katerina Chatzimeletiou
- The London Bridge Fertility, Gynaecology and Genetics Centre, 1 St Thomas Street, London Bridge, London, SE1 9RY, UK
| | - Anna Mantzouratou
- Department of Obstetrics and Gynaecology, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| | - Alan Handyside
- The London Bridge Fertility, Gynaecology and Genetics Centre, 1 St Thomas Street, London Bridge, London, SE1 9RY, UK
| | - Joy Delhanty
- Department of Obstetrics and Gynaecology, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| | - Darren K. Griffin
- Department of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
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Unneberg P, Claverie JM. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PLoS One 2007; 2:e254. [PMID: 17330142 PMCID: PMC1804257 DOI: 10.1371/journal.pone.0000254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 02/06/2007] [Indexed: 11/18/2022] Open
Abstract
Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology.
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Affiliation(s)
- Per Unneberg
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique (CNRS) UPR-2589, Institut de Biologie Structurale et Microbiologie, Marseille, France.
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Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol 2006; 18:307-16. [PMID: 16687245 DOI: 10.1016/j.ceb.2006.04.007] [Citation(s) in RCA: 475] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 04/10/2006] [Indexed: 11/17/2022]
Abstract
Understanding nuclear architecture is indispensable for understanding the cell-type-dependent orchestration of active and silent genes and other nuclear functions, such as RNA splicing, DNA replication and repair. Yet, while it is now generally agreed that chromosomes in the cell nucleus are organized as chromosome territories, present models of chromosome territory architecture differ widely with respect to the possible functional implications of dynamic changes of this architecture during the cell cycle and terminal cell differentiation.
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Affiliation(s)
- Thomas Cremer
- Department of Biology II, Ludwig-Maximilians-University, Grosshadernerstrasse 2, D-82152, Martinsried, Germany.
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