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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024. [PMID: 38618985 DOI: 10.1111/jmi.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023; 42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2-10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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Affiliation(s)
- Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Shih-Ya Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Jan Neumann
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Ole Kröger
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Filip Sadlo
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Jorg Imhoff
- Neuroconsult GmbH, 69120 Heidelberg, Germany
| | - Michael J Hendzel
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany.
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3
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The influence of high-order chromatin state in the regulation of stem cell fate. Biochem Soc Trans 2022; 50:1809-1822. [DOI: 10.1042/bst20220763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, genomic DNA is hierarchically compacted by histones into chromatin, which is initially assembled by the nucleosome and further folded into orderly and flexible structures that include chromatin fiber, chromatin looping, topologically associated domains (TADs), chromosome compartments, and chromosome territories. These distinct structures and motifs build the three-dimensional (3D) genome architecture, which precisely controls spatial and temporal gene expression in the nucleus. Given that each type of cell is characterized by its own unique gene expression profile, the state of high-order chromatin plays an essential role in the cell fate decision. Accumulating evidence suggests that the plasticity of high-order chromatin is closely associated with stem cell fate. In this review, we summarize the biological roles of the state of high-order chromatin in embryogenesis, stem cell differentiation, the maintenance of stem cell identity, and somatic cell reprogramming. In addition, we highlight the roles of epigenetic factors and pioneer transcription factors (TFs) involved in regulating the state of high-order chromatin during the determination of stem cell fate and discuss how H3K9me3-heterochromatin restricts stem cell fate. In summary, we review the most recent progress in research on the regulatory functions of high-order chromatin dynamics in the determination and maintenance of stem cell fate.
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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Furth N, Shema E. It’s all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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Lv X, Jin K, Sun G, Ledesma-Amaro R, Liu L. Microscopy imaging of living cells in metabolic engineering. Trends Biotechnol 2021; 40:752-765. [PMID: 34799183 DOI: 10.1016/j.tibtech.2021.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023]
Abstract
Microscopy imaging of living cells is becoming a pivotal, noninvasive, and highly specific tool in metabolic engineering to visualize molecular dynamics in industrial microorganisms. This review describes the different microscopy methods, from fluorescence to super resolution, with application in microbial bioengineering. Firstly, the role and importance of microscopy imaging is analyzed in the context of strain design. Then, the advantages and disadvantages of different microscopy technologies are discussed, including confocal laser scanning microscopy (CLSM), spatial light interference microscopy (SLIM), and super-resolution microscopy, followed by their applications in synthetic biology. Finally, the future perspectives of live-cell imaging and their potential to transform microbial systems are analyzed. This review provides theoretical guidance and highlights the importance of microscopy in understanding and engineering microbial metabolism.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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Malashicheva A, Perepelina K. Diversity of Nuclear Lamin A/C Action as a Key to Tissue-Specific Regulation of Cellular Identity in Health and Disease. Front Cell Dev Biol 2021; 9:761469. [PMID: 34722546 PMCID: PMC8548693 DOI: 10.3389/fcell.2021.761469] [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: 08/19/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
A-type lamins are the main structural components of the nucleus, which are mainly localized at the nucleus periphery. First of all, A-type lamins, together with B-type lamins and proteins of the inner nuclear membrane, form a stiff structure-the nuclear lamina. Besides maintaining the nucleus cell shape, A-type lamins play a critical role in many cellular events, such as gene transcription and epigenetic regulation. Nowadays it is clear that lamins play a very important role in determining cell fate decisions. Various mutations in genes encoding A-type lamins lead to damages of different types of tissues in humans, collectively known as laminopathies, and it is clear that A-type lamins are involved in the regulation of cell differentiation and stemness. However, the mechanisms of this regulation remain unclear. In this review, we discuss how A-type lamins can execute their regulatory role in determining the differentiation status of a cell. We have summarized recent data focused on lamin A/C action mechanisms in regulation of cell differentiation and identity development of stem cells of different origin. We also discuss how this knowledge can promote further research toward a deeper understanding of the role of lamin A/C mutations in laminopathies.
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Affiliation(s)
- Anna Malashicheva
- Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Kseniya Perepelina
- Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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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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Hoboth P, Šebesta O, Hozák P. How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription. Int J Mol Sci 2021; 22:6694. [PMID: 34206594 PMCID: PMC8269275 DOI: 10.3390/ijms22136694] [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: 06/07/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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10
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Ahmad A, Frindel C, Rousseau D. Detecting Differences of Fluorescent Markers Distribution in Single Cell Microscopy: Textural or Pointillist Feature Space? Front Robot AI 2021; 7:39. [PMID: 33501207 PMCID: PMC7805927 DOI: 10.3389/frobt.2020.00039] [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: 07/30/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
We consider the detection of change in spatial distribution of fluorescent markers inside cells imaged by single cell microscopy. Such problems are important in bioimaging since the density of these markers can reflect the healthy or pathological state of cells, the spatial organization of DNA, or cell cycle stage. With the new super-resolved microscopes and associated microfluidic devices, bio-markers can be detected in single cells individually or collectively as a texture depending on the quality of the microscope impulse response. In this work, we propose, via numerical simulations, to address detection of changes in spatial density or in spatial clustering with an individual (pointillist) or collective (textural) approach by comparing their performances according to the size of the impulse response of the microscope. Pointillist approaches show good performances for small impulse response sizes only, while all textural approaches are found to overcome pointillist approaches with small as well as with large impulse response sizes. These results are validated with real fluorescence microscopy images with conventional resolution. This, a priori non-intuitive result in the perspective of the quest of super-resolution, demonstrates that, for difference detection tasks in single cell microscopy, super-resolved microscopes may not be mandatory and that lower cost, sub-resolved, microscopes can be sufficient.
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Affiliation(s)
- Ali Ahmad
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France.,Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé, CNRS UMR 5220-INSERM U1206, Université Lyon 1, INSA de Lyon, Lyon, France
| | - Carole Frindel
- Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé, CNRS UMR 5220-INSERM U1206, Université Lyon 1, INSA de Lyon, Lyon, France
| | - David Rousseau
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
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Hoboth P, Sztacho M, Šebesta O, Schätz M, Castano E, Hozák P. Nanoscale mapping of nuclear phosphatidylinositol phosphate landscape by dual-color dSTORM. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158890. [PMID: 33513445 DOI: 10.1016/j.bbalip.2021.158890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Current models of gene expression, which are based on single-molecule localization microscopy, acknowledge protein clustering and the formation of transcriptional condensates as a driving force of gene expression. However, these models largely omit the role of nuclear lipids and amongst them nuclear phosphatidylinositol phosphates (PIPs) in particular. Moreover, the precise distribution of nuclear PIPs in the functional sub-nuclear domains remains elusive. The direct stochastic optical reconstruction microscopy (dSTORM) provides an unprecedented resolution in biological imaging. Therefore, its use for imaging in the densely crowded cell nucleus is desired but also challenging. Here we present a dual-color dSTORM imaging and image analysis of nuclear PI(4,5)P2, PI(3,4)P2 and PI(4)P distribution while preserving the context of nuclear architecture. In the nucleoplasm, PI(4,5)P2 and PI(3,4)P2 co-pattern in close proximity with the subset of RNA polymerase II foci. PI(4,5)P2 is surrounded by fibrillarin in the nucleoli and all three PIPs are dispersed within the matrix formed by the nuclear speckle protein SON. PI(4,5)P2 is the most abundant nuclear PIP, while PI(4)P is a precursor for the biosynthesis of PI(4,5)P2 and PI(3,4)P2. Therefore, our data are relevant for the understanding the roles of nuclear PIPs and provide further evidence for the model in which nuclear PIPs represent a localization signal for the formation of lipo-ribonucleoprotein hubs in the nucleus. The discussed experimental pipeline is applicable for further functional studies on the role of other nuclear PIPs in the regulation of gene expression and beyond.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Martin Schätz
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Enrique Castano
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic; Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, division BIOCEV, Průmyslová 595, 252 20 Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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G. Keller S, Kamiya M, Urano Y. Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes. Molecules 2020; 25:E5964. [PMID: 33339370 PMCID: PMC7766215 DOI: 10.3390/molecules25245964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.
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Affiliation(s)
- Sascha G. Keller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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13
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Fiorentino G, Parrilli A, Garagna S, Zuccotti M. Three-Dimensional Micro-Computed Tomography of the Adult Mouse Ovary. Front Cell Dev Biol 2020; 8:566152. [PMID: 33195196 PMCID: PMC7604317 DOI: 10.3389/fcell.2020.566152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
In the mouse ovary, folliculogenesis proceeds through eight main growth stages, from small primordial type 1 (T1) to fully grown antral T8 follicles. Most of our understanding of this process was obtained with approaches that disrupted the ovary three-dimensional (3D) integrity. Micro-Computed Tomography (microCT) allows the maintenance of the organ structure and a true in-silico 3D reconstruction, with cubic voxels and isotropic resolution, giving a precise spatial mapping of its functional units. Here, we developed a robust method that, by combining an optimized contrast procedure with microCT imaging of the tiny adult mouse ovary, allowed 3D mapping and counting of follicles, from pre-antral secondary T4 (53.2 ± 12.7 μm in diameter) to antral T8 (321.0 ± 21.3 μm) and corpora lutea, together with the major vasculature branches. Primordial and primary follicles (T1–T3) could not be observed. Our procedure highlighted, with unprecedent details, the main functional compartments of the growing follicle: granulosa, antrum, cumulus cells, zona pellucida, and oocyte with its nucleus. The results describe a homogeneous distribution of all follicle types between the ovary dorsal and ventral regions. Also, they show that each of the eight sectors, virtually segmented along the dorsal-ventral axis, houses an equal number of each follicle type. Altogether, these data suggest that follicle recruitment is homogeneously distributed all-over the ovarian surface. This topographic reconstruction builds sound bases for modeling follicles position and, prospectively, could contribute to our understanding of folliculogenesis dynamics, not only under normal conditions, but, importantly, during aging, in the presence of pathologies or after hormones or drugs administration.
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Affiliation(s)
- Giulia Fiorentino
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Annapaola Parrilli
- Center for X-ray Analytics, Empa-Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
| | - Silvia Garagna
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Maurizio Zuccotti
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
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14
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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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: 43] [Impact Index Per Article: 10.8] [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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Li G. The 3D organization of genome in the nucleus: from the nucleosome to the 4D nucleome. SCIENCE CHINA-LIFE SCIENCES 2020; 63:791-794. [PMID: 32394246 DOI: 10.1007/s11427-020-1723-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Guohong Li
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
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17
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Ghosh SK, Jost D. Genome organization via loop extrusion, insights from polymer physics models. Brief Funct Genomics 2020; 19:119-127. [PMID: 31711163 DOI: 10.1093/bfgp/elz023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
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Affiliation(s)
- Surya K Ghosh
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007 Lyon, France
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18
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Heller JP, Odii T, Zheng K, Rusakov DA. Imaging tripartite synapses using super-resolution microscopy. Methods 2020; 174:81-90. [PMID: 31153907 PMCID: PMC7144327 DOI: 10.1016/j.ymeth.2019.05.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 01/02/2023] Open
Abstract
Astroglia are vital facilitators of brain development, homeostasis, and metabolic support. In addition, they are also essential to the formation and regulation of synaptic circuits. Due to the extraordinary complex, nanoscopic morphology of astrocytes, the underlying cellular mechanisms have been poorly understood. In particular, fine astrocytic processes that can be found in the vicinity of synapses have been difficult to study using traditional imaging techniques. Here, we describe a 3D three-colour super-resolution microscopy approach to unravel the nanostructure of tripartite synapses. The method is based on the SMLM technique direct stochastic optical reconstruction microscopy (dSTORM) which uses conventional fluorophore-labelled antibodies. This approach enables reconstructing the nanoscale localisation of individual astrocytic glutamate transporter (GLT-1) molecules surrounding presynaptic (bassoon) and postsynaptic (Homer1) protein localisations in fixed mouse brain sections. However, the technique is readily adaptable to other types of targets and tissues.
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Affiliation(s)
- Janosch Peter Heller
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Tuamoru Odii
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Physiology, Faculty of Basic Medical Sciences, Alex Ekwueme Federal University Ndufu-Alike Ikwo, PMB 1010 Abakaliki, Nigeria
| | - Kaiyu Zheng
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
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19
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Badawi Y, Nishimune H. Super-resolution microscopy for analyzing neuromuscular junctions and synapses. Neurosci Lett 2020; 715:134644. [PMID: 31765730 PMCID: PMC6937598 DOI: 10.1016/j.neulet.2019.134644] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022]
Abstract
Super-resolution microscopy techniques offer subdiffraction limited resolution that is two- to ten-fold improved compared to that offered by conventional confocal microscopy. This breakthrough in resolution for light microscopy has contributed to new findings in neuroscience and synapse biology. This review will focus on the Structured Illumination Microscopy (SIM), Stimulated emission depletion (STED) microscopy, and Stochastic optical reconstruction microscopy (STORM) / Single molecule localization microscopy (SMLM) techniques and compare them for the better understanding of their differences and their suitability for the analysis of synapse biology. In addition, we will discuss a few practical aspects of these microscopic techniques, including resolution, image acquisition speed, multicolor capability, and other advantages and disadvantages. Tips for the improvement of microscopy will be introduced; for example, information resources for recommended dyes, the limitations of multicolor analysis, and capabilities for live imaging. In addition, we will summarize how super-resolution microscopy has been used for analyses of neuromuscular junctions and synapses.
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Affiliation(s)
- Yomna Badawi
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Hiroshi Nishimune
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS, 66160, USA.
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20
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Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA. H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. eLife 2019; 8:49278. [PMID: 31573510 PMCID: PMC6795522 DOI: 10.7554/elife.49278] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.
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Affiliation(s)
- Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Cheryl L Smith
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Karen G Wong
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Rajan Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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21
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Allgayer H, Leupold JH, Patil N. Defining the "Metastasome": Perspectives from the genome and molecular landscape in colorectal cancer for metastasis evolution and clinical consequences. Semin Cancer Biol 2019; 60:1-13. [PMID: 31362074 DOI: 10.1016/j.semcancer.2019.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Metastasis still poses the highest challenge for personalized therapy in cancer, partly due to a still incomplete understanding of its molecular evolution. We recently presented the most comprehensive whole-genome study of colorectal metastasis vs. matched primary tumors and suggested novel components of disease progression and metastasis evolution, some of them potentially relevant for targeted therapy. In this review, we try to put these findings into perspective with latest discoveries of colleagues and recent literature, and propose a systematic international team effort to collectively define the "metastasome", a term we introduce to summarize all genomic, epigenomic, transcriptomic, further -omic, molecular and functional characteristics rendering metastases different from primary tumors. Based on recent discoveries, we propose a revised metastasis model for colorectal cancer which is based on a common ancestor clone, early dissemination but flexible early or late stage clonal separation paralleling stromal interactions. Furthermore, we discuss hypotheses on site-specific metastasis, colorectal cancer progression, metastasis-targeted diagnosis and therapy, and metastasis prevention based on latest metastasome data.
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Affiliation(s)
- Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany.
| | - Jörg H Leupold
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
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22
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Birk UJ. Super-Resolution Microscopy of Chromatin. Genes (Basel) 2019; 10:E493. [PMID: 31261775 PMCID: PMC6678334 DOI: 10.3390/genes10070493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.
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Affiliation(s)
- Udo J Birk
- University of Applied Sciences HTW Chur, Pulvermühlestrasse 57, 7004 Chur, Switzerland.
- Institut für Physik, Universität Mainz, 55122 Mainz, Germany.
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23
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Lin R, Clowsley AH, Lutz T, Baddeley D, Soeller C. 3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples. Methods 2019; 174:56-71. [PMID: 31129290 DOI: 10.1016/j.ymeth.2019.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 12/29/2022] Open
Abstract
Assessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time- and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.
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Affiliation(s)
- Ruisheng Lin
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Alexander H Clowsley
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Tobias Lutz
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - David Baddeley
- Department of Cell Biology, Yale University, USA; Bioengineering Institute, University of Auckland, New Zealand
| | - Christian Soeller
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom.
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24
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Bucevičius J, Keller-Findeisen J, Gilat T, Hell SW, Lukinavičius G. Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin. Chem Sci 2019; 10:1962-1970. [PMID: 30881625 PMCID: PMC6385482 DOI: 10.1039/c8sc05082a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Hoechst conjugates to fluorescent dyes are popular DNA stains for live-cell imaging, but the relationship between their structure and performance remains elusive. This study of carboxyrhodamine-Hoechst 33258 conjugates reveals that a minimal change in the attachment point of the dye has dramatic effects on the properties of the final probe. All tested 6'-carboxyl dye-containing probes exhibited dual-mode binding to DNA and formed a dimmer complex at high DNA concentrations. The 5'-carboxyl dye-containing probes exhibited single-mode binding to DNA which translated into increased brightness and lower cytotoxicity. Up to 10-fold brighter nuclear staining by the newly developed probes allowed acquisition of stimulated emission depletion (STED) nanoscopy images of outstanding quality in living and fixed cells. Therefore we were able to estimate a diameter of ∼155 nm of the heterochromatin exclusion zones in the nuclear pore region in living cells and intact chicken erythrocytes and to localize telomeres relative to heterochromatin in living U-2 OS cells. Employing the highly efficient probes for two-color STED allowed visualization of DNA and tubulin structures in intact nucleated erythrocytes - a system where imaging is greatly hampered by high haemoglobin absorbance.
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Affiliation(s)
- Jonas Bucevičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Tanja Gilat
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Stefan W Hell
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Gražvydas Lukinavičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
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25
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, NCI, United States; Department of Computational Medicine and Bioinformatics, University of Michigan, United States
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, United States; Department of Mathematics, University of Michigan, United States
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26
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Smith PJ, Darzynkiewicz Z, Errington RJ. Nuclear cytometry and chromatin organization. Cytometry A 2018; 93:771-784. [PMID: 30144297 DOI: 10.1002/cyto.a.23521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.
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Affiliation(s)
- Paul J Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, Valhalla, New York, 10595
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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27
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Sarmento MJ, Oneto M, Pelicci S, Pesce L, Scipioni L, Faretta M, Furia L, Dellino GI, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Exploiting the tunability of stimulated emission depletion microscopy for super-resolution imaging of nuclear structures. Nat Commun 2018; 9:3415. [PMID: 30143630 PMCID: PMC6109149 DOI: 10.1038/s41467-018-05963-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/27/2018] [Indexed: 11/23/2022] Open
Abstract
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
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Affiliation(s)
- Maria J Sarmento
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | - Michele Oneto
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Luca Pesce
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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28
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Gray-level co-occurrence matrix analysis of chromatin architecture in periportal and perivenous hepatocytes. Histochem Cell Biol 2018; 151:75-83. [PMID: 30140953 DOI: 10.1007/s00418-018-1714-5] [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] [Accepted: 08/21/2018] [Indexed: 02/05/2023]
Abstract
Periportal hepatocytes (PPHs) and perivenous hepatocytes (PVHs) in standard optical microscopy appear to be morphologically identical. However, the functional properties of these two cell populations and their roles in liver lobules are not the same. Despite significant differences in gene expression between these two hepatocyte populations, it is still unclear whether the differences are present at the higher levels of chromatin organization. In this study, we present results, indicating that periportal and perivenous hepatocytes, when stained using toluidine blue histological dye, have different chromatin textural patterns quantified with gray-level co-occurrence matrix (GLCM) method. Hepatic tissue was obtained from ten male, healthy mice. Chromatin structures were analyzed using GLCM. For each structure, we measured the values of angular second moment, inverse difference moment, GLCM Contrast, GLCM Variance, and GLCM Sum Variance. The results indicate that there is a statistically significant difference in all GLCM mathematical parameters except the contrast. In addition, some chromatin GLCM features were in correlation with serum aminotransferase levels in perivenous, but not in periportal hepatocytes. To the best of our knowledge, this is the first study to test the nuclear morphological differences between hepatocytes using GLCM and to investigate the respective relation with serum liver enzymes.
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29
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Abstract
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automated GO-CC annotation of proteins suffer from the inconsistency of individual GO-CC term predictions. Here, we present FGGA-CC+, a class of hierarchical graph-based classifiers for the consistent GO-CC annotation of protein coding genes at the subcellular compartment or macromolecular complex levels. Aiming to boost the accuracy of GO-CC predictions, we make use of the protein localization knowledge in the GO-Biological Process (GO-BP) annotations to boost the accuracy of GO-CC prediction. As a result, FGGA-CC+ classifiers are built from annotation data in both the GO-CC and GO-BP ontologies. Due to their graph-based design, FGGA-CC+ classifiers are fully interpretable and their predictions amenable to expert analysis. Promising results on protein annotation data from five model organisms were obtained. Additionally, successful validation results in the annotation of a challenging subset of tandem duplicated genes in the tomato non-model organism were accomplished. Overall, these results suggest that FGGA-CC+ classifiers can indeed be useful for satisfying the huge demand of GO-CC annotation arising from ubiquitous high throughout sequencing and proteomic projects.
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30
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Emerging views of the nucleus as a cellular mechanosensor. Nat Cell Biol 2018; 20:373-381. [PMID: 29467443 DOI: 10.1038/s41556-018-0038-y] [Citation(s) in RCA: 328] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
The ability of cells to respond to mechanical forces is critical for numerous biological processes. Emerging evidence indicates that external mechanical forces trigger changes in nuclear envelope structure and composition, chromatin organization and gene expression. However, it remains unclear if these processes originate in the nucleus or are downstream of cytoplasmic signals. Here we discuss recent findings that support a direct role of the nucleus in cellular mechanosensing and highlight novel tools to study nuclear mechanotransduction.
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31
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Goodin MM. Protein Localization and Interaction Studies in Plants: Toward Defining Complete Proteomes by Visualization. Adv Virus Res 2017; 100:117-144. [PMID: 29551133 DOI: 10.1016/bs.aivir.2017.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein interaction and localization studies in plants are a fundamental component of achieving mechanistic understanding of virus:plant interactions at the systems level. Many such studies are conducted using transient expression assays in leaves of Nicotiana benthamiana, the most widely used experimental plant host in virology, examined by laser-scanning confocal microscopy. This chapter provides a workflow for protein interaction and localization experiments, with particular attention to the many control and supporting assays that may also need to be performed. Basic principles of microscopy are introduced to aid researchers in the early stages of adding imaging techniques to their experimental repertoire. Three major types of imaging-based experiments are discussed in detail: (i) protein localization using autofluorescent proteins, (ii) colocalization studies, and (iii) bimolecular fluorescence complementation, with emphasis on judicious interpretation of the data obtained from these approaches. In addition to establishing a general framework for protein localization experiments in plants, the need for proteome-scale localization projects is discussed, with emphasis on nuclear-localized proteins.
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