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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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2
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Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
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Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
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3
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Chromosome territory reorganization through artificial chromosome fusion is compatible with cell fate determination and mouse development. Cell Discov 2023; 9:11. [PMID: 36693846 PMCID: PMC9873915 DOI: 10.1038/s41421-022-00511-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/18/2022] [Indexed: 01/26/2023] Open
Abstract
Chromosomes occupy discrete spaces in the interphase cell nucleus, called chromosome territory. The structural and functional relevance of chromosome territory remains elusive. We fused chromosome 15 and 17 in mouse haploid embryonic stem cells (haESCs), resulting in distinct changes of territories in the cognate chromosomes, but with little effect on gene expression, pluripotency and gamete functions of haESCs. The karyotype-engineered haESCs were successfully implemented in generating heterozygous (2n = 39) and homozygous (2n = 38) mouse models. Mice containing the fusion chromosome are fertile, and their representative tissues and organs display no phenotypic abnormalities, suggesting unscathed development. These results indicate that the mammalian chromosome architectures are highly resilient, and reorganization of chromosome territories can be readily tolerated during cell differentiation and mouse development.
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4
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Purshouse K, Friman ET, Boyle S, Dewari PS, Grant V, Hamdan A, Morrison GM, Brennan PM, Beentjes SV, Pollard SM, Bickmore WA. Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells. eLife 2022; 11:e80207. [PMID: 36476408 PMCID: PMC9728993 DOI: 10.7554/elife.80207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022] Open
Abstract
Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size, and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional hubs, and that this underpins their elevated transcriptional activity. Here, we use super-resolution imaging and quantitative image analysis to evaluate GBM stem cells harbouring distinct ecDNA species (EGFR, CDK4, PDGFRA). We find no evidence that ecDNA routinely cluster with one another or closely interact with transcriptional hubs. Cells with EGFR-containing ecDNA have increased EGFR transcriptional output, but transcription per gene copy is similar in ecDNA compared to the endogenous chromosomal locus. These data suggest that it is the increased copy number of oncogene-harbouring ecDNA that primarily drives high levels of oncogene transcription, rather than specific interactions of ecDNA with each other or with high concentrations of the transcriptional machinery.
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Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
| | - Pooran Singh Dewari
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Vivien Grant
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Alhafidz Hamdan
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Gillian M Morrison
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Paul M Brennan
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
- Centre for Clinical Brain Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Sjoerd V Beentjes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
- School of Mathematics, University of EdinburghEdinburghUnited Kingdom
| | - Steven M Pollard
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
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5
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Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Rep 2022; 41:111730. [PMID: 36450242 PMCID: PMC9793828 DOI: 10.1016/j.celrep.2022.111730] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/14/2022] [Accepted: 11/04/2022] [Indexed: 12/02/2022] Open
Abstract
Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments-with multiple active genes simultaneously colocalizing within the same B compartment-and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.
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Affiliation(s)
- Isabel N Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Joanna W Jachowicz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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6
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Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell 2022; 33:ar72. [PMID: 35476603 PMCID: PMC9635277 DOI: 10.1091/mbc.e21-11-0593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chromosome structure and nuclear organization are important factors in the regulation of gene expression. Transcription of a gene is influenced by local and global chromosome features such as chromatin condensation status. The relationship between the 3D position of a gene in the nucleus and its activity is less clear. Here we used high-throughput imaging to perform a large-scale analysis of the spatial location of nearly 100 hypoxia-responsive genes to determine whether their location and activity state are correlated. Radial distance analysis demonstrated that the majority of Hypoxia-Inducible Factor (HIF)- and CREB-dependent hypoxia-responsive genes are located in the intermediate region of the nucleus, and some of them changed their radial position in hypoxia. Analysis of the relative distances among a subset of HIF target genes revealed that some gene pairs altered their relative location to each other on hypoxic treatment, suggesting higher-order chromatin rearrangements. While these changes in location occurred in response to hypoxic activation of the target genes, they did not correlate with the extent of their activation. These results suggest that induction of the hypoxia-responsive gene expression program is accompanied by spatial alterations of the genome, but that radial and relative gene positions are not directly related to gene activity.
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Affiliation(s)
- Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan.,Department of Pharmacology, School of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Elizabeth H Finn
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Hiroyuki Sato
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akihiro Hirakawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tom Misteli
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
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7
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:1368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
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8
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Yadav M, Jalan M, Srivastava M. Enhancer dependent repositioning of TCRb locus with respect to the chromosome territory. J Mol Biol 2022; 434:167509. [PMID: 35202629 DOI: 10.1016/j.jmb.2022.167509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022]
Abstract
Intranuclear position of several genes is dynamically altered during development concordant with their activation. To understand this dynamic, but non-random, nuclear organization, it is important to identify the relevant regulatory elements and trans acting factors. Murine TCRb locus gets activated during thymic development. Enhancer Eb is important for VDJ recombination at TCRb locus as it is critically required establishment of recombination center. Our analysis revealed that TCRb locus gets located out of the chromosome territory specifically in developing thymocytes. Further, CRISPR/Cas9 based deletion mutagenesis established an unambiguous role of enhancer Eb in defining TCRb location relative to chromosome territory. The ability to reposition the target locus relative to chromosome territory highlights a novel aspect pertaining to activity of enhancers which may contribute to their ability to regulate gene expression. Additionally, our observations have implications for understanding the role of enhancers in three-dimensional genome organization and function.
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Affiliation(s)
- Monika Yadav
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
| | - Manisha Jalan
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
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9
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022; 24:327-339. [PMID: 35177821 DOI: 10.1038/s41556-022-00847-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
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Affiliation(s)
- Susanne Leidescher
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Johannes Ribisel
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Ullrich
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Yana Feodorova
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Department of Medical Biology, Medical University of Plovdiv; Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Erica Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Sebastian Bultmann
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Stephanie Link
- BioMedizinisches Center, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Thanisch
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christopher Mulholland
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Heinrich Leonhardt
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irina Solovei
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.
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10
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The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model. Genes (Basel) 2021; 12:genes12101524. [PMID: 34680920 PMCID: PMC8535310 DOI: 10.3390/genes12101524] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 12/18/2022] Open
Abstract
The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.
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11
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Jin X, Fudenberg G, Pollard KS. Genome-wide variability in recombination activity is associated with meiotic chromatin organization. Genome Res 2021; 31:1561-1572. [PMID: 34301629 PMCID: PMC8415379 DOI: 10.1101/gr.275358.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022]
Abstract
Recombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, whereas variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, although PRDM9 binding peaks are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favored loci, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity. We propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Geoff Fudenberg
- Gladstone Institutes, San Francisco, California 94158, USA.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, California 94158, USA.,University of California San Francisco, San Francisco, California 94143, USA.,Chan-Zuckerberg Biohub, San Francisco, California 94158, USA
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12
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Bertero A. RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. Front Genet 2021; 12:645863. [PMID: 33732290 PMCID: PMC7957078 DOI: 10.3389/fgene.2021.645863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Three-dimensional (3D) genome organization has emerged as an important layer of gene regulation in development and disease. The functional properties of chromatin folding within individual chromosomes (i.e., intra-chromosomal or in cis) have been studied extensively. On the other hand, interactions across different chromosomes (i.e., inter-chromosomal or in trans) have received less attention, being often regarded as background noise or technical artifacts. This viewpoint has been challenged by emerging evidence of functional relationships between specific trans chromatin interactions and epigenetic control, transcription, and splicing. Therefore, it is an intriguing possibility that the key processes involved in the biogenesis of RNAs may both shape and be in turn influenced by inter-chromosomal genome architecture. Here I present the rationale behind this hypothesis, and discuss a potential experimental framework aimed at its formal testing. I present a specific example in the cardiac myocyte, a well-studied post-mitotic cell whose development and response to stress are associated with marked rearrangements of chromatin topology both in cis and in trans. I argue that RNA polymerase II clusters (i.e., transcription factories) and foci of the cardiac-specific splicing regulator RBM20 (i.e., splicing factories) exemplify the existence of trans-interacting chromatin domains (TIDs) with important roles in cellular homeostasis. Overall, I propose that inter-molecular 3D proximity between co-regulated nucleic acids may be a pervasive functional mechanism in biology.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
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13
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Singchat W, Ahmad SF, Laopichienpong N, Suntronpong A, Panthum T, Griffin DK, Srikulnath K. Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome. Cells 2020; 9:cells9112386. [PMID: 33142713 PMCID: PMC7692289 DOI: 10.3390/cells9112386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence: ; Tel.: +66-2562-5644
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14
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Abstract
Current methods for chromosome painting via fluorescence in situ hybridization (FISH) are costly, time-consuming, and limited in complexity. In contrast to conventional sources of probe, Oligopaints are computationally designed, synthesized on microarrays, and amplified by PCR. This approach allows for precise control over the sequences they target, which can range from a few kilobases to entire chromosomes with the same basic protocol. We have utilized the flexibility and scalability of Oligopaints to generate low-cost and renewable chromosome paints for Drosophila, mouse, and human chromosomes. These Oligopaint libraries can be customized to label any genomic feature(s) in a chromosome-wide manner. Additionally, this method is compatible with sequential FISH to label entire genomes with a single denaturation step. Here, we outline a protocol and considerations to scale the Oligopaint technology for fluorescent labeling of whole chromosomes.
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15
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Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet 2020; 36:273-287. [PMID: 32007290 PMCID: PMC7197267 DOI: 10.1016/j.tig.2019.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.
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Affiliation(s)
- Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Sedona Murphy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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16
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Crosetto N, Bienko M. Radial Organization in the Mammalian Nucleus. Front Genet 2020; 11:33. [PMID: 32117447 PMCID: PMC7028756 DOI: 10.3389/fgene.2020.00033] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, most of the genetic material is contained within a highly specialized organelle-the nucleus. A large body of evidence indicates that, within the nucleus, chromatinized DNA is spatially organized at multiple length scales. The higher-order organization of chromatin is crucial for proper execution of multiple genome functions, including DNA replication and transcription. Here, we review our current knowledge on the spatial organization of chromatin in the nucleus of mammalian cells, focusing in particular on how chromatin is radially arranged with respect to the nuclear lamina. We then discuss the possible mechanisms by which the radial organization of chromatin in the cell nucleus is established. Lastly, we propose a unifying model of nuclear spatial organization, and suggest novel approaches to test it.
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Affiliation(s)
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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17
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Kumar Y, Sengupta D, Bickmore WA. Recent advances in the spatial organization of the mammalian genome. J Biosci 2020. [DOI: 10.1007/s12038-019-9968-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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18
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Kumar Y, Sengupta D, Bickmore W. Recent advances in the spatial organization of the mammalian genome. J Biosci 2020; 45:18. [PMID: 31965996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mammalian genome is complex and presents a dynamic structural organization that reflects function. Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but not limited to transcription, replication and repair, and in many biological contexts such as early development, differentiation and physiological adaptations. However, there is limited understating of how 3D organization of the mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad of genomics methods -- ropelled by next-generation sequencing -- have advanced our knowledge of genome organization to a great extent. In this review, we discuss nuclear compartments in general and recent advances in the understanding of how mammalian genome is organized in these compartments with an emphasis on dynamics at the nuclear periphery.
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Affiliation(s)
- Yatendra Kumar
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road South, Edinburgh EH42XU, UK
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19
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Oluwadare O, Highsmith M, Cheng J. An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data. Biol Proced Online 2019; 21:7. [PMID: 31049033 PMCID: PMC6482566 DOI: 10.1186/s12575-019-0094-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/01/2019] [Indexed: 01/08/2023] Open
Abstract
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.
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Affiliation(s)
- Oluwatosin Oluwadare
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
| | - Max Highsmith
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
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20
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Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
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Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
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21
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The structural and functional roles of CTCF in the regulation of cell type-specific and human disease-associated super-enhancers. Genes Genomics 2018; 41:257-265. [PMID: 30456521 DOI: 10.1007/s13258-018-0768-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Super-enhancers play critical roles in cell-type specific gene controls and human disease progression. CCCTC-binding factor (CTCF), a transcriptional repressor that insulates the expression of neighboring genes and is involved in chromatin interactions, is frequently present in the boundary regions of or within super-enhancers. However, the structural and functional roles of CTCF in regulating super-enhancers remain elusive. OBJECTIVE To provide a comprehensive review describing the distinct chromatin features and functional roles of CTCF within super-enhancers. METHODS This review compares the various tools used to study the three-dimensional (3D) chromatin architecture of super-enhancers; summarizes the chromatin features of CTCF within cell-type specific super-enhancers and their in vivo biological activities, as determined by CRISPR/Cas9 genome editing; and describes the structural and functional activities of CTCF within human disease-associated super-enhancers. CONCLUSION This review provides fundamental insights into the regulatory mechanisms of super-enhancers and facilitates studies of tissue-specific developmental processes and human disease progression.
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22
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Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol 2018; 218:27-38. [PMID: 30181316 PMCID: PMC6314556 DOI: 10.1083/jcb.201806052] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
Maass et al. review interchromosomal interactions, which, like intrachromosomal interactions, are emerging as important regulators of genome organization and gene expression. Nuclei require a precise three- and four-dimensional organization of DNA to establish cell-specific gene-expression programs. Underscoring the importance of DNA topology, alterations to the nuclear architecture can perturb gene expression and result in disease states. More recently, it has become clear that not only intrachromosomal interactions, but also interchromosomal interactions, a less studied feature of chromosomes, are required for proper physiological gene-expression programs. Here, we review recent studies with emerging insights into where and why cross-chromosomal communication is relevant. Specifically, we discuss how long noncoding RNAs (lncRNAs) and three-dimensional gene positioning are involved in genome organization and how low-throughput (live-cell imaging) and high-throughput (Hi-C and SPRITE) techniques contribute to understand the fundamental properties of interchromosomal interactions.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA.,University of Colorado, BioFrontiers, Department of Biochemistry, Boulder, CO
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23
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Balajee AS, Hande MP. History and evolution of cytogenetic techniques: Current and future applications in basic and clinical research. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:3-12. [PMID: 30389159 DOI: 10.1016/j.mrgentox.2018.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022]
Abstract
Chromosomes are the vehicles of genes, which are the functional units of a cell's nucleus. In humans, there are more than 20,000 genes that are distributed among 46 chromosomes in somatic cells. The study of chromosome structure and function is known as cytogenetics which is historically a field of hybrid science encompassing cytology and genetics. The field of cytogenetics has undergone rapid developments over the last several decades from classical Giemsa staining of chromosomes to 3-dimensional spatial organization of chromosomes with a high resolution mapping of gene structure at the nucleotide level. Improved molecular cytogenetic techniques have opened up exciting possibilities for understanding the chromosomal/molecular basis of various human diseases including cancer and tissue degeneration. This review summaries the history and evolution of various cytogenetic techniques and their current and future applications in diverse areas of basic research and medical diagnostics.
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Affiliation(s)
- Adayabalam S Balajee
- Cytogenetics Biodosimetry Laboratory, Radiation Emergency Assistance Center and Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, 1299, Bethel Valley Road, Oak Ridge, TN 37830, USA.
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine and Tembusu College, National University of Singapore, 117593, Singapore.
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24
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Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell 2018; 174:744-757.e24. [PMID: 29887377 PMCID: PMC6548320 DOI: 10.1016/j.cell.2018.05.024] [Citation(s) in RCA: 546] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/18/2018] [Accepted: 05/10/2018] [Indexed: 11/22/2022]
Abstract
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.
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Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barbara Tabak
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ali Palla
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jan Marten Schmidt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth Detmar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mason M Lai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Erik Aznauryan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela Russell
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Christine Cheng
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Patrick McDonel
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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25
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Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CHL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L. Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. Cell 2018; 174:363-376.e16. [PMID: 29887381 PMCID: PMC6046268 DOI: 10.1016/j.cell.2018.05.035] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/07/2017] [Accepted: 05/15/2018] [Indexed: 01/08/2023]
Abstract
Visualization of the transcriptome and the nuclear organization in situ has been challenging for single-cell analysis. Here, we demonstrate a multiplexed single-molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome-profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories, and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hr in mouse embryonic stem cells, as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured.
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Affiliation(s)
- Sheel Shah
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA; UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Wen Zhou
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Eric Lubeck
- Department of Biochemistry and Molecular Biophysics, Caltech, Pasadena, CA 91125, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Chee-Huat Linus Eng
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Noushin Koulena
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Christopher Cronin
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Christoph Karp
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Eric J Liaw
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mina Amin
- UC Riverside School of Medicine, University of Riverside, Riverside, CA 92521, USA
| | - Long Cai
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA.
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26
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A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation. Sci Rep 2018; 8:10150. [PMID: 29977047 PMCID: PMC6033925 DOI: 10.1038/s41598-018-28173-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 12/28/2022] Open
Abstract
The integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development.
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27
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Abstract
It is well known that the chromosomes are organized in the nucleus and this spatial arrangement of genome play a crucial role in gene regulation and genome stability. Different techniques have been developed and applied to uncover the intrinsic mechanism of genome architecture, especially the chromosome conformation capture (3C) and 3C-derived methods. 3C and 3C-derived techniques provide us approaches to perform high-throughput chromatin architecture assays at the genome scale. However, the advantage and disadvantage of current methodologies of C-technologies have not been discussed extensively. In this review, we described and compared the methodologies of C-technologies used in genome organization studies with an emphasis on Hi-C method. We also discussed the crucial challenges facing current genome architecture studies based on 3C and 3C-derived technologies and the direction of future technologies to address currently outstanding questions in the field. These latest news contribute to our current understanding of genome structure, and provide a comprehensive reference for researchers to choose the appropriate method in future application. We consider that these constantly improving technologies will offer a finer and more accurate contact profiles of entire genome and ultimately reveal specific molecular machines govern its shape and function.
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28
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Maya‐Mendoza A, Jackson DA. Labeling DNA Replication Foci to Visualize Chromosome Territories In Vivo. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/cpcb.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Dean A. Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, The University of Manchester Manchester United Kingdom
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29
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How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
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30
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Transcription-dependent radial distribution of TCF7L2 regulated genes in chromosome territories. Chromosoma 2017; 126:655-667. [PMID: 28343235 DOI: 10.1007/s00412-017-0629-6] [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: 11/11/2016] [Revised: 02/20/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
Abstract
Human chromosomes occupy distinct territories in the interphase nucleus. Such chromosome territories (CTs) are positioned according to gene density. Gene-rich CTs are generally located in the center of the nucleus, while gene-poor CTs are positioned more towards the nuclear periphery. However, the association between gene expression levels and the radial positioning of genes within the CT is still under debate. In the present study, we performed three-dimensional fluorescence in situ hybridization experiments in the colorectal cancer cell lines DLD-1 and LoVo using whole chromosome painting probes for chromosomes 8 and 11 and BAC clones targeting four genes with different expression levels assessed by gene expression arrays and RT-PCR. Our results confirmed that the two over-expressed genes, MYC on chromosome 8 and CCND1 on chromosome 11, are located significantly further away from the center of the CT compared to under-expressed genes on the same chromosomes, i.e., DLC1 and SCN3B. When CCND1 expression was reduced after silencing the major transcription factor of the WNT/β-catenin signaling pathway, TCF7L2, the gene was repositioned and mostly detected in the interior of the CT. Thus, we suggest a non-random distribution in which over-expressed genes are located more towards the periphery of the respective CTs.
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Pueschel R, Coraggio F, Meister P. From single genes to entire genomes: the search for a function of nuclear organization. Development 2016; 143:910-23. [PMID: 26980791 DOI: 10.1242/dev.129007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The existence of different domains within the nucleus has been clear from the time, in the late 1920s, that heterochromatin and euchromatin were discovered. The observation that heterochromatin is less transcribed than euchromatin suggested that microscopically identifiable structures might correspond to functionally different domains of the nucleus. Until 15 years ago, studies linking gene expression and subnuclear localization were limited to a few genes. As we discuss in this Review, new genome-wide techniques have now radically changed the way nuclear organization is analyzed. These have provided a much more detailed view of functional nuclear architecture, leading to the emergence of a number of new paradigms of chromatin folding and how this folding evolves during development.
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Affiliation(s)
- Ringo Pueschel
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Francesca Coraggio
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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Maurer-Alcalá XX, Katz LA. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata. Genome Biol Evol 2016; 8:1634-42. [PMID: 27189988 PMCID: PMC4943175 DOI: 10.1093/gbe/evw099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst
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Vaquerizas JM, Akhtar A, Luscombe NM. Large-scale nuclear architecture and transcriptional control. Subcell Biochem 2016; 52:279-95. [PMID: 21557088 DOI: 10.1007/978-90-481-9069-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transcriptional regulation is one the most basic mechanisms for controlling gene expression. Over the past few years, much research has been devoted to understanding the interplay between transcription factors, histone modifications and associated enzymes required to achieve this control. However, it is becoming increasingly apparent that the three-dimensional conformation of chromatin in the interphase nucleus also plays a critical role in regulating transcription. Chromatin localisation in the nucleus is highly organised, and early studies described strong interactions between chromatin and sub-nuclear components. Single-gene studies have shed light on how chromosomal architecture affects gene expression. Lately, this has been complemented by whole-genome studies that have determined the global chromatin conformation of living cells in interphase. These studies have greatly expanded our understanding of nuclear architecture and its interplay with different physiological processes. Despite these advances, however, most of the mechanisms used to impose the three-dimensional chromatin structure remain unknown. Here, we summarise the different levels of chromatin organisation in the nucleus and discuss current efforts into characterising the mechanisms that govern it.
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Joyce EF, Erceg J, Wu CT. Pairing and anti-pairing: a balancing act in the diploid genome. Curr Opin Genet Dev 2016; 37:119-128. [PMID: 27065367 DOI: 10.1016/j.gde.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 12/22/2022]
Abstract
The presence of maternal and paternal homologs appears to be much more than just a doubling of genetic material. We know this because genomes have evolved elaborate mechanisms that permit homologous regions to sense and then respond to each other. One way in which homologs communicate is to come into contact and, in fact, Dipteran insects such as Drosophila excel at this task, aligning all pairs of maternal and paternal chromosomes, end-to-end, in essentially all somatic tissues throughout development. Here, we reexamine the widely held tenet that extensive somatic pairing of homologous sequences cannot occur in mammals and suggest, instead, that pairing may be a widespread and significant potential that has gone unnoticed in mammals because they expend considerable effort to prevent it. We then extend this discussion to interchromosomal interactions, in general, and speculate about the potential of nuclear organization and pairing to impact inheritance.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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Fritz A, Barutcu AR, Martin-Buley L, vanWijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus. J Cell Biochem 2016; 117:9-19. [PMID: 26192137 PMCID: PMC4715719 DOI: 10.1002/jcb.25280] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.
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Affiliation(s)
- Andrew Fritz
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Lori Martin-Buley
- University of Vermont Cancer Center, 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
| | - Sayyed K. Zaidi
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B. Lian
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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Affiliation(s)
- Huy Q. Nguyen
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
| | - Giovanni Bosco
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
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Fraser J, Williamson I, Bickmore WA, Dostie J. An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev 2015; 79:347-72. [PMID: 26223848 PMCID: PMC4517094 DOI: 10.1128/mmbr.00006-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dostie
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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Strongin DE, Groudine M, Politz JCR. Nucleolar tethering mediates pairing between the IgH and Myc loci. Nucleus 2015; 5:474-81. [PMID: 25482199 PMCID: PMC4164489 DOI: 10.4161/nucl.36233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gene loci on different chromosomes can preferentially colocalize in the cell nucleus. However, many of the mechanisms mediating this spatial proximity remain to be elucidated. The IgH locus on Chromosome 12 and the Myc locus on Chromosome 15 are a well-studied model for gene colocalization in murine B cells, where the two loci are positioned in close proximity at a higher than expected frequency. These gene loci are also partners in the chromosomal translocation that causes murine plasmacytoma and Burkitt’s lymphoma. Because both Chromosome 12 and Chromosome 15 carry nucleolar organizer regions (NORs) in the most commonly studied mouse strains, we hypothesized that NOR-mediated tethering of the IgH and Myc loci to shared nucleoli could serve as a mechanism to drive IgH:Myc colocalization. Using mouse strains that naturally carry nucleolar organizer regions (NORs) on different sets of chromosomes, we establish that IgH and Myc are positioned proximal to nucleoli in a NOR dependent manner and show that their joint association with nucleoli significantly increases the frequency of IgH and Myc pairing. Thus we demonstrate that simple nucleolar tethering can increase the colocalization frequency of genes on NOR-bearing chromosomes.
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Affiliation(s)
- Daniel E Strongin
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA
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Chromatin at the nuclear periphery and the regulation of genome functions. Histochem Cell Biol 2015; 144:111-22. [PMID: 26170147 DOI: 10.1007/s00418-015-1346-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 01/01/2023]
Abstract
Chromatin is not randomly organized in the nucleus, and its spatial organization participates in the regulation of genome functions. However, this spatial organization is also not entirely fixed and modifications of chromatin architecture are implicated in physiological processes such as differentiation or senescence. One of the most striking features of chromatin architecture is the concentration of heterochromatin at the nuclear periphery. A closer examination of the association of chromatin at the nuclear periphery reveals that heterochromatin accumulates at the nuclear lamina, whereas nuclear pores are usually devoid of heterochromatin. After summarizing the current techniques used to study the attachment of chromatin at the nuclear lamina or the nuclear pores, we review the mechanisms underlying these attachments, their plasticity and their consequences on the regulation of gene expression, DNA repair and replication.
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40
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Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. BMC Genomics 2015; 16:121. [PMID: 25887659 PMCID: PMC4369351 DOI: 10.1186/s12864-015-1236-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
Background Several recently developed experimental methods, each an extension of the chromatin conformation capture (3C) assay, have enabled the genome-wide profiling of chromatin contacts between pairs of genomic loci in 3D. Especially in complex eukaryotes, data generated by these methods, coupled with other genome-wide datasets, demonstrated that non-random chromatin folding correlates strongly with cellular processes such as gene expression and DNA replication. Results We describe a genome architecture assay, tethered multiple 3C (TM3C), that maps genome-wide chromatin contacts via a simple protocol of restriction enzyme digestion and religation of fragments upon agarose gel beads followed by paired-end sequencing. In addition to identifying contacts between pairs of loci, TM3C enables identification of contacts among more than two loci simultaneously. We use TM3C to assay the genome architectures of two human cell lines: KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line. We confirm that the contact frequency maps produced by TM3C exhibit features characteristic of existing genome architecture datasets, including the expected scaling of contact probabilities with genomic distance, megabase scale chromosomal compartments and sub-megabase scale topological domains. We also confirm that TM3C captures several known cell type-specific contacts, ploidy shifts and translocations, such as Philadelphia chromosome formation (Ph+) in KBM7. We confirm a subset of the triple contacts involving the IGF2-H19 imprinting control region (ICR) using PCR analysis for KBM7 cells. Our genome-wide analysis of pairwise and triple contacts demonstrates their preference for linking open chromatin regions to each other and for linking regions with higher numbers of DNase hypersensitive sites (DHSs) to each other. For near-haploid KBM7 cells, we infer whole genome 3D models that exhibit clustering of small chromosomes with each other and large chromosomes with each other, consistent with previous studies of the genome architectures of other human cell lines. Conclusion TM3C is a simple protocol for ascertaining genome architecture and can be used to identify simultaneous contacts among three or four loci. Application of TM3C to a near-haploid human cell line revealed large-scale features of chromosomal organization and multi-way chromatin contacts that preferentially link regions of open chromatin. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1236-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA.
| | - Thanh H Vu
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - Michael J Zeitz
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - Nelle Varoquaux
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré, Fontainebleau, 77300, France. .,Institut Curie, Paris, F-75248, France. .,U900, INSERM, ParisF-75248, France.
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, 94305, CA, USA.
| | - Jean-Philippe Vert
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré, Fontainebleau, 77300, France. .,Institut Curie, Paris, F-75248, France. .,U900, INSERM, ParisF-75248, France.
| | - Andrew R Hoffman
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA. .,Department of Computer Science and Engineering, University of Washington, Seattle, 98195, WA, USA.
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41
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Williamson I, Berlivet S, Eskeland R, Boyle S, Illingworth RS, Paquette D, Dostie J, Bickmore WA. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev 2014; 28:2778-91. [PMID: 25512564 PMCID: PMC4265680 DOI: 10.1101/gad.251694.114] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/30/2014] [Indexed: 01/28/2023]
Abstract
Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods.
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Affiliation(s)
- Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Soizik Berlivet
- Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montréal, Québec H3G1Y6, Canada
| | - Ragnhild Eskeland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Illingworth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | | | | | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
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Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T. 4D Chromatin dynamics in cycling cells. Nucleus 2014. [DOI: 10.4161/nucl.11969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
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Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
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46
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Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 2014; 7:8. [PMID: 25057298 PMCID: PMC4108088 DOI: 10.1186/1756-8935-7-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/11/2014] [Indexed: 12/31/2022] Open
Abstract
Background A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs). Results We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an ‘autosomal Barr body’ with less compacted chromatin and incomplete RNAP II exclusion. Conclusions 3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform compaction of the Barr body at the nucleosome level. The localization of distinct Xist RNA foci at boundaries of the rudimentary ANC may be considered as snap-shots of a dynamic interaction with silenced genes. Enrichment of SAF-A within Xi territories and its close spatial association with Xist RNA suggests their cooperative function for structural organization of Xi.
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Affiliation(s)
- Daniel Smeets
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Yolanda Markaki
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Volker J Schmid
- Institute of Statistics, Ludwig Maximilians University (LMU), Munich, Germany
| | - Felix Kraus
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Andrea Cerase
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Sterr
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Susanne Fiedler
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Justin Demmerle
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jens Popken
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Heinrich Leonhardt
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Thomas Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Lothar Schermelleh
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Marion Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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Alexander JM, Lomvardas S. Nuclear architecture as an epigenetic regulator of neural development and function. Neuroscience 2014; 264:39-50. [PMID: 24486963 PMCID: PMC4006947 DOI: 10.1016/j.neuroscience.2014.01.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/11/2014] [Accepted: 01/22/2014] [Indexed: 12/23/2022]
Abstract
The nervous system of higher organisms is characterized by an enormous diversity of cell types that function in concert to carry out a myriad of neuronal functions. Differences in connectivity, and subsequent physiology of the connected neurons, are a result of differences in transcriptional programs. The extraordinary complexity of the nervous system requires an equally complex regulatory system. It is well established that transcription factor combinations and the organization of cis-regulatory sequences control commitment to differentiation programs and preserve a nuclear plasticity required for neuronal functions. However, an additional level of regulation is provided by epigenetic controls. Among various epigenetic processes, nuclear organization and the control of genome architecture emerge as an efficient and powerful form of gene regulation that meets the unique needs of the post-mitotic neuron. Here, we present an outline of how nuclear architecture affects transcription and provide examples from the recent literature where these principles are used by the nervous system.
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Affiliation(s)
- J M Alexander
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - S Lomvardas
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA.
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Razin SV, Gavrilov AA. Chromatin without the 30-nm fiber: constrained disorder instead of hierarchical folding. Epigenetics 2014; 9:653-7. [PMID: 24561903 PMCID: PMC4063823 DOI: 10.4161/epi.28297] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several hierarchical levels of DNA packaging are believed to exist in chromatin, starting from a 10-nm chromatin fiber that is further packed into a 30-nm fiber. Transitions between the 30-nm and 10-nm fibers are thought to be essential for the control of chromatin transcriptional status. However, recent studies demonstrate that in the nuclei, DNA is packed in tightly associated 10-nm fibers that are not compacted into 30-nm fibers. Additionally, the accessibility of DNA in chromatin depends on the local mobility of nucleosomes rather than on decompaction of chromosome regions. These findings argue for reconsidering the hierarchical model of chromatin packaging and some of the basic definitions of chromatin. In particular, chromatin domains should be considered as three-dimensional objects, which may include genomic regions that do not necessarily constitute a continuous domain on the DNA chain.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences; Moscow, Russia; Faculty of Biology; M.V. Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Moscow, Russia
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Abstract
Odorants are detected by odorant receptors, which are located on olfactory sensory neurons of the nose. Each olfactory sensory neuron expresses one single odorant receptor gene allele from a large family of odorant receptor genes. To gain insight into the mechanisms underlying this monogenic and monoallelic expression, we examined the 3D nuclear organization of olfactory sensory neurons and determined the positions of homologous odorant receptor gene alleles in relation to different nuclear compartments. Our results show that olfactory neurons exhibit a singular nuclear architecture that is characterized by a large centrally localized constitutive heterochromatin block and by the presence of prominent facultative heterochromatin domains that are localized around this constitutive heterochromatin block. We also found that the two homologous alleles of a given odorant receptor gene are frequently segregated to separate compartments in the nucleus, with one of the alleles localized to the constitutive heterochromatin block and the other one localized to the more plastic facultative heterochromatin, or next to it. Our findings suggest that this nuclear compartmentalization may play a critical role in the expression of odorant receptor genes.
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Thanisch K, Schneider K, Morbitzer R, Solovei I, Lahaye T, Bultmann S, Leonhardt H. Targeting and tracing of specific DNA sequences with dTALEs in living cells. Nucleic Acids Res 2013; 42:e38. [PMID: 24371265 PMCID: PMC3973286 DOI: 10.1093/nar/gkt1348] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.
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Affiliation(s)
- Katharina Thanisch
- Department of Biology II, Humanbiology and Bioimaging, Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany and Department of Biology I, Genetics, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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