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Doležalová A, Beránková D, Koláčková V, Hřibová E. Insight into chromatin compaction and spatial organization in rice interphase nuclei. FRONTIERS IN PLANT SCIENCE 2024; 15:1358760. [PMID: 38863533 PMCID: PMC11165205 DOI: 10.3389/fpls.2024.1358760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Chromatin organization and its interactions are essential for biological processes, such as DNA repair, transcription, and DNA replication. Detailed cytogenetics data on chromatin conformation, and the arrangement and mutual positioning of chromosome territories in interphase nuclei are still widely missing in plants. In this study, level of chromatin condensation in interphase nuclei of rice (Oryza sativa) and the distribution of chromosome territories (CTs) were analyzed. Super-resolution, stimulated emission depletion (STED) microscopy showed different levels of chromatin condensation in leaf and root interphase nuclei. 3D immuno-FISH experiments with painting probes specific to chromosomes 9 and 2 were conducted to investigate their spatial distribution in root and leaf nuclei. Six different configurations of chromosome territories, including their complete association, weak association, and complete separation, were observed in root meristematic nuclei, and four configurations were observed in leaf nuclei. The volume of CTs and frequency of their association varied between the tissue types. The frequency of association of CTs specific to chromosome 9, containing NOR region, is also affected by the activity of the 45S rDNA locus. Our data suggested that the arrangement of chromosomes in the nucleus is connected with the position and the size of the nucleolus.
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Affiliation(s)
| | | | | | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Science, Centre of Plants Structural and Functional Genomics, Olomouc, Czechia
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2
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Sun B, Kim H, Mello CC, Priess JR. The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods. PLoS Genet 2023; 19:e1010804. [PMID: 37384599 PMCID: PMC10309623 DOI: 10.1371/journal.pgen.1010804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL polyproteins. Because gRNA often includes splice acceptor and donor sequences used to splice viral mRNAs, retroelements must overcome host mechanisms that retain intron-containing RNAs in the nucleus. Here we examine gRNA expression in Cer1, an LTR retrotransposon in C. elegans which somehow avoids silencing and is highly expressed in germ cells. Newly exported Cer1 gRNA associates rapidly with the Cer1 GAG protein, which has structural similarity with retroviral GAG proteins. gRNA export requires CERV (C. elegans regulator of viral expression), a novel protein encoded by a spliced Cer1 mRNA. CERV phosphorylation at S214 is essential for gRNA export, and phosphorylated CERV colocalizes with nuclear gRNA at presumptive sites of transcription. By electron microscopy, tagged CERV proteins surround clusters of distinct, linear fibrils that likely represent gRNA molecules. Single fibrils, or groups of aligned fibrils, also localize near nuclear pores. During the C. elegans self-fertile period, when hermaphrodites fertilize oocytes with their own sperm, CERV concentrates in two nuclear foci that are coincident with gRNA. However, as hermaphrodites cease self-fertilization, and can only produce cross-progeny, CERV undergoes a remarkable transition to form giant nuclear rods or cylinders that can be up to 5 microns in length. We propose a novel mechanism of rod formation, in which stage-specific changes in the nucleolus induce CERV to localize to the nucleolar periphery in flattened streaks of protein and gRNA; these streaks then roll up into cylinders. The rods are a widespread feature of Cer1 in wild strains of C. elegans, but their function is not known and might be limited to cross-progeny. We speculate that the adaptive strategy Cer1 uses for the identical self-progeny of a host hermaphrodite might differ for heterozygous cross-progeny sired by males. For example, mating introduces male chromosomes which can have different, or no, Cer1 elements.
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Affiliation(s)
- Bing Sun
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Haram Kim
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Craig C. Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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3
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Hübner B, von Otter E, Ahsan B, Wee ML, Henriksson S, Ludwig A, Sandin S. Ultrastructure and nuclear architecture of telomeric chromatin revealed by correlative light and electron microscopy. Nucleic Acids Res 2022; 50:5047-5063. [PMID: 35489064 PMCID: PMC9122609 DOI: 10.1093/nar/gkac309] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022] Open
Abstract
Telomeres, the ends of linear chromosomes, are composed of repetitive DNA sequences, histones and a protein complex called shelterin. How DNA is packaged at telomeres is an outstanding question in the field with significant implications for human health and disease. Here, we studied the architecture of telomeres and their spatial association with other chromatin domains in different cell types using correlative light and electron microscopy. To this end, the shelterin protein TRF1 or TRF2 was fused in tandem to eGFP and the peroxidase APEX2, which provided a selective and electron-dense label to interrogate telomere organization by transmission electron microscopy, electron tomography and scanning electron microscopy. Together, our work reveals, for the first time, ultrastructural insight into telomere architecture. We show that telomeres are composed of a dense and highly compacted mesh of chromatin fibres. In addition, we identify marked differences in telomere size, shape and chromatin compaction between cancer and non-cancer cells and show that telomeres are in direct contact with other heterochromatin regions. Our work resolves the internal architecture of telomeres with unprecedented resolution and advances our understanding of how telomeres are organized in situ.
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Affiliation(s)
- Barbara Hübner
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Eric von Otter
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Bilal Ahsan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Mei Ling Wee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Sara Henriksson
- Umeå Centre for Electron Microscopy, Umeå University, Chemical Biological Centre (KBC) Building, Linnaeus väg 6, SE-90736 Umeå, Sweden
| | - Alexander Ludwig
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:cells11081368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 0] [Impact Index Per Article: 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;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
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Lorber D, Volk T. Evaluation of chromatin mesoscale organization. APL Bioeng 2022; 6:010902. [PMID: 35071965 PMCID: PMC8758204 DOI: 10.1063/5.0069286] [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] [Received: 08/30/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Chromatin organization in the nucleus represents an important aspect of transcription regulation. Most of the studies so far focused on the chromatin structure in cultured cells or in fixed tissue preparations. Here, we discuss the various approaches for deciphering chromatin 3D organization with an emphasis on the advantages of live imaging approaches.
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Affiliation(s)
- Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Current Understanding of the Neutrophil Transcriptome in Health and Disease. Cells 2021; 10:cells10092406. [PMID: 34572056 PMCID: PMC8469435 DOI: 10.3390/cells10092406] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
Neutrophils are key cells of the innate immune system. It is now understood that this leukocyte population is diverse in both the basal composition and functional plasticity. Underlying this plasticity is a post-translational framework for rapidly achieving early activation states, but also a transcriptional capacity that is becoming increasingly recognized by immunologists. Growing interest in the contribution of neutrophils to health and disease has resulted in more efforts to describe their transcriptional activity. Whilst initial efforts focused predominantly on understanding the existing biology, investigations with advanced methods such as single cell RNA sequencing to understand interactions of the entire immune system are revealing higher flexibility in neutrophil transcription than previously thought possible and multiple transition states. It is now apparent that neutrophils utilise many forms of RNA in the regulation of their function. This review collates current knowledge on the nuclei structure and gene expression activity of human neutrophils across homeostasis and disease, before highlighting knowledge gaps that are research priority areas.
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Lang F, Contreras-Gerenas MF, Gelléri M, Neumann J, Kröger O, Sadlo F, Berniak K, Marx A, Cremer C, Wagenknecht HA, Allgayer H. Tackling Tumour Cell Heterogeneity at the Super-Resolution Level in Human Colorectal Cancer Tissue. Cancers (Basel) 2021; 13:cancers13153692. [PMID: 34359592 PMCID: PMC8345115 DOI: 10.3390/cancers13153692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Tumour cell heterogeneity is the most fundamental problem in cancer diagnosis and therapy. Micro-diagnostic technologies able to differentiate the heterogeneous molecular, especially metastatic, potential of single cells or cell clones already within early primary tumours of carcinoma patients would be of utmost importance. Single molecule localisation microscopy (SMLM) has recently allowed the imaging of subcellular features at the nanoscale. However, the technology has mostly been limited to cultured cell lines only. We introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma patient tissue sections, illustrating, as a first example, changes in nuclear chromatin nanostructure and microRNA intracellular distribution within carcinoma cells as opposed to normal cells, chromatin accessibility and microRNAs having been shown to be critical in gene regulation and metastasis. We believe this technology to have an enormous potential for future differential diagnosis between individual cells in the tissue context. Abstract Tumour cell heterogeneity, and its early individual diagnosis, is one of the most fundamental problems in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) resolves subcellular features but has been limited to cultured cell lines only. Since nuclear chromatin architecture and microRNAs are critical in metastasis, we introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma (CRC) patient tissue sections. Chromatin density profiles proved to differ for cells in normal and carcinoma colorectal tissues. In tumour sections, nuclear size and chromatin compaction percentages were significantly different in carcinoma versus normal epithelial and other cells of colorectal tissue. SMLM analysis in nuclei from normal colorectal tissue revealed abrupt changes in chromatin density profiles at the nanoscale, features not detected by conventional widefield microscopy. SMLM for microRNAs relevant for metastasis was achieved in colorectal cancer tissue at the nuclear level. Super-resolution microscopy with quantitative image evaluation algorithms provide powerful tools to analyse chromatin nanostructure and microRNAs of individual cells from normal and tumour tissue at the nanoscale. Our new perspectives improve the differential diagnosis of normal and (metastatically relevant) tumour cells at the single-cell level within the heterogeneity of primary tumours of patients.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - María F. Contreras-Gerenas
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Jan Neumann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Ole Kröger
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Filip Sadlo
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 Street, 30-387 Krakow, Poland;
| | - Alexander Marx
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Theodor-Kutzer-Ufer 1, 68167 Mannheim, Germany;
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
- Institute of Pharmacy & Molecular Biotechnology, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Correspondence: ; Tel.: +49-(0)621-383-71630/-1406/-71635; Fax: +49-(0)621-383-71631
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Mendonca A, Sánchez OF, Xie J, Carneiro A, Lin L, Yuan C. Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194725. [PMID: 34174495 DOI: 10.1016/j.bbagrm.2021.194725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
The 3D spatial organization of the genome controls gene expression and cell functionality. Heterochromatin (HC), which is the densely compacted and largely silenced part of the chromatin, is the driver for the formation and maintenance of nuclear organization in the mammalian nucleus. It is functionally divided into highly compact constitutive heterochromatin (cHC) and transcriptionally poised facultative heterochromatin (fHC). Long regarded as a static structure, the highly dynamic nature of the heterochromatin is being slowly understood and studied. These changes in HC occur on various temporal scales during the cell cycle and differentiation processes. Most methods that capture information about the heterochromatin are static techniques that cannot provide a readout of how the HC organization evolves with time. The delineation of specific areas such as fHC are also rendered difficult due to its diffusive nature and lack of specific features. Another degree of complexity in characterizing changes in heterochromatin occurs due to the heterogeneity in the HC organization of individual cells, necessitating single cell studies. Overall, there is a need for live cell compatible tools that can stably track the heterochromatin as it undergoes re-organization. In this work, we present an approach to track cHC and fHC based on the epigenetic hallmarks associated with them. Unlike conventional immunostaining approaches, we use small recombinant protein probes that allow us to dynamically monitor the HC by binding to modifications specific to the cHC and fHC, such as H3K9me3, DNA methylation and H3K27me3. We demonstrate the use of the probes to follow the changes in HC induced by drug perturbations at the single cell level. We also use the probe sets combinatorically to simultaneously track chromatin regions enriched in two selected epigenetic modifications using a FRET based approach that enabled us tracking distinctive chromatin features in situ.
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Affiliation(s)
- Agnes Mendonca
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Ana Carneiro
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47906, USA.
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Prakash K, Diederich B, Reichelt S, Heintzmann R, Schermelleh L. Super-resolution structured illumination microscopy: past, present and future. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200143. [PMID: 33896205 PMCID: PMC8366908 DOI: 10.1098/rsta.2020.0143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structured illumination microscopy (SIM) has emerged as an essential technique for three-dimensional (3D) and live-cell super-resolution imaging. However, to date, there has not been a dedicated workshop or journal issue covering the various aspects of SIM, from bespoke hardware and software development and the use of commercial instruments to biological applications. This special issue aims to recap recent developments as well as outline future trends. In addition to SIM, we cover related topics such as complementary super-resolution microscopy techniques, computational imaging, visualization and image processing methods. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kirti Prakash
- National Physical Laboratory, TW11 0LW Teddington, UK
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Benedict Diederich
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, Jena, Germany
| | - Stefanie Reichelt
- CRUK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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10
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Amiad-Pavlov D, Lorber D, Bajpai G, Reuveny A, Roncato F, Alon R, Safran S, Volk T. Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization. SCIENCE ADVANCES 2021; 7:7/23/eabf6251. [PMID: 34078602 PMCID: PMC8172175 DOI: 10.1126/sciadv.abf6251] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/15/2021] [Indexed: 05/12/2023]
Abstract
Live imaging of chromatin in an intact organism reveals a novel mode of mesoscale chromatin organization at nuclear periphery.
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Affiliation(s)
- Daria Amiad-Pavlov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Adriana Reuveny
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Roncato
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Alon
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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11
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Ventura JA, Donoghue JF, Nowell CJ, Cann LM, Day LRJ, Smyth LML, Forrester HB, Rogers PAW, Crosbie JC. The γH2AX DSB marker may not be a suitable biodosimeter to measure the biological MRT valley dose. Int J Radiat Biol 2021; 97:642-656. [PMID: 33617395 DOI: 10.1080/09553002.2021.1893854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/31/2020] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE γH2AX biodosimetry has been proposed as an alternative dosimetry method for microbeam radiation therapy (MRT) because conventional dosimeters, such as ionization chambers, lack the spatial resolution required to accurately measure the MRT valley dose. Here we investigated whether γH2AX biodosimetry should be used to measure the biological valley dose of MRT-irradiated mammalian cells. MATERIALS AND METHODS We irradiated human skin fibroblasts and mouse skin flaps with synchrotron MRT and broad beam (BB) radiation. BB doses of 1-5 Gy were used to generate a calibration curve in order to estimate the biological MRT valley dose using the γH2AX assay. RESULTS Our key finding was that MRT induced a non-linear dose response compared to BB, where doses 2-3 times greater showed the same level of DNA DSB damage in the valley in cell and tissue studies. This indicates that γH2AX may not be an appropriate biodosimeter to estimate the biological valley doses of MRT-irradiated samples. We also established foci yields of 5.9 ± 0 . 04 and 27.4 ± 2 . 5 foci/cell/Gy in mouse skin tissue and human fibroblasts respectively, induced by BB. Using Monte Carlo simulations, a linear dose response was seen in cell and tissue studies and produced predicted peak-to-valley dose ratios (PVDRs) of ∼30 and ∼107 for human fibroblasts and mouse skin tissue respectively. CONCLUSIONS Our report highlights novel MRT radiobiology, attempts to explain why γH2AX may not be an appropriate biodosimeter and suggests further studies aimed at revealing the biological and cellular communication mechanisms that drive the normal tissue sparing effect, which is characteristic of MRT.
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Affiliation(s)
- Jessica A Ventura
- Department of Obstetrics and Gynaecology, Royal Women's Hospital, University of Melbourne, Parkville, Australia
| | - Jacqueline F Donoghue
- Department of Obstetrics and Gynaecology, Royal Women's Hospital, University of Melbourne, Parkville, Australia
| | - Cameron J Nowell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Leonie M Cann
- Department of Obstetrics and Gynaecology, Royal Women's Hospital, University of Melbourne, Parkville, Australia
| | - Liam R J Day
- School of Science, RMIT University, Melbourne, Australia
| | - Lloyd M L Smyth
- Department of Obstetrics and Gynaecology, Royal Women's Hospital, University of Melbourne, Parkville, Australia
| | - Helen B Forrester
- School of Science, RMIT University, Melbourne, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Peter A W Rogers
- Department of Obstetrics and Gynaecology, Royal Women's Hospital, University of Melbourne, Parkville, Australia
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Keenan CR, Mlodzianoski MJ, Coughlan HD, Bediaga NG, Naselli G, Lucas EC, Wang Q, de Graaf CA, Hilton DJ, Harrison LC, Smyth GK, Rogers KL, Boudier T, Allan RS, Johanson TM. Chromosomes distribute randomly to, but not within, human neutrophil nuclear lobes. iScience 2021; 24:102161. [PMID: 33665577 PMCID: PMC7905186 DOI: 10.1016/j.isci.2021.102161] [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: 10/12/2020] [Revised: 11/24/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
The proximity pattern and radial distribution of chromosome territories within spherical nuclei are random and non-random, respectively. Whether this distribution pattern is conserved in the partitioned or lobed nuclei of polymorphonuclear cells is unclear. Here we use chromosome paint technology to examine the chromosome territories of all 46 chromosomes in hundreds of single human neutrophils - an abundant and famously polymorphonuclear immune cell. By comparing the distribution of chromosomes to randomly shuffled controls and validating with orthogonal chromosome conformation capture technology, we show for the first time that human chromosomes randomly distribute to neutrophil nuclear lobes, while maintaining a non-random radial distribution within these lobes. Furthermore, we demonstrate that chromosome length correlates with three-dimensional volume not only in neutrophils but other human immune cells. This work demonstrates that chromosomes are largely passive passengers during the neutrophil lobing process but are able to subsequently maintain their macro-level organization within lobes.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael J. Mlodzianoski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hannah D. Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Naiara G. Bediaga
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gaetano Naselli
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Erin C. Lucas
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Qike Wang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Carolyn A. de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Douglas J. Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Leonard C. Harrison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kelly L. Rogers
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thomas Boudier
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Institute of Biology Paris-Seine, Sorbonne Université, Paris, France
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Timothy M. Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Corresponding author
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13
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Coskun AF, Han G, Ganesh S, Chen SY, Clavé XR, Harmsen S, Jiang S, Schürch CM, Bai Y, Hitzman C, Nolan GP. Nanoscopic subcellular imaging enabled by ion beam tomography. Nat Commun 2021; 12:789. [PMID: 33542220 PMCID: PMC7862654 DOI: 10.1038/s41467-020-20753-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 01/30/2023] Open
Abstract
Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices. Here, a mathematical and technical framework for three-dimensional (3D) subcellular MIBI is presented. Ion-beam tomography (IBT) compiles ion beam images that are acquired iteratively across successive, multiple scans, and later assembled into a 3D format without loss of depth resolution. Algorithmic deconvolution, tailored for ion beams, is then applied to the transformed ion image series, yielding 4-fold enhanced ion beam data cubes. To further generate 3D sub-ion-beam-width precision visuals, isolated ion molecules are localized in the raw ion beam images, creating an approach coined as SILM, secondary ion beam localization microscopy, providing sub-25 nm accuracy in original ion images. Using deep learning, a parameter-free reconstruction method for ion beam tomograms with high accuracy is developed for low-density targets. In cultured cancer cells and tissues, IBT enables accessible visualization of 3D volumetric distributions of genomic regions, RNA transcripts, and protein factors with 5 nm axial resolution using isotope-enrichments and label-free elemental analyses. Multiparameter imaging of subcellular features at near macromolecular resolution is implemented by the IBT tools as a general biocomputation pipeline for imaging mass spectrometry.
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Affiliation(s)
- Ahmet F. Coskun
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA USA ,grid.213917.f0000 0001 2097 4943Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA USA
| | - Guojun Han
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Shambavi Ganesh
- grid.213917.f0000 0001 2097 4943Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA USA ,grid.213917.f0000 0001 2097 4943School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA USA
| | - Shih-Yu Chen
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Xavier Rovira Clavé
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Stefan Harmsen
- grid.168010.e0000000419368956Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA USA ,grid.25879.310000 0004 1936 8972Present Address: Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Sizun Jiang
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Christian M. Schürch
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA ,grid.411544.10000 0001 0196 8249Present Address: Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Yunhao Bai
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA USA
| | - Chuck Hitzman
- grid.168010.e0000000419368956Department of Materials Science and Engineering, Stanford University, Stanford, CA USA
| | - Garry P. Nolan
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
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14
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Strickfaden H. Reflections on the organization and the physical state of chromatin in eukaryotic cells. Genome 2020; 64:311-325. [PMID: 33306433 DOI: 10.1139/gen-2020-0132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In recent years, our perception of chromatin structure and organization in the cell nucleus has changed in fundamental ways. The 30 nm chromatin fiber has lost its status as an essential in vivo structure. Hi-C and related biochemical methods, advanced electron and super-resolved fluorescence microscopy, together with concepts from soft matter physics, have revolutionized the field. A comprehensive understanding of the structural and functional interactions that regulate cell cycle and cell type specific nuclear functions appears within reach, but it requires the integration of top-down and bottom-up approachs. In this review, I present an update on nuclear architecture studies with an emphasis on organization and the controversy regarding the physical state of chromatin in cells.
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Affiliation(s)
- Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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15
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Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
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Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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16
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Mai S. Introduction to the special issue "3D nuclear architecture of the genome". Genes Chromosomes Cancer 2019; 58:405-406. [PMID: 30851140 DOI: 10.1002/gcc.22747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sabine Mai
- Department of Cell Biology, Research Institute of Oncology and Hematology, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
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17
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Delaney CE, Methot SP, Guidi M, Katic I, Gasser SM, Padeken J. Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65. J Cell Biol 2019; 218:820-838. [PMID: 30737265 PMCID: PMC6400574 DOI: 10.1083/jcb.201811038] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
Delaney et al. show that the unstructured domain cofactor LIN-65 is essential for the stable formation of heterochromatic foci. It stably interacts with the H3K9 methyltransferase MET-2/SETDB1 and modulates MET-2 nuclear localization, activity, and H3K9me-mediated silencing in C. elegans. The segregation of the genome into accessible euchromatin and histone H3K9-methylated heterochromatin helps silence repetitive elements and tissue-specific genes. In Caenorhabditis elegans, MET-2, the homologue of mammalian SETDB1, catalyzes H3K9me1 and me2, yet like SETDB1, its regulation is enigmatic. Contrary to the cytosolic enrichment of overexpressed MET-2, we show that endogenous MET-2 is nuclear throughout development, forming perinuclear foci in a cell cycle–dependent manner. Mass spectrometry identified two cofactors that bind MET-2: LIN-65, a highly unstructured protein, and ARLE-14, a conserved GTPase effector. All three factors colocalize in heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9 dimethylation, dispersion of heterochromatic foci, and derepression of MET-2 targets. Mutation of met-2 or lin-65 also disrupts the perinuclear anchoring of genomic heterochromatin. Loss of LIN-65, like that of MET-2, compromises temperature stress resistance and germline integrity, which are both linked to promiscuous repeat transcription and gene expression.
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Affiliation(s)
- Colin E Delaney
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stephen P Methot
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Micol Guidi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Iskra Katic
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland .,University of Basel, Faculty of Natural Sciences, Basel, Switzerland
| | - Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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18
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Cremer M, Cremer T. Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences. Genes Chromosomes Cancer 2019; 58:427-436. [DOI: 10.1002/gcc.22714] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marion Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
| | - Thomas Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
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19
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Neriec N, Percipalle P. Sorting mRNA Molecules for Cytoplasmic Transport and Localization. Front Genet 2018; 9:510. [PMID: 30459808 PMCID: PMC6232293 DOI: 10.3389/fgene.2018.00510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/12/2018] [Indexed: 01/03/2023] Open
Abstract
In eukaryotic cells, gene expression is highly regulated at many layers. Nascent RNA molecules are assembled into ribonucleoprotein complexes that are then released into the nucleoplasmic milieu and transferred to the nuclear pore complex for nuclear export. RNAs are then either translated or transported to the cellular periphery. Emerging evidence indicates that RNA-binding proteins play an essential role throughout RNA biogenesis, from the gene to polyribosomes. However, the sorting mechanisms that regulate whether an RNA molecule is immediately translated or sent to specialized locations for translation are unclear. This question is highly relevant during development and differentiation when cells acquire a specific identity. Here, we focus on the RNA-binding properties of heterogeneous nuclear ribonucleoproteins (hnRNPs) and how these mechanisms are believed to play an essential role in RNA trafficking in polarized cells. Further, by focusing on the specific hnRNP protein CBF-A/hnRNPab and its naturally occurring isoforms, we propose a model on how hnRNP proteins are capable of regulating gene expression both spatially and temporally throughout the RNA biogenesis pathway, impacting both healthy and diseased cells.
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Affiliation(s)
- Nathalie Neriec
- Biology Department, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Biology Department, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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20
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Szczurek A, Contu F, Hoang A, Dobrucki J, Mai S. Aqueous mounting media increasing tissue translucence improve image quality in Structured Illumination Microscopy of thick biological specimen. Sci Rep 2018; 8:13971. [PMID: 30228281 PMCID: PMC6143540 DOI: 10.1038/s41598-018-32191-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023] Open
Abstract
Structured Illumination Microscopy (SIM) is a super-resolution microscopy method that has significantly advanced studies of cellular structures. It relies on projection of illumination patterns onto a fluorescently labelled biological sample. The information derived from the sample is then shifted to a detectable band, and in the process of image calculation in Fourier space the resolution is doubled. Refractive index homogeneity along the optical path is crucial to maintain a highly modulated illumination pattern necessary for high-quality SIM. This applies in particular to thick samples consisting of large cells and tissues. Surprisingly, sample mounting media for SIM have not undergone a significant evolution for almost a decade. Through identification and systematic evaluation of a number of non-hazardous, water-soluble chemical components of mounting media, we demonstrate an unprecedented improvement in SIM-image quality. Mounting solutions presented in this research are capable of reducing abundant light scattering which constitutes the limiting factor in 3D-SIM imaging of large Hodgkin's lymphoma and embryonic stem cells as well as 10 µm tissue sections. Moreover, we demonstrate usefulness of some of the media in single molecule localisation microscopy. The results presented here are of importance for standardisation of 3D-SIM data acquisition pipelines for an expanding community of users.
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Affiliation(s)
- Aleksander Szczurek
- University of Manitoba, Cancer Care Manitoba, Winnipeg, 675 McDermot Ave, R3E 0V9, Canada
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Gronostajowa 7, 30-387, Poland
| | - Fabio Contu
- University of Manitoba, Cancer Care Manitoba, Winnipeg, 675 McDermot Ave, R3E 0V9, Canada
- University of Cagliari, Unit of Biology and Genetics, Department of Biomedical Sciences, S. P. Monserrato, Sestu Km 0.700, Cagliari, 09042, Italy
| | - Agnieszka Hoang
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Gronostajowa 7, 30-387, Poland
| | - Jurek Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Gronostajowa 7, 30-387, Poland
| | - Sabine Mai
- University of Manitoba, Cancer Care Manitoba, Winnipeg, 675 McDermot Ave, R3E 0V9, Canada.
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21
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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22
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Lomiento M, Mammoli F, Mazza EMC, Bicciato S, Ferrari S. Chromosome positioning in interphase nuclei of hematopoietic stem cell and myeloid precursor. Hematol Rep 2018; 10:7515. [PMID: 29721254 PMCID: PMC5907646 DOI: 10.4081/hr.2018.7515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
Human myelopoiesis is an intriguing biological process during which multipotent stem cells limit their differentiation potential generating precursors that evolve into terminally differentiated cells. The differentiation process is correlated with differential gene expression and changes in nuclear architecture. In interphase, chromosomes are distinct entities known as chromosome territories and they show a radial localization that could result in a constrain of inter-homologous distance. This element plays a role in genome stability and gene expression. Here, we provide the first experimental evidence of 3D chromosomal arrangement considering two steps of human normal myelopoiesis. Specifically, multicolor 3D-FISH and 3D image analysis revealed that, in both normal human hematopoietic stem cells and myelod precursors CD14-, chromosomal position is correlated with gene density. However, we observed that inter-homologue distances are totally different during differentiation. This could be associated with differential gene expression that we found comparing the two cell types. Our results disclose an unprecedented framework relevant for deciphering the genomic mechanisms at the base of normal human myelopoiesis.
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Affiliation(s)
- Mariana Lomiento
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabiana Mammoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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23
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Kocanova S, Goiffon I, Bystricky K. 3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines. Methods 2018; 142:3-15. [PMID: 29501423 DOI: 10.1016/j.ymeth.2018.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/19/2017] [Accepted: 02/14/2018] [Indexed: 11/28/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
| | - Isabelle Goiffon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France.
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
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24
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Super resolution imaging of chromatin in pluripotency, differentiation, and reprogramming. Curr Opin Genet Dev 2017; 46:186-193. [DOI: 10.1016/j.gde.2017.07.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/10/2017] [Accepted: 07/24/2017] [Indexed: 12/23/2022]
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25
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Ryabichko SS, Ibragimov AN, Lebedeva LA, Kozlov EN, Shidlovskii YV. Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus. Acta Naturae 2017; 9:42-51. [PMID: 29340216 PMCID: PMC5762827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Indexed: 11/21/2022] Open
Abstract
In recent decades, novel microscopic methods commonly referred to as super- resolution microscopy have been developed. These methods enable the visualization of a cell with a resolution of up to 10 nm. The application of these methods is of great interest in studying the structure and function of the cell nucleus. The review describes the main achievements in this field.
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Affiliation(s)
- S. S. Ryabichko
- Institute of Gene Biology RAS, Vavilova Str. 34/5, Moscow, 119334, Russia
| | - A. N. Ibragimov
- Institute of Gene Biology RAS, Vavilova Str. 34/5, Moscow, 119334, Russia
| | - L. A. Lebedeva
- Institute of Gene Biology RAS, Vavilova Str. 34/5, Moscow, 119334, Russia
| | - E. N. Kozlov
- Institute of Gene Biology RAS, Vavilova Str. 34/5, Moscow, 119334, Russia
| | - Y. V. Shidlovskii
- Institute of Gene Biology RAS, Vavilova Str. 34/5, Moscow, 119334, Russia
- I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8, bldg. 2, Moscow, 119048 , Russia
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26
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Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res 2017; 45:e56. [PMID: 28082388 PMCID: PMC5416826 DOI: 10.1093/nar/gkw1301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.
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Affiliation(s)
| | - Ludger Klewes
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Jun Xing
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Amine Gourram
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Hans Knecht
- Département de Médecine, CHUS, Université de Sherbrooke, 3001-12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada.,Department of Medicine, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sabine Mai
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Christoph Cremer
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany.,Kirchhoff Institute of Physics (KIP), and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Germany
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27
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Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics Chromatin 2017; 10:39. [PMID: 28784182 PMCID: PMC5547466 DOI: 10.1186/s13072-017-0146-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks. RESULTS Using 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[-] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[-]) are enriched toward the compacted interior of CDCs (INC). CONCLUSIONS Our results add further evidence in support of the ANC-INC network model. The different 3D topographies of DHS[+] and DHS[-] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an 'open,' active and 'closed,' inactive state.
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28
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Schmid VJ, Cremer M, Cremer T. Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. Methods 2017; 123:33-46. [PMID: 28323041 DOI: 10.1016/j.ymeth.2017.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/16/2017] [Accepted: 03/10/2017] [Indexed: 01/20/2023] Open
Abstract
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data.
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Affiliation(s)
- Volker J Schmid
- BioImaging Group, Department of Statistics, Ludwig Maximilians-Universität München, Ludwigstrasse 33, 80539 Munich, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians-Universität München, Großhadernerstrasse 2, 82152 Martinsried, Germany.
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians-Universität München, Großhadernerstrasse 2, 82152 Martinsried, Germany.
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29
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Skinner BM, Johnson EEP. Nuclear morphologies: their diversity and functional relevance. Chromosoma 2017; 126:195-212. [PMID: 27631793 PMCID: PMC5371643 DOI: 10.1007/s00412-016-0614-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/17/2016] [Indexed: 12/20/2022]
Abstract
Studies of chromosome and genome biology often focus on condensed chromatin in the form of chromosomes and neglect the non-dividing cells. Even when interphase nuclei are considered, they are often then treated as interchangeable round objects. However, different cell types can have very different nuclear shapes, and these shapes have impacts on cellular function; indeed, many pathologies are linked with alterations to nuclear shape. In this review, we describe some of the nuclear morphologies beyond the spherical and ovoid. Many of the leukocytes of the immune system have lobed nuclei, which aid their flexibility and migration; smooth muscle cells have a spindle shaped nucleus, which must deform during muscle contractions; spermatozoa have highly condensed nuclei which adopt varied shapes, potentially associated with swimming efficiency. Nuclei are not passive passengers within the cell. There are clear effects of nuclear shape on the transcriptional activity of the cell. Recent work has shown that regulation of gene expression can be influenced by nuclear morphology, and that cells can drastically remodel their chromatin during differentiation. The link between the nucleoskeleton and the cytoskeleton at the nuclear envelope provides a mechanism for transmission of mechanical forces into the nucleus, directly affecting chromatin compaction and organisation.
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Affiliation(s)
- Benjamin M Skinner
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
| | - Emma E P Johnson
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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30
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Sathitruangsak C, Righolt CH, Klewes L, Tung Chang D, Kotb R, Mai S. Distinct and shared three-dimensional chromosome organization patterns in lymphocytes, monoclonal gammopathy of undetermined significance and multiple myeloma. Int J Cancer 2017; 140:400-410. [PMID: 27711972 PMCID: PMC5132008 DOI: 10.1002/ijc.30461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/11/2016] [Accepted: 09/29/2016] [Indexed: 12/24/2022]
Abstract
The consistent appearance of specific chromosomal translocations in multiple myeloma has suggested that the positioning of chromosomes in the interphase nucleus might play a role in the occurrence of particular chromosomal rearrangements associated with malignant transformation. Using fluorescence in situ hybridization, we have determined the positions of selected chromosome pairs (18 and 19, 9 and 22, 4 and 14, 14 and 16, 11 and 14) in interphase nuclei of myeloma cells compared to normal lymphocytes of treatment-naïve patients. All chromosome pairs were arranged in a nonrandom pattern. Chromosomes commonly involved in myeloma-associated translocations (4 and 14, 14 and 16, 11 and 14) were found in close spatial proximity, and this is correlated with the occurrence of overlapping chromosome territories. The spatial distribution of chromosomes may increase the possibility of chromosomal translocations in multiple myeloma.
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Affiliation(s)
- Chirawadee Sathitruangsak
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Division of Medical OncologyDepartment of Internal MedicinePrince of Songkla UniversitySongkhlaThailand
| | - Christiaan H. Righolt
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Ludger Klewes
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
| | - Doris Tung Chang
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Rami Kotb
- Department of HaematologyCancerCare ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
- Department of Physiology and PathophysiologyUniversity of ManitobaWinnipegManitobaCanada
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31
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Banday S, Farooq Z, Rashid R, Abdullah E, Altaf M. Role of Inner Nuclear Membrane Protein Complex Lem2-Nur1 in Heterochromatic Gene Silencing. J Biol Chem 2016; 291:20021-9. [PMID: 27451393 DOI: 10.1074/jbc.m116.743211] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 11/06/2022] Open
Abstract
Heterochromatin in the fission yeast Schizosaccharomyces pombe is clustered at the nuclear periphery and interacts with a number of nuclear membrane proteins. However, the significance and the factors that sequester heterochromatin at the nuclear periphery are not fully known. Here, we report that an inner nuclear membrane protein complex Lem2-Nur1 is essential for heterochromatin-mediated gene silencing. We found that Lem2 is physically associated with another inner nuclear membrane protein, Nur1, and deletion of either lem2 or nur1 causes silencing defect at centromeres, telomeres, and rDNA loci. We analyzed the genome-wide association of Lem2 using ChIP sequencing and we found that it binds to the central core region of centromeres, in striking contrast to Chp1, a component of pericentromeric heterochromatin, which binds H3K9me-rich chromatin in neighboring sequences. The recruitment of Lem2 and Nur1 to silent regions of the genome is dependent on H3K9 methyltransferase, Clr4. Finally, we show that the Lem2-Nur1 complex regulates the local balance between the underln]Snf2/HDAC-containing repressor complex (SHREC) histone deacetylase complex and the anti-silencing protein Epe1. These findings uncover a novel role for Lem2-Nur1 as a key functional link between localization at the nuclear periphery and heterochromatin-mediated gene silencing.
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Affiliation(s)
- Shahid Banday
- From the Chromatin and Epigenetics Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Zeenat Farooq
- From the Chromatin and Epigenetics Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Romana Rashid
- From the Chromatin and Epigenetics Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Ehsaan Abdullah
- From the Chromatin and Epigenetics Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Mohammad Altaf
- From the Chromatin and Epigenetics Laboratory, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
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32
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Gonzalez-Sandoval A, Gasser SM. Mechanism of chromatin segregation to the nuclear periphery in C. elegans embryos. WORM 2016; 5:e1190900. [PMID: 27695653 DOI: 10.1080/21624054.2016.1190900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
In eukaryotic organisms, gene regulation occurs in the context of chromatin. In the interphase nucleus, euchromatin and heterochromatin occupy distinct space during cell differentiation, with heterochromatin becoming enriched at the nuclear and nucleolar peripheries. This organization is thought to fine-tune gene expression. To elucidate the mechanisms that govern this level of genome organization, screens were carried out in C. elegans which monitored the loss of heterochromatin sequestration at the nuclear periphery. This led to the identification of a novel chromodomain protein, CEC-4 (Caenorhabditis elegans chromodomain protein 4) that mediates the anchoring of H3K9 methylation-bearing chromatin at the nuclear periphery in early to mid-stage embryos. Surprisingly, the loss of CEC-4 does not derepress genes found in heterochromatic domains, nor does it affect differentiation under standard laboratory conditions. On the other hand, CEC-4 contributes to the efficiency with which muscle differentiation is induced following ectopic expression of the master regulator, HLH-1. This is one of the first phenotypes specifically attributed to the ablation of heterochromatin anchoring.
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Affiliation(s)
- Adriana Gonzalez-Sandoval
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
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33
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Solovei I, Thanisch K, Feodorova Y. How to rule the nucleus: divide et impera. Curr Opin Cell Biol 2016; 40:47-59. [PMID: 26938331 DOI: 10.1016/j.ceb.2016.02.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/14/2023]
Abstract
Genome-wide molecular studies have provided new insights into the organization of nuclear chromatin by revealing the presence of chromatin domains of differing transcriptional activity, frequency of cis-interactions, proximity to scaffolding structures and replication timing. These studies have not only brought our understanding of genome function to a new level, but also offered functional insight for many phenomena observed in microscopic studies. In this review, we discuss the major principles of nuclear organization based on the spatial segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell differentiation and development. We hope to unite the existing molecular and microscopic data on genome organization to get a holistic view of the nucleus, and propose a model, in which repeat repertoire together with scaffolding structures blueprint the functional nuclear architecture.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany.
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
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34
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Harr JC, Gonzalez-Sandoval A, Gasser SM. Histones and histone modifications in perinuclear chromatin anchoring: from yeast to man. EMBO Rep 2016; 17:139-55. [PMID: 26792937 PMCID: PMC4783997 DOI: 10.15252/embr.201541809] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023] Open
Abstract
It is striking that within a eukaryotic nucleus, the genome can assume specific spatiotemporal distributions that correlate with the cell's functional states. Cell identity itself is determined by distinct sets of genes that are expressed at a given time. On the level of the individual gene, there is a strong correlation between transcriptional activity and associated histone modifications. Histone modifications act by influencing the recruitment of non-histone proteins and by determining the level of chromatin compaction, transcription factor binding, and transcription elongation. Accumulating evidence also shows that the subnuclear position of a gene or domain correlates with its expression status. Thus, the question arises whether this spatial organization results from or determines a gene's chromatin status. Although the association of a promoter with the inner nuclear membrane (INM) is neither necessary nor sufficient for repression, the perinuclear sequestration of heterochromatin is nonetheless conserved from yeast to man. How does subnuclear localization influence gene expression? Recent work argues that the common denominator between genome organization and gene expression is the modification of histones and in some cases of histone variants. This provides an important link between local chromatin structure and long-range genome organization in interphase cells. In this review, we will evaluate how histones contribute to the latter, and discuss how this might help to regulate genes crucial for cell differentiation.
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Affiliation(s)
- Jennifer C Harr
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Adriana Gonzalez-Sandoval
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Faculty of Natural Sciences, University of Basel, Basel, Switzerland
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