1
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Bruštíková K, Ryabchenko B, Žáčková S, Šroller V, Forstová J, Horníková L. Mouse polyomavirus infection induces lamin reorganisation. FEBS J 2024. [PMID: 39288210 DOI: 10.1111/febs.17275] [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: 04/04/2024] [Revised: 07/02/2024] [Accepted: 09/06/2024] [Indexed: 09/19/2024]
Abstract
The nuclear lamina is a dense network of intermediate filaments beneath the inner nuclear membrane. Composed of A-type lamins (lamin A/C) and B-type lamins (lamins B1 and B2), the nuclear lamina provides a scaffold for the nuclear envelope and chromatin, thereby maintaining the structural integrity of the nucleus. A-type lamins are also found inside the nucleus where they interact with chromatin and participate in gene regulation. Viruses replicating in the cell nucleus have to overcome the nuclear envelope during the initial phase of infection and during the nuclear egress of viral progeny. Here, we focused on the role of lamins in the replication cycle of a dsDNA virus, mouse polyomavirus. We detected accumulation of the major capsid protein VP1 at the nuclear periphery, defects in nuclear lamina staining and different lamin A/C phosphorylation patterns in the late phase of mouse polyomavirus infection, but the nuclear envelope remained intact. An absence of lamin A/C did not affect the formation of replication complexes but did slow virus propagation. Based on our findings, we propose that the nuclear lamina is a scaffold for replication complex formation and that lamin A/C has a crucial role in the early phases of infection with mouse polyomavirus.
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Affiliation(s)
- Kateřina Bruštíková
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Boris Ryabchenko
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sandra Žáčková
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vojtěch Šroller
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lenka Horníková
- Department of Genetics and Microbiology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
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2
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Fabian-Morales E, Rodríguez A, Gudiño A, Herrera LA, Frias S. Profiling Chromosome Topological Features by Super-Resolution 3D Structured Illumination Microscopy. Methods Mol Biol 2024; 2825:213-237. [PMID: 38913312 DOI: 10.1007/978-1-0716-3946-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) and fluorescence in situ hybridization on three-dimensional preserved cells (3D-FISH) have proven to be robust and efficient methodologies for analyzing nuclear architecture and profiling the genome's topological features. These methods have allowed the simultaneous visualization and evaluation of several target structures at super-resolution. In this chapter, we focus on the application of 3D-SIM for the visualization of 3D-FISH preparations of chromosomes in interphase, known as Chromosome Territories (CTs). We provide a workflow and detailed guidelines for sample preparation, image acquisition, and image analysis to obtain quantitative measurements for profiling chromosome topological features. In parallel, we address a practical example of these protocols in the profiling of CTs 9 and 22 involved in the translocation t(9;22) in Chronic Myeloid Leukemia (CML). The profiling of chromosome topological features described in this chapter allowed us to characterize a large-scale topological disruption of CTs 9 and 22 that correlates directly with patients' response to treatment and as a possible potential change in the inheritance systems. These findings open new insights into how the genome structure is associated with the response to cancer treatments, highlighting the importance of microscopy in analyzing the topological features of the genome.
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MESH Headings
- Humans
- In Situ Hybridization, Fluorescence/methods
- Imaging, Three-Dimensional/methods
- Translocation, Genetic
- Chromosomes/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Interphase/genetics
- Chromosomes, Human/genetics
- Image Processing, Computer-Assisted/methods
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Affiliation(s)
- Eunice Fabian-Morales
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
- Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | - Adriana Gudiño
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico.
- Escuela de Medicina y Ciencias de la Salud, Instituto Tecnológico y de Estudios Superiores de Monterrey, Mexico City, Mexico.
| | - Sara Frias
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico.
- Laboratorio de Citogenética, Instituto Nacional de Pediatría (INP), Mexico City, Mexico.
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3
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Chong S, Graham TGW, Dugast-Darzacq C, Dailey GM, Darzacq X, Tjian R. Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. Mol Cell 2022; 82:2084-2097.e5. [PMID: 35483357 DOI: 10.1016/j.molcel.2022.04.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/14/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023]
Abstract
Gene activation by mammalian transcription factors (TFs) requires multivalent interactions of their low-complexity domains (LCDs), but how such interactions regulate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS::FLI1 requires a narrow optimum of LCD-LCD interactions to activate its target genes associated with GGAA microsatellites. Increasing LCD-LCD interactions toward putative LLPS represses transcription of these genes in patient-derived cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS::FLI1 into a well-documented LLPS compartment, the nucleolus, inhibits EWS::FLI1-driven transcription and oncogenic transformation. Our findings show how altering the balance of LCD-LCD interactions can influence transcriptional regulation and suggest a potential therapeutic strategy for targeting disease-causing TFs.
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Affiliation(s)
- Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Thomas G W Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA.
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4
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022; 24:327-339. [PMID: 35177821 DOI: 10.1038/s41556-022-00847-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
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Affiliation(s)
- Susanne Leidescher
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Johannes Ribisel
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Ullrich
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Yana Feodorova
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Department of Medical Biology, Medical University of Plovdiv; Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Erica Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Sebastian Bultmann
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Stephanie Link
- BioMedizinisches Center, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Thanisch
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christopher Mulholland
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Heinrich Leonhardt
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irina Solovei
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.
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5
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Yu Z, Potapova TA. Superresolution Microscopy for Visualization of Physical Contacts Between Chromosomes at Nanoscale Resolution. Methods Mol Biol 2022; 2458:359-375. [PMID: 35103978 DOI: 10.1007/978-1-0716-2140-0_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This protocol describes the fluorescence in situ hybridization (FISH) of DNA probes on mitotic chromosome spreads optimized for two super-resolution microscopy approaches-structured illumination microscopy (SIM) and stimulated emission depletion (STED). It is based on traditional DNA FISH methods that can be combined with immunofluorescence labeling (Immuno-FISH). This technique previously allowed us to visualize ribosomal DNA linkages between human acrocentric chromosomes and provided information about the activity status of linked rDNA loci. Compared to the conventional wide-field and confocal microscopy, the quality of SIM and STED data depends a lot more on the optimal specimen preparation, choice of fluorophores, and quality of the fluorescent labeling. This protocol highlights details that make specimens suitable for super-resolution microscopy and tips for good imaging practices.
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Affiliation(s)
- Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA
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6
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Fabian-Morales E, Vallejo-Escamilla D, Gudiño A, Rodríguez A, González-Barrios R, Rodríguez Torres YL, Castro Hernández C, de la Torre-Luján AH, Oliva-Rico DA, Ornelas Guzmán EC, López Saavedra A, Frias S, Herrera LA. Large-scale topological disruption of chromosome territories 9 and 22 is associated with nonresponse to treatment in CML. Int J Cancer 2021; 150:1455-1470. [PMID: 34913480 PMCID: PMC9303775 DOI: 10.1002/ijc.33903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/07/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm defined by the presence of t(9;22) translocation whose origin has been associated with the tridimensional genome organization. This rearrangement leads to the fusion of BCR and ABL1 genes giving rise to a chimeric protein with constitutive kinase activity. Imatinib, a tyrosine kinase inhibitor (TKI), is used as a first‐line treatment for CML, though ~40% of CML patients do not respond. Here, using structured illumination microscopy (SIM) and 3D reconstruction, we studied the 3D organization patterns of the ABL1 and BCR genes, and their chromosome territories (CTs) CT9 and CT22, in CD34+ cells from CML patients that responded or not to TKI. We found that TKI resistance in CML is associated with high levels of structural disruption of CT9 and CT22 in CD34+ cells, increased CT volumes (especially for CT22), intermingling between CT9 and CT22, and an open‐chromatin epigenetic mark in CT22. Altogether our results suggest that large‐scale disruption of CT9 and CT22 correlates with the clinical response of CML patients, which could be translated into a potential prognostic marker of response to treatment in this disease and provide novel insights into the mechanisms underlying resistance to TKI in CML.
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Affiliation(s)
- Eunice Fabian-Morales
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - David Vallejo-Escamilla
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Adriana Gudiño
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Yameli L Rodríguez Torres
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Clementina Castro Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | | | - Diego A Oliva-Rico
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Erandhi C Ornelas Guzmán
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alejandro López Saavedra
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Sara Frias
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Laboratorio de Citogenética, Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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7
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Alić I, Goh PA, Murray A, Portelius E, Gkanatsiou E, Gough G, Mok KY, Koschut D, Brunmeir R, Yeap YJ, O'Brien NL, Groet J, Shao X, Havlicek S, Dunn NR, Kvartsberg H, Brinkmalm G, Hithersay R, Startin C, Hamburg S, Phillips M, Pervushin K, Turmaine M, Wallon D, Rovelet-Lecrux A, Soininen H, Volpi E, Martin JE, Foo JN, Becker DL, Rostagno A, Ghiso J, Krsnik Ž, Šimić G, Kostović I, Mitrečić D, Francis PT, Blennow K, Strydom A, Hardy J, Zetterberg H, Nižetić D. Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene dose-sensitive AD suppressor in human brain. Mol Psychiatry 2021; 26:5766-5788. [PMID: 32647257 PMCID: PMC8190957 DOI: 10.1038/s41380-020-0806-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/18/2020] [Accepted: 05/29/2020] [Indexed: 11/15/2022]
Abstract
A population of more than six million people worldwide at high risk of Alzheimer's disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of β-amyloid-(Aβ)-precursor-protein gene. We report AD-like pathology in cerebral organoids grown in vitro from non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar Aβ deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss. Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome 21 gene BACE2, but prevented by combined chemical β and γ-secretase inhibition. We found that T21 organoids secrete increased proportions of Aβ-preventing (Aβ1-19) and Aβ-degradation products (Aβ1-20 and Aβ1-34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2-trisomy and cross-inhibited by clinically trialled BACE1 inhibitors. Combined, our data prove the physiological role of BACE2 as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in ~30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.
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Grants
- MR/S011277/1 Medical Research Council
- MR/L501542/1 Medical Research Council
- G-0907 Parkinson's UK
- MR/N026004/1 Medical Research Council
- MR/R024901/1 Medical Research Council
- Wellcome Trust
- 217199 Wellcome Trust
- G0901254 Medical Research Council
- MR/T002581/1 Medical Research Council
- RF1 AG059695 NIA NIH HHS
- G0701075 Medical Research Council
- 098330 Wellcome Trust
- William Harvey Academy Fellowship, co-funded by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° 608765
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- National Research Foundation Singapore (National Research Foundation-Prime Minister’s office, Republic of Singapore)
- BrightFocus Foundation (BrightFocus)
- Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)
- Svenska Forskningsrådet Formas (Swedish Research Council Formas)
- KB holds the Torsten Söderberg Professorship in Medicine at the Royal Swedish Academy of Sciences, and is supported by the Swedish Alzheimer Foundation (#AF-742881), Hjärnfonden, Sweden (#FO2017-0243), and the Swedish State Support for Clinical Research (#ALFGBG-715986).
- Wellcome Trust (Wellcome)
- JH received funding from the Dementia Research Institute, an anonymous foundation and the Dolby foundation
- HZ is a Wallenberg Academy Fellow supported by grants from the Swedish Research Council, the European Research Council, Swedish State Support for Clinical Research (ALFGBG-720931) the UK Dementia Research Institute at UCL
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Affiliation(s)
- Ivan Alić
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Pollyanna A Goh
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- LonDownS Consortium, London, UK
| | - Aoife Murray
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
| | - Eleni Gkanatsiou
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
| | - Gillian Gough
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Kin Y Mok
- LonDownS Consortium, London, UK
- Dementia Research Institute & Reta Lila Weston Institute, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - David Koschut
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Reinhard Brunmeir
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Niamh L O'Brien
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- LonDownS Consortium, London, UK
| | - Jürgen Groet
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
- LonDownS Consortium, London, UK
| | - Xiaowei Shao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Steven Havlicek
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - N Ray Dunn
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Hlin Kvartsberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
| | - Rosalyn Hithersay
- LonDownS Consortium, London, UK
- Division of Psychiatry, University College London, London, WC1E 6BT, UK
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Carla Startin
- LonDownS Consortium, London, UK
- Division of Psychiatry, University College London, London, WC1E 6BT, UK
| | - Sarah Hamburg
- LonDownS Consortium, London, UK
- Division of Psychiatry, University College London, London, WC1E 6BT, UK
| | - Margaret Phillips
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Mark Turmaine
- Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - David Wallon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Neurology and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne Rovelet-Lecrux
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Neurology and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Hilkka Soininen
- University of Eastern Finland, Institute of Clinical Medicine/Neurology, Kuopio, FI-70211, Finland
| | - Emanuela Volpi
- School of Life Sciences, University of Westminster, London, W1W 6UW, UK
| | - Joanne E Martin
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - David L Becker
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Agueda Rostagno
- Department of Pathology & Department of Psychiatry, New York University School of Medicine, New York, NY, 10016, USA
| | - Jorge Ghiso
- Department of Pathology & Department of Psychiatry, New York University School of Medicine, New York, NY, 10016, USA
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Goran Šimić
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Ivica Kostović
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Dinko Mitrečić
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Paul T Francis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
| | - Andre Strydom
- LonDownS Consortium, London, UK
- Division of Psychiatry, University College London, London, WC1E 6BT, UK
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - John Hardy
- LonDownS Consortium, London, UK
- Dementia Research Institute & Reta Lila Weston Institute, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, S-405 30, Sweden
- Dementia Research Institute & Reta Lila Weston Institute, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Dean Nižetić
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- The Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, E1 2AT, UK.
- LonDownS Consortium, London, UK.
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8
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Ryabchenko B, Soldatova I, Šroller V, Forstová J, Huérfano S. Immune sensing of mouse polyomavirus DNA by p204 and cGAS DNA sensors. FEBS J 2021; 288:5964-5985. [PMID: 33969628 PMCID: PMC8596513 DOI: 10.1111/febs.15962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/20/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
The mechanism by which DNA viruses interact with different DNA sensors and their connection with the activation of interferon (IFN) type I pathway are poorly understood. We investigated the roles of protein 204 (p204) and cyclic guanosine-adenosine synthetase (cGAS) sensors during infection with mouse polyomavirus (MPyV). The phosphorylation of IFN regulatory factor 3 (IRF3) and the stimulator of IFN genes (STING) proteins and the upregulation of IFN beta (IFN-β) and MX Dynamin Like GTPase 1 (MX-1) genes were detected at the time of replication of MPyV genomes in the nucleus. STING knockout abolished the IFN response. Infection with a mutant virus that exhibits defective nuclear entry via nucleopores and that accumulates in the cytoplasm confirmed that replication of viral genomes in the nucleus is required for IFN induction. The importance of both DNA sensors, p204 and cGAS, in MPyV-induced IFN response was demonstrated by downregulation of the IFN pathway observed in p204-knockdown and cGAS-knockout cells. Confocal microscopy revealed the colocalization of p204 with MPyV genomes in the nucleus. cGAS was found in the cytoplasm, colocalizing with viral DNA leaked from the nucleus and with DNA within micronucleus-like bodies, but also with the MPyV genomes in the nucleus. However, 2'3'-Cyclic guanosine monophosphate-adenosine monophosphate synthesized by cGAS was detected exclusively in the cytoplasm. Biochemical assays revealed no evidence of functional interaction between cGAS and p204 in the nucleus. Our results provide evidence for the complex interactions of MPyV and DNA sensors including the sensing of viral genomes in the nucleus by p204 and of leaked viral DNA and micronucleus-like bodies in the cytoplasm by cGAS.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Irina Soldatova
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Vojtech Šroller
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Jitka Forstová
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Sandra Huérfano
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
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9
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Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021; 17:e9653. [PMID: 34232558 PMCID: PMC8262488 DOI: 10.15252/msb.20209653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
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Affiliation(s)
- Liangqi Xie
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - Zhe Liu
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
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10
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Suv4-20h2 protects against influenza virus infection by suppression of chromatin loop formation. iScience 2021; 24:102660. [PMID: 34169237 PMCID: PMC8209278 DOI: 10.1016/j.isci.2021.102660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/20/2021] [Accepted: 05/26/2021] [Indexed: 01/03/2023] Open
Abstract
The spatial organization of chromatin is known to be highly dynamic in response to environmental stress. However, it remains unknown how chromatin dynamics contributes to or modulates disease pathogenesis. Here, we show that upon influenza virus infection, the H4K20me3 methyltransferase Suv4-20h2 binds the viral protein NP, which results in the inactivation of Suv4-20h2 and the dissociation of cohesin from Suv4-20h2. Inactivation of Suv4-20h2 by viral infection or genetic deletion allows the formation of an active chromatin loop at the HoxC8-HoxC6 loci coincident with cohesin loading. HoxC8 and HoxC6 proteins in turn enhance viral replication by inhibiting the Wnt-β-catenin mediated interferon response. Importantly, loss of Suv4-20h2 augments the pathology of influenza infection in vivo. Thus, Suv4-20h2 acts as a safeguard against influenza virus infection by suppressing cohesin-mediated loop formation. H4K20me3 methyltransferase Suv4-20h2 suppresses influenza viral replication Influenza virus NP protein binds to Suv4-20h2 and causes dissociation from cohesin Suv4-20h2 inactivation generates cohesion-mediated loop formation at HoxC8 -HoxC6 HoxC8-HoxC6 enhance viral replication by suppressing Wnt/β-catenin signaling
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11
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Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics 2020; 21:511. [PMID: 33167851 PMCID: PMC7654587 DOI: 10.1186/s12859-020-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations. RESULTS A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells. CONCLUSIONS Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.
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Affiliation(s)
- Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Tongye Shen
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
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12
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Mauch-Mücke K, Schön K, Paulus C, Nevels MM. Evidence for Tethering of Human Cytomegalovirus Genomes to Host Chromosomes. Front Cell Infect Microbiol 2020; 10:577428. [PMID: 33117732 PMCID: PMC7561393 DOI: 10.3389/fcimb.2020.577428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/17/2020] [Indexed: 11/27/2022] Open
Abstract
Tethering of viral genomes to host chromosomes has been recognized in a variety of DNA and RNA viruses. It can occur during both the productive cycle and latent infection and may impact viral genomes in manifold ways including their protection, localization, transcription, replication, integration, and segregation. Tethering is typically accomplished by dedicated viral proteins that simultaneously associate with both the viral genome and cellular chromatin via nucleic acid, histone and/or non-histone protein interactions. Some of the most prominent tethering proteins have been identified in DNA viruses establishing sustained latent infections, including members of the papillomaviruses and herpesviruses. Herpesvirus particles have linear genomes that circularize in infected cell nuclei and usually persist as extrachromosomal episomes. In several γ-herpesviruses, tethering facilitates the nuclear retention and faithful segregation of viral episomes during cell division, thus contributing to persistence of these viruses in the absence of infectious particle production. However, it has not been studied whether the genomes of human Cytomegalovirus (hCMV), the prototypical β-herpesvirus, are tethered to host chromosomes. Here we provide evidence by fluorescence in situ hybridization that hCMV genomes associate with the surface of human mitotic chromosomes following infection of both non-permissive myeloid and permissive fibroblast cells. This chromosome association occurs at lower frequency in the absence of the immediate-early 1 (IE1) proteins, which bind to histones and have been implicated in the maintenance of hCMV episomes. Our findings point to a mechanism of hCMV genome maintenance through mitosis and suggest a supporting but non-essential role of IE1 in this process.
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Affiliation(s)
- Katrin Mauch-Mücke
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Kathrin Schön
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Christina Paulus
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Michael M Nevels
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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13
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Preparing Map of Chromosome Territory Distribution Frequency. Methods Mol Biol 2020. [PMID: 32820406 DOI: 10.1007/978-1-0716-0664-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The chromosomes in mammalian interphase nuclei are organized into domains called chromosome territories that play a major role in nuclear organization. Here we propose a methodology that combines the use of micro-patterning of adhesive molecules to impose single-cell geometry, with visualization of chromosome territories. This allows obtaining a representative statistical map of the absolute positions of chromosome territories relative to the geometry imposed to the cell population by combining the signal from each cell.
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14
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Zhao B, Chaturvedi P, Zimmerman DL, Belmont AS. Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. ACS Synth Biol 2020; 9:1100-1116. [PMID: 32216371 DOI: 10.1021/acssynbio.9b00457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Achieving stable expression of a single transgene in mammalian cells remains challenging; even more challenging is obtaining simultaneous stable expression of multiple transgenes at reproducible, relative expression levels. Previously, we attained copy-number-dependent, chromosome-position-independent expression of reporter minigenes by embedding them within a BAC "scaffold" containing the mouse Msh3-Dhfr locus (DHFR BAC). Here, we extend this "BAC TG-EMBED" approach. First, we report a toolkit of endogenous promoters capable of driving transgene expression over a 0.01- to 5-fold expression range relative to the CMV promoter, allowing fine-tuning of relative expression levels of multiple reporter genes. Second, we demonstrate little variation in expression level and long-term expression stability of a reporter gene embedded in BACs containing either transcriptionally active or inactive genomic regions, making the choice of BAC scaffolds more flexible. Third, we present a novel BAC assembly scheme, "BAC-MAGIC", for inserting multiple transgenes into BAC scaffolds, which is much more time-efficient than traditional galK-based methods. As a proof-of-principle for our improved BAC TG-EMBED toolkit, we simultaneously fluorescently labeled three nuclear compartments at reproducible, relative intensity levels in 94% of stable clones after a single transfection using a DHFR BAC scaffold containing 4 transgenes assembled with BAC-MAGIC. Our extended BAC TG-EMBED toolkit and BAC-MAGIC method provide an efficient, versatile platform for stable simultaneous expression of multiple transgenes at reproducible, relative levels.
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Affiliation(s)
- Binhui Zhao
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Pankaj Chaturvedi
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - David L. Zimmerman
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew S. Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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15
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Huo X, Ji L, Zhang Y, Lv P, Cao X, Wang Q, Yan Z, Dong S, Du D, Zhang F, Wei G, Liu Y, Wen B. The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation. Mol Cell 2019; 77:368-383.e7. [PMID: 31677973 DOI: 10.1016/j.molcel.2019.10.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/24/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022]
Abstract
Interphase chromatin is hierarchically organized into higher-order architectures that are essential for gene functions, yet the biomolecules that regulate these 3D architectures remain poorly understood. Here, we show that scaffold attachment factor B (SAFB), a nuclear matrix (NM)-associated protein with RNA-binding functions, modulates chromatin condensation and stabilizes heterochromatin foci in mouse cells. SAFB interacts via its R/G-rich region with heterochromatin-associated repeat transcripts such as major satellite RNAs, which promote the phase separation driven by SAFB. Depletion of SAFB leads to changes in 3D genome organization, including an increase in interchromosomal interactions adjacent to pericentromeric heterochromatin and a decrease in genomic compartmentalization, which could result from the decondensation of pericentromeric heterochromatin. Collectively, we reveal the integrated roles of NM-associated proteins and repeat RNAs in the 3D organization of heterochromatin, which may shed light on the molecular mechanisms of nuclear architecture organization.
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Affiliation(s)
- Xiangru Huo
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Luzhang Ji
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yuwen Zhang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pin Lv
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xuan Cao
- CAS Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qianfeng Wang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zixiang Yan
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Duo Du
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Liu
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bo Wen
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.
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16
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Multicolor Laser Scanning Confocal Immunofluorescence Microscopy of DNA Damage Response Biomarkers. Methods Mol Biol 2019. [PMID: 31473966 DOI: 10.1007/978-1-4939-9646-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
DNA damage through endogenous and environmental toxicants is a constant threat to both a human's ability to pass on intact genetic information to its offspring as well as in somatic cells for its own survival. To counter these threats posed by DNA damage, cells have evolved a series of highly choreographed mechanisms-collectively defined as the DNA-damage response (DDR)-to sense DNA lesions, signal their presence, and mediate their repair. Thus, regular DDR signaling cascades are vital to prevent the initiation and progression of many human diseases including cancer. Consequently, quantitative assessment of DNA damage and response became an important biomarker for assessment of human health and disease risk in biomonitoring studies. However, most quantitative DNA damage biomarker techniques require dissolution of the nuclear architecture and hence loss of spatial information. Laser scanning confocal immunofluorescence microscopy (LSCIM) of three-dimensionally preserved nuclei can be, quantitative and maintain the spatial information. Here we describe the experimental protocols to quantify individual key events of the DDR cascade in three-dimensionally preserved nuclei by LSCIM with high resolution, using the simultaneous detection of Rad50 as well as phosphorylated H2AX and ATM and in somatic and germ cells as an example.
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17
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Dynamics of the spatial orientation of the pericentromeric heterochromatin regions in the polytene chromosomes of ovarian nurse cells in the Drosophila melanogaster (Diptera: Drosophilidae) oogenesis. THE NUCLEUS 2019. [DOI: 10.1007/s13237-019-00275-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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18
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Gelali E, Girelli G, Matsumoto M, Wernersson E, Custodio J, Mota A, Schweitzer M, Ferenc K, Li X, Mirzazadeh R, Agostini F, Schell JP, Lanner F, Crosetto N, Bienko M. iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nat Commun 2019; 10:1636. [PMID: 30967549 PMCID: PMC6456570 DOI: 10.1038/s41467-019-09616-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/19/2019] [Indexed: 11/23/2022] Open
Abstract
DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.
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Affiliation(s)
- Eleni Gelali
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Gabriele Girelli
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Masahiro Matsumoto
- R&D division, Medical Business Group, Sony Imaging Products & Solutions, Inc., Tokyo, 108-0075, Japan
| | - Erik Wernersson
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Joaquin Custodio
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Ana Mota
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Maud Schweitzer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Katalin Ferenc
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Xinge Li
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - John P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, SE-14186, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, SE-14186, Stockholm, Sweden
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden.
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden.
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19
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Bejarano DA, Peng K, Laketa V, Börner K, Jost KL, Lucic B, Glass B, Lusic M, Müller B, Kräusslich HG. HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the nuclear pore complex. eLife 2019; 8:41800. [PMID: 30672737 PMCID: PMC6400501 DOI: 10.7554/elife.41800] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
Nuclear entry of HIV-1 replication complexes through intact nuclear pore complexes is critical for successful infection. The host protein cleavage-and-polyadenylation-specificity-factor-6 (CPSF6) has been implicated in different stages of early HIV-1 replication. Applying quantitative microscopy of HIV-1 reverse-transcription and pre-integration-complexes (RTC/PIC), we show that CPSF6 is strongly recruited to nuclear replication complexes but absent from cytoplasmic RTC/PIC in primary human macrophages. Depletion of CPSF6 or lack of CPSF6 binding led to accumulation of HIV-1 subviral complexes at the nuclear envelope of macrophages and reduced infectivity. Two-color stimulated-emission-depletion microscopy indicated that under these circumstances HIV-1 complexes are retained inside the nuclear pore and undergo CA-multimer dependent CPSF6 clustering adjacent to the nuclear basket. We propose that nuclear entry of HIV-1 subviral complexes in macrophages is mediated by consecutive binding of Nup153 and CPSF6 to the hexameric CA lattice. Viruses are miniscule parasites that hijack the resources of a cell to make more of themselves. For many, this involves getting inside the nucleus, the fortress that protects the cell’s genetic information. To do so, viruses need to first find a way through a double-layered membrane called the nuclear envelope, which only opens up when a cell divides. Yet, the human immunodeficiency virus type 1 (HIV-1) can infect cells that no longer divide, and in which the nucleus’ walls never come down. The virus cores then head for the nuclear pores, heavily guarded holes in the nuclear envelope that allow the cell's own molecules to go in and out of the nucleus. But HIV-1 is too big to fit through, as its genetic information is encased in a capsid, a coat made of a complex assembly of proteins. However, research shows that these capsid proteins can bind to host proteins at the pore or even inside the nucleus. For example, the capsid protein can recognize the pore protein Nup153, or the nuclear protein CPSF6. These interactions could help the virus make its way in, but how these events unfold is still unclear. To explore this, Bejarano, Peng et al. attached fluorescent labels to HIV-1 and watched as it infected non-dividing cells. Rather than completely get rid of their capsid before they crossed the pores, the virus particles hung on to a large part of their lattice. This remaining coat then attached to CPSF6; when this protein was missing or could not bind to capsid proteins, the viral complexes got stuck in the nuclear pores. This suggests that the capsid lattice could first interact with Nup153 inside the pores: then, CPSF6 would take over, knocking Nup153 away and pulling HIV-1 into the nucleus. Armed with this knowledge, virologists and drug developers could try to block HIV-1 from entering the cell’s nucleus; they could also start to dissect how drugs that target the HIV-1 capsid work. Ultimately, HIV-1 may serve as a model to unravel how large objects can pass the nuclear pore, which may help us understand how molecules are constantly trafficked in and out of the nucleus.
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Affiliation(s)
| | - Ke Peng
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - K Laurence Jost
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Bojana Lucic
- German Center for Infection Research, Heidelberg, Germany.,Department of Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany
| | - Bärbel Glass
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- German Center for Infection Research, Heidelberg, Germany.,Department of Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases Virology, University of Heidelberg, Heidelberg, Germany
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20
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Stachecka J, Nowacka-Woszuk J, Kolodziejski PA, Szczerbal I. The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis. Chromosome Res 2019; 27:271-284. [PMID: 30656515 PMCID: PMC6733831 DOI: 10.1007/s10577-019-09604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 01/27/2023]
Abstract
Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene’s nuclear positioning for its activity during in vitro adipogenesis in the pig. We used an established system of differentiation of mesenchymal stem cells derived from bone marrow and adipose tissue into adipocytes. The differentiation process was carried out for 7 days, and the cells were examined using the 3D DNA/immuno-FISH and RNA/DNA-FISH approaches. PPARG transcript level was measured using real-time PCR, and PPARγ activity was detected with colorimetric assay. Changes in the nuclear location of the PPARG gene were observed when we compared undifferentiated mesenchymal stem cells with mature adipocytes. The gene moved from the nuclear periphery to the nuclear center as its transcriptional activity increased. The RNA/DNA-FISH approach shows that differences in primary transcript production correlated with the allele’s nuclear positioning. Transcriptionally active alleles preferentially occupy the central part of the nucleus, while inactive alleles are found on the nuclear periphery. We also show that transcription of PPARG begins with one allele, but that both alleles are active in later stages of differentiation. Our results provide evidence that functionally distinct alleles of the PPARG gene are positioned in different parts of the cell nucleus. This confirms the importance of nuclear architecture to the regulation of PPARG gene transcription, and thus to the fate of the adipose cell.
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Affiliation(s)
- Joanna Stachecka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Pawel A Kolodziejski
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637, Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
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21
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Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J Cell Biol 2018; 217:4025-4048. [PMID: 30154186 PMCID: PMC6219710 DOI: 10.1083/jcb.201807108] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023] Open
Abstract
Chen et al. present TSA-Seq, a new mapping method that measures cytological distances relative to spatially distinct nuclear subcompartments. From novel nuclear organization maps of human cells, they identify transcription hot zones of high gene density that are near nuclear speckles and enriched in highly expressed genes, housekeeping genes, and genes with low transcriptional pausing. While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a “cytological ruler” for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription “hot zones.” Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.
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Affiliation(s)
- Yu Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Yang Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Eva K Brinkman
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Robert Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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22
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Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 2018; 361:eaar2555. [PMID: 29930090 PMCID: PMC6961784 DOI: 10.1126/science.aar2555] [Citation(s) in RCA: 618] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/12/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity sequence domains (LCDs), but how these LCDs drive transactivation remains unclear. We used live-cell single-molecule imaging to reveal that TF LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF LCD hubs stabilize DNA binding, recruit RNA polymerase II (RNA Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the RNA Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for drugs targeting gene regulatory interactions implicated in disease.
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Affiliation(s)
- Shasha Chong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sambashiva Banala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
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23
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Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc Natl Acad Sci U S A 2018; 115:E2183-E2192. [PMID: 29463736 PMCID: PMC5877937 DOI: 10.1073/pnas.1714530115] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications.
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Affiliation(s)
- Brian J Beliveau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115;
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Jocelyn Y Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115;
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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24
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Evdokimova VN, Gandhi M, Nikitski AV, Bakkenist CJ, Nikiforov YE. Nuclear myosin/actin-motored contact between homologous chromosomes is initiated by ATM kinase and homology-directed repair proteins at double-strand DNA breaks to suppress chromosome rearrangements. Oncotarget 2018; 9:13612-13622. [PMID: 29568381 PMCID: PMC5862602 DOI: 10.18632/oncotarget.24434] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/30/2018] [Indexed: 01/10/2023] Open
Abstract
We provide evidence for a mechanism of DNA repair that requires nuclear myosin/actin-dependent contact between homologous chromosomes to prevent formation of chromosomal rearrangement in human cells. We recently showed that DNA double strand breaks (DSBs) induced by γ-rays or endonucleases cause ATM-dependent contact formation between homologous chromosomes at damaged sites of transcriptionally active chromatin in G0/G1-phase cells. Here, we report that the mechanism of contact generation between homologous chromosomes also requires homology-directed repair proteins, including BRCA1, RAD51 and RAD52, and nuclear myosin/actin-motors. Moreover, inhibition of ATM kinase or deficiency in nuclear actin polymerization causes carcinogenic RET/PTC chromosome rearrangements after DSBs induction in human cells. These data suggest that DSBs in transcriptionally active euchromatin in G0/G1-phase cells are repaired through a mechanism that requires contact formation between homologous chromosomes and that this mechanism is mediated by HDR proteins and nuclear myosin/actin motors.
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Affiliation(s)
| | - Manoj Gandhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | | | - Christopher J Bakkenist
- Department of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
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25
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Abstract
DNA fluorescence in situ hybridization (DNA FISH) has emerged as a powerful microscopy technique that allows a unique view into the composition and arrangement of the genetic material in its natural context-be it the cell nucleus in interphase, or chromosomes in metaphase spreads. The core principle of DNA FISH is the ability of fluorescently labeled DNA probes (either double- or single-stranded DNA fragments) to bind to their complementary sequences in situ in cells or tissues, revealing the location of their target as fluorescence signals detectable with a fluorescence microscope. Numerous variants and improvements of the original DNA FISH method as well as a vast repertoire of applications have been described since its inception more than 4 decades ago. In recent years, the development of many new fluorescent dyes together with drastic advancements in methods for probe generation (Boyle et al., Chromosome Res 19:901-909, 2011; Beliveau et al., Proc Natl Acad Sci U S A 109:21301-21306, 2012; Bienko et al., Nat Methods 10:122-124, 2012), as well as improvements in the resolution of microscopy technologies, have boosted the number of DNA FISH applications, particularly in the field of genome architecture (Markaki et al., Bioessays 34:412-426, 2012; Beliveau et al., Nat Commun 6:7147, 2015). However, despite these remarkable steps forward, choosing which type of DNA FISH sample preparation protocol, probe design, hybridization procedure, and detection method is best suited for a given application remains still challenging for many research labs, preventing a more widespread use of this powerful technology. Here, we present a comprehensive platform to help researchers choose which DNA FISH protocol is most suitable for their particular application. In addition, we describe computational pipelines that can be implemented for efficient DNA FISH probe design and for signal quantification. Our goal is to make DNA FISH a versatile and streamlined technique that can be easily implemented by both research and diagnostic labs.
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26
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Botchkarev VA. The Molecular Revolution in Cutaneous Biology: Chromosomal Territories, Higher-Order Chromatin Remodeling, and the Control of Gene Expression in Keratinocytes. J Invest Dermatol 2017; 137:e93-e99. [PMID: 28411854 DOI: 10.1016/j.jid.2016.04.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 03/05/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
Three-dimensional organization of transcription in the nucleus and mechanisms controlling the global chromatin folding, including spatial interactions between the genes, noncoding genome elements, and epigenetic and transcription machinery, are essential for establishing lineage-specific gene expression programs during cell differentiation. Spatial chromatin interactions in the nucleus involving gene promoters and distal regulatory elements are currently considered major forces that drive cell differentiation and genome evolution in general, and such interactions are substantially reorganized during many pathological conditions. During terminal differentiation of the epidermal keratinocytes, the nucleus undergoes programmed transformation from highly active status, associated with execution of the genetic program of epidermal barrier formation, to a fully inactive condition and finally becomes a part of the keratinized cells of the cornified epidermal layer. This transition is accompanied by marked remodeling of the three-dimensional nuclear organization and microanatomy, including changes in the spatial arrangement of lineage-specific genes, nuclear bodies, and heterochromatin. This mini-review highlights the important landmarks in the accumulation of our current knowledge on three-dimensional organization of the nucleus, spatial arrangement of the genes, and their distal regulatory elements, and it provides an update on the mechanisms that control higher-order chromatin remodeling in the context of epidermal keratinocyte differentiation in the skin.
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Affiliation(s)
- Vladimir A Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK; Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA.
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27
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Urbanek MO, Michalak M, Krzyzosiak WJ. 2D and 3D FISH of expanded repeat RNAs in human lymphoblasts. Methods 2017; 120:49-57. [PMID: 28404480 DOI: 10.1016/j.ymeth.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022] Open
Abstract
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible. RNA imaging techniques have been utilized for investigating the role of mutant RNAs in a number of human disorders caused by simple microsatellite expansions. These diseases include myotonic dystrophy type 1 and 2, amyotrophic lateral sclerosis/frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and Huntington's disease. Mutant RNAs with expanded repeats tend to aggregate predominantly within cell nuclei, forming structures called RNA foci. In this study, we demonstrate methods for fluorescent visualization of RNAs in both fixed and living cells using the example of RNAs containing various expanded repeat tracts (CUG, CCUG, GGGGCC, CGG, and CAG) from experiment design to image analysis. We describe in detail 2D and 3D fluorescence in situ hybridization (FISH) protocols for imaging expanded repeats RNAs, and we review briefly live imaging techniques used to characterize RNA foci formed by mutant RNAs. These methods could be used to image the entire cellular pathway of RNAs, from transcription to degradation.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Michal Michalak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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28
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van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. Small chromosomal regions position themselves autonomously according to their chromatin class. Genome Res 2017; 27:922-933. [PMID: 28341771 PMCID: PMC5453326 DOI: 10.1101/gr.213751.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/22/2017] [Indexed: 11/24/2022]
Abstract
The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
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Affiliation(s)
- Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute & Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.,Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josien C Haan
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Dominika Bijos
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - An Weuts
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Koen Theunis
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Sjoerd J B Holwerda
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Parveen Kumar
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Boris Joffe
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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29
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Abstract
Dissecting the complex network of epigenetic modifications requires tools that combine precise recognition of DNA sequences with the capability to modify epigenetic marks. The CRISPR/Cas system has been proven to be a valuable addition to existing methodologies that fulfill these tasks. So far, sequence-specific editing of epigenetic modifications such as DNA methylation and histone posttranslational modifications relied on direct fusions of enzymatically inactivated Cas9 (dCas9) with epigenetic effectors. Here, we report a novel, modular system that facilitates the recruitment of any GFP-tagged protein to desired genomic loci. By fusing dCas9 to a GFP-binding nanobody (GBP) we demonstrate that prevalent epigenetic modifications at mouse major satellite repeats can be erased or set de novo by recruiting GFP-coupled catalytic domains of TET1 and DNMT3A, respectively. Furthermore, we construct an inducible expression system that enables a temporally controlled expression of both GBP-dCas9 and the effector protein. Thus, our approach further expands the CRISPR/Cas toolbox for site-specific manipulation of epigenetic modifications with a modular and easy-to-use system.
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Affiliation(s)
- Tobias Anton
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
| | - Sebastian Bultmann
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
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30
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Abstract
Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architecture. Although DNA FISH is commonly used for confirming 3C-based findings, the two techniques are conceptually and technically different and comparing their results is not trivial. Here, we discuss both 3C-based techniques and DNA FISH approaches to highlight their similarities and differences. We then describe the technical biases that affect each approach, and review the available reports that address their compatibility. Finally, we propose an experimental scheme for comparison of 3C and DNA FISH results.
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Affiliation(s)
- Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.
| | - Edith Heard
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex 05, France. .,Collège de France, Paris, 75005, France.
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31
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Abstract
Chromatin structure and function are determined by a plethora of proteins whose genome-wide distribution is typically assessed by immunoprecipitation (ChIP). Here, we developed a novel tool to investigate the local chromatin environment at specific DNA sequences. We combined the programmable DNA binding of dCas9 with the promiscuous biotin ligase BirA* (CasID) to biotinylate proteins in the direct vicinity of specific loci. Subsequent streptavidin-mediated precipitation and mass spectrometry identified both known and previously unknown chromatin factors associated with repetitive telomeric, major satellite and minor satellite DNA. With super-resolution microscopy, we confirmed the localization of the putative transcription factor ZNF512 at chromocenters. The versatility of CasID facilitates the systematic elucidation of functional protein complexes and locus-specific chromatin composition.
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Affiliation(s)
- Elisabeth Schmidtmann
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
| | - Tobias Anton
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
| | - Pascaline Rombaut
- b Gene Center and Department of Biochemistry , LMU Munich , Munich , Germany
| | - Franz Herzog
- b Gene Center and Department of Biochemistry , LMU Munich , Munich , Germany
| | - Heinrich Leonhardt
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
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32
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Kulashreshtha M, Mehta IS, Kumar P, Rao BJ. Chromosome territory relocation during DNA repair requires nuclear myosin 1 recruitment to chromatin mediated by ϒ-H2AX signaling. Nucleic Acids Res 2016; 44:8272-91. [PMID: 27365048 PMCID: PMC5041470 DOI: 10.1093/nar/gkw573] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/03/2016] [Indexed: 11/22/2022] Open
Abstract
During DNA damage response (DDR), certain gene rich chromosome territories (CTs) relocate to newer positions within interphase nuclei and revert to their native locations following repair. Such dynamic relocation of CTs has been observed under various cellular conditions, however, the underlying mechanistic basis of the same has remained largely elusive. In this study, we aim to understand the temporal and molecular details of such crosstalk between DDR signaling and CT relocation dynamics. We demonstrate that signaling at DNA double strand breaks (DSBs) by the phosphorylated histone variant (ϒ-H2AX) is a pre-requisite for damage induced CT relocation, as cells deficient in ϒ-H2AX signaling fail to exhibit such a response. Inhibition of Rad51 or DNA Ligase IV mediated late steps of double strand break repair does not seem to abrogate CT relocation completely. Upon DNA damage, an increase in the levels of chromatin bound motor protein nuclear myosin 1 (NM1) ensues, which appears to be functionally linked to ϒ-H2AX signaling. Importantly, the motor function of NM1 is essential for its recruitment to chromatin and CT relocation following damage. Taking these observations together, we propose that early DDR sensing and signaling result in NM1 recruitment to chromosomes which in turn guides DNA damage induced CT relocation.
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Affiliation(s)
- Mugdha Kulashreshtha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Ishita S Mehta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India UM-DAE Centre for Excellence in Basic Sciences, Biological Sciences, Kalina Campus, Santacruz (E), Mumbai, Maharashtra 400098, India
| | - Pradeep Kumar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India UM-DAE Centre for Excellence in Basic Sciences, Biological Sciences, Kalina Campus, Santacruz (E), Mumbai, Maharashtra 400098, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
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33
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Clements CS, Bikkul U, Ahmed MH, Foster HA, Godwin LS, Bridger JM. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence In Situ Hybridization. Methods Mol Biol 2016; 1411:387-406. [PMID: 27147055 DOI: 10.1007/978-1-4939-3530-7_24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH.
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Affiliation(s)
- Craig S Clements
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Ural Bikkul
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Mai Hassan Ahmed
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Helen A Foster
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Lauren S Godwin
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK
| | - Joanna M Bridger
- Division of Biosciences, College of Life and Health Sciences, Brunel University London, Uxbridge, London, UB8 3PH, UK.
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Fritz A, Barutcu AR, Martin-Buley L, vanWijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus. J Cell Biochem 2016; 117:9-19. [PMID: 26192137 PMCID: PMC4715719 DOI: 10.1002/jcb.25280] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.
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Affiliation(s)
- Andrew Fritz
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Lori Martin-Buley
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Sayyed K. Zaidi
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B. Lian
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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35
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Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics 2015; 16:982. [PMID: 26589460 PMCID: PMC4654810 DOI: 10.1186/s12864-015-2137-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022] Open
Abstract
Background Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. Results A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. Conclusions Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2137-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
| | | | - Emily S Wong
- The European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Nathalie Harder
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Erik Splinter
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Elzo de Wit
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Melanie A Eckersley-Maslin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Thomas Ried
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, 50 South Drive, Bldg. 50, Rm. 1408, Bethesda, MD, 20892, USA.
| | - Roland Eils
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Karl Rohr
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Alea Mills
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Paul Flicek
- The European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Anirvan M Sengupta
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ, 08854-8019, USA.
| | - David L Spector
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
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36
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Mulholland CB, Smets M, Schmidtmann E, Leidescher S, Markaki Y, Hofweber M, Qin W, Manzo M, Kremmer E, Thanisch K, Bauer C, Rombaut P, Herzog F, Leonhardt H, Bultmann S. A modular open platform for systematic functional studies under physiological conditions. Nucleic Acids Res 2015; 43:e112. [PMID: 26007658 PMCID: PMC4787826 DOI: 10.1093/nar/gkv550] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/14/2015] [Indexed: 12/15/2022] Open
Abstract
Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1, Dnmt3a, Dnmt3b, Tet1, Tet2, Tet3 and Uhrf1, we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions.
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Affiliation(s)
- Christopher B Mulholland
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Martha Smets
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Elisabeth Schmidtmann
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Susanne Leidescher
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Yolanda Markaki
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Mario Hofweber
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Weihua Qin
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Massimiliano Manzo
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Elisabeth Kremmer
- Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Institute of Molecular Immunology, Marchioninistrasse 25, 81377 Munich, Germany
| | - Katharina Thanisch
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Christina Bauer
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Pascaline Rombaut
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig Maximilians University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Heinrich Leonhardt
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
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Ollion J, Loll F, Cochennec J, Boudier T, Escudé C. Proliferation-dependent positioning of individual centromeres in the interphase nucleus of human lymphoblastoid cell lines. Mol Biol Cell 2015; 26:2550-60. [PMID: 25947134 PMCID: PMC4571307 DOI: 10.1091/mbc.e14-05-1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 04/27/2015] [Indexed: 01/01/2023] Open
Abstract
Centromeres are not randomly distributed in interphase nuclei. High-throughput imaging provides an accurate characterization of how their organization varies as a function of the proliferation state in human lymphoblastoid cells. The results suggest the existence of mechanisms that drive the nuclear positioning of centromeres. The cell nucleus is a highly organized structure and plays an important role in gene regulation. Understanding the mechanisms that sustain this organization is therefore essential for understanding genome function. Centromeric regions (CRs) of chromosomes have been known for years to adopt specific nuclear positioning patterns, but the significance of this observation is not yet completely understood. Here, using a combination of fluorescence in situ hybridization and immunochemistry on fixed human cells and high-throughput imaging, we directly and quantitatively investigated the nuclear positioning of specific human CRs. We observe differential attraction of individual CRs toward both the nuclear border and the nucleoli, the former being enhanced in nonproliferating cells and the latter being enhanced in proliferating cells. Similar positioning patterns are observed in two different lymphoblastoid cell lines. Moreover, the positioning of CRs differs from that of noncentromeric regions, and CRs display specific orientations within chromosome territories. These results suggest the existence of not-yet-characterized mechanisms that drive the nuclear positioning of CRs and therefore pave the way toward a better understanding of how CRs affect nuclear organization.
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Affiliation(s)
- Jean Ollion
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - François Loll
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Julien Cochennec
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Thomas Boudier
- Université Pierre et Marie Curie, Sorbonne Universités, 75005 Paris, France
| | - Christophe Escudé
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
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Nuclear architecture dictates HIV-1 integration site selection. Nature 2015; 521:227-31. [PMID: 25731161 DOI: 10.1038/nature14226] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/09/2015] [Indexed: 12/23/2022]
Abstract
Long-standing evidence indicates that human immunodeficiency virus type 1 (HIV-1) preferentially integrates into a subset of transcriptionally active genes of the host cell genome. However, the reason why the virus selects only certain genes among all transcriptionally active regions in a target cell remains largely unknown. Here we show that HIV-1 integration occurs in the outer shell of the nucleus in close correspondence with the nuclear pore. This region contains a series of cellular genes, which are preferentially targeted by the virus, and characterized by the presence of active transcription chromatin marks before viral infection. In contrast, the virus strongly disfavours the heterochromatic regions in the nuclear lamin-associated domains and other transcriptionally active regions located centrally in the nucleus. Functional viral integrase and the presence of the cellular Nup153 and LEDGF/p75 integration cofactors are indispensable for the peripheral integration of the virus. Once integrated at the nuclear pore, the HIV-1 DNA makes contact with various nucleoporins; this association takes part in the transcriptional regulation of the viral genome. These results indicate that nuclear topography is an essential determinant of the HIV-1 life cycle.
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Peng K, Muranyi W, Glass B, Laketa V, Yant SR, Tsai L, Cihlar T, Müller B, Kräusslich HG. Quantitative microscopy of functional HIV post-entry complexes reveals association of replication with the viral capsid. eLife 2014; 3:e04114. [PMID: 25517934 PMCID: PMC4293571 DOI: 10.7554/elife.04114] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022] Open
Abstract
The steps from HIV-1 cytoplasmic entry until integration of the reverse transcribed genome are currently enigmatic. They occur in ill-defined reverse-transcription- and pre-integration-complexes (RTC, PIC) with various host and viral proteins implicated. In this study, we report quantitative detection of functional RTC/PIC by labeling nascent DNA combined with detection of viral integrase. We show that the viral CA (capsid) protein remains associated with cytoplasmic RTC/PIC but is lost on nuclear PIC in a HeLa-derived cell line. In contrast, nuclear PIC were almost always CA-positive in primary human macrophages, indicating nuclear import of capsids or capsid-like structures. We further show that the CA-targeted inhibitor PF74 exhibits a bimodal mechanism, blocking RTC/PIC association with the host factor CPSF6 and nuclear entry at low, and abrogating reverse transcription at high concentrations. The newly developed system is ideally suited for studying retroviral post-entry events and the roles of host factors including DNA sensors and signaling molecules.
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Affiliation(s)
- Ke Peng
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Walter Muranyi
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Bärbel Glass
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | | | - Luong Tsai
- Gilead Sciences Inc., Foster City, United States
| | - Tomas Cihlar
- Gilead Sciences Inc., Foster City, United States
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
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40
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Anton T, Bultmann S, Leonhardt H, Markaki Y. Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system. Nucleus 2014; 5:163-72. [PMID: 24637835 PMCID: PMC4049922 DOI: 10.4161/nucl.28488] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Labeling and tracing of specific sequences in living cells has been a major challenge in studying the spatiotemporal dynamics of native chromatin. Here we repurposed the prokaryotic CRISPR/Cas adaptive immunity system to specifically detect endogenous genomic loci in mouse embryonic stem cells. We constructed a catalytically inactive version of the Cas9 endonuclease, fused it with eGFP (dCas9-eGFP) and co-expressed small guide RNAs (gRNAs) to target pericentric, centric, and telomeric repeats, which are enriched in distinct nuclear structures. With major satellite specific gRNAs we obtained a characteristic chromocenter (CC) pattern, while gRNAs targeting minor satellites and telomeres highlighted smaller foci coinciding with centromere protein B (CENP-B) and telomeric repeat-binding factor 2 (TRF2), respectively. DNA sequence specific labeling by gRNA/dCas9-eGFP complexes was directly shown with 3D-fluorescent in situ hybridization (3D-FISH). Structured illumination microscopy (3D-SIM) of gRNA/dCas9-eGFP expressing cells revealed chromatin ultrastructures and demonstrated the potential of this approach for chromatin conformation studies by super resolution microscopy. This programmable dCas9 labeling system opens new perspectives to study functional nuclear architecture.
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Affiliation(s)
- Tobias Anton
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
| | - Yolanda Markaki
- Department of Biology II; Center for Integrated Protein Science Munich (CIPSM); Ludwig Maximilians University Munich; Planegg-Martinsried, Germany
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41
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Carri NG, Bermúdez SN, Fiore L, Napoli JD, Scicolone G. Anaglyph of Retinal Stem Cells And Developing Axons: Selective Volume Enhancement In Microscopy Images. Anat Rec (Hoboken) 2014; 297:770-80. [DOI: 10.1002/ar.22889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/07/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Néstor Gabriel Carri
- Laboratorio de Biología Molecular del Desarrollo, lnstituto Multidisciplinario de Biología Celular; IMBICE La Plata Argentina
| | - Sebastián Noo Bermúdez
- Laboratorio de Biología Molecular del Desarrollo, lnstituto Multidisciplinario de Biología Celular; IMBICE La Plata Argentina
| | - Luciano Fiore
- Laboratorio de Neurobiologia del Desarrollo Instituto de Biología Celular y Neurosciencia “Prof. Eduardo De Robertis” (UBA-CONICET); Facultad de Medicina, Universidad de Buenos Aires; Ciudad Buenos Aires Argentina
| | - Jennifer Di Napoli
- Laboratorio de Neurobiologia del Desarrollo Instituto de Biología Celular y Neurosciencia “Prof. Eduardo De Robertis” (UBA-CONICET); Facultad de Medicina, Universidad de Buenos Aires; Ciudad Buenos Aires Argentina
| | - Gabriel Scicolone
- Laboratorio de Neurobiologia del Desarrollo Instituto de Biología Celular y Neurosciencia “Prof. Eduardo De Robertis” (UBA-CONICET); Facultad de Medicina, Universidad de Buenos Aires; Ciudad Buenos Aires Argentina
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Liu MH, Cheung E. Estrogen receptor-mediated long-range chromatin interactions and transcription in breast cancer. Mol Cell Endocrinol 2014; 382:624-632. [PMID: 24071518 DOI: 10.1016/j.mce.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
Estrogen induces the binding of ERα to thousands of locations in the breast cancer genome, preferring intergenic and distal regions rather than near the promoters of estrogen-regulated genes. With recent technological innovations in mapping and characterization of global chromatin organization, evidence now indicates ERα mediates long-range chromatin interactions to control gene transcription. The principles that govern how ERα communicates with their putative target genes via chromosomal interactions are also beginning to unravel. Herein, we summarize our current knowledge on the functional significance of chromatin looping in estrogen-mediated transcription. ERα collaborative factors and other players that contribute to define the genomic interactions in breast cancer cells will also be discussed. Defects in chromatin organization are emerging key players in diseases such as cancer, thus understanding how ERα-mediated chromatin looping affects genome organization will clarify the receptor's role in estrogen responsive pathways sensitive to defects in chromatin organization.
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Affiliation(s)
- Mei Hui Liu
- Food Science and Technology Programme, Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
| | - Edwin Cheung
- Cancer Biology and Pharmacology, Genome Institute of Singapore, A∗STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore.
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43
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Lusic M, Marini B, Ali H, Lucic B, Luzzati R, Giacca M. Proximity to PML nuclear bodies regulates HIV-1 latency in CD4+ T cells. Cell Host Microbe 2013; 13:665-77. [PMID: 23768491 DOI: 10.1016/j.chom.2013.05.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/05/2013] [Accepted: 04/26/2013] [Indexed: 12/21/2022]
Abstract
Nuclear bodies (NBs), characterized by the presence of the promyelocytic leukemia (PML) protein, are important components of the nuclear architecture, contributing to genetic and epigenetic control of gene expression. In investigating the mechanisms mediating HIV-1 latency, we determined that silenced but transcriptionally competent HIV-1 proviruses reside in close proximity to PML NBs and that this association inhibits HIV-1 gene expression. PML binds to the latent HIV-1 promoter, which coincides with transcriptionally inactive facultative heterochromatic marks, notably H3K9me2, at the viral genome. PML degradation and NB disruption result in strong activation of viral transcription as well as release of G9a, the major methyltransferase responsible for H3K9me2, and loss of facultative heterochromatin marks from the proviral DNA. Additionally, HIV-1 transcriptional activation requires proviral displacement from PML NBs by active nuclear actin polymerization. Thus, nuclear topology and active gene movement mediate HIV-1 transcriptional regulation and have implications for controlling HIV-1 latency and eradication.
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Affiliation(s)
- Marina Lusic
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology ICGEB, 34149 Trieste, Italy.
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44
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Thanisch K, Schneider K, Morbitzer R, Solovei I, Lahaye T, Bultmann S, Leonhardt H. Targeting and tracing of specific DNA sequences with dTALEs in living cells. Nucleic Acids Res 2013; 42:e38. [PMID: 24371265 PMCID: PMC3973286 DOI: 10.1093/nar/gkt1348] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.
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Affiliation(s)
- Katharina Thanisch
- Department of Biology II, Humanbiology and Bioimaging, Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany and Department of Biology I, Genetics, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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45
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Laubenthal J, Gdula MR, Dhawan A, Anderson D. Multicolor laser scanning confocal immunofluorescence microscopy of DNA damage response biomarkers. Methods Mol Biol 2013; 1044:311-23. [PMID: 23896884 DOI: 10.1007/978-1-62703-529-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA damage through endogenous and environmental toxicants is a constant threat to both a human's ability to pass on intact genetic information to its offspring as well as somatic cells for their own survival. To counter these threats posed by DNA damage, cells have evolved a series of highly choreographed mechanisms--collectively defined as the DNA damage response (DDR)--to sense DNA lesions, signal their presence, and mediate their repair. Thus, regular DDR signalling cascades are vital to prevent the initiation and progression of many human diseases including cancer. Consequently, quantitative assessment of DNA damage and response became an important biomarker for assessment of human health and disease risk in biomonitoring studies. However, most quantitative DNA damage biomarker techniques require dissolution of the nuclear architecture and hence loss of spatial information. Laser scanning confocal immunofluorescence microscopy (LSCIM) of three-dimensionally preserved nuclei can be quantitative and maintain the spatial information. Here we describe the experimental protocols to quantify individual key events of the DDR cascade in three-dimensionally preserved nuclei by LSCIM with high resolution, using the simultaneous detection of Rad50 as well as phosphorylated H2AX and ATM and in somatic and germ cells as an example.
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Affiliation(s)
- Julian Laubenthal
- Medical Sciences Division, School of Life Sciences, University of Bradford, Bradford, UK
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46
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Kosulin K, Hoffmann F, Clauditz TS, Wilczak W, Dobner T. Presence of adenovirus species C in infiltrating lymphocytes of human sarcoma. PLoS One 2013; 8:e63646. [PMID: 23671688 PMCID: PMC3646006 DOI: 10.1371/journal.pone.0063646] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
Human adenoviruses are known to persist in T-lymphocytes of tonsils, adenoids and intestinal tract. The oncogenic potential of different adenovirus types has been widely studied in rodents, in which adenovirus inoculation can induce multiple tumors such as undifferentiated sarcomas, adenocarcinomas and neuroectodermal tumors. However, the oncogenic potential of this virus has never been proven in human subjects. Using a highly sensitive broad-spectrum qRT-PCR, we have screened a set of different human sarcomas including leiomyosarcoma, liposarcoma and gastro intestinal stroma tumors. Primers binding the viral oncogene E1A and the capsid-coding gene Hexon were used to detect the presence of adenovirus DNA in tumor samples. We found that 18% of the tested leiomyosarcomas and 35% of the liposarcomas were positive for the presence of adenovirus DNA, being species C types the most frequently detected adenoviruses. However, only in one sample of the gastro intestinal stroma tumors the virus DNA could be detected. The occurrence of adenovirus in the tumor sections was confirmed by subsequent fluorescence in-situ-hybridization analysis and co-staining with the transcription factor Bcl11b gives evidence for the presence of the virus in infiltrating T-lymphocytes within the tumors. Together these data underline, for the first time, the persistence of adenovirus in T-lymphocytes infiltrated in muscular and fatty tissue tumor samples. If an impaired immune system leads to the viral persistence and reactivation of the virus is involved in additional diseases needs further investigation.
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Affiliation(s)
- Karin Kosulin
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Molecular Virology, Hamburg, Germany
| | - Franziska Hoffmann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Molecular Virology, Hamburg, Germany
| | | | - Waldemar Wilczak
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Dobner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Molecular Virology, Hamburg, Germany
- * E-mail:
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47
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Chaumeil J, Micsinai M, Skok JA. Combined immunofluorescence and DNA FISH on 3D-preserved interphase nuclei to study changes in 3D nuclear organization. J Vis Exp 2013:e50087. [PMID: 23407477 DOI: 10.3791/50087] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fluorescent in situ hybridization using DNA probes on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA FISH) represents the most direct way to visualize the location of gene loci, chromosomal sub-regions or entire territories in individual cells. This type of analysis provides insight into the global architecture of the nucleus as well as the behavior of specific genomic loci and regions within the nuclear space. Immunofluorescence, on the other hand, permits the detection of nuclear proteins (modified histones, histone variants and modifiers, transcription machinery and factors, nuclear sub-compartments, etc). The major challenge in combining immunofluorescence and 3D DNA FISH is, on the one hand to preserve the epitope detected by the antibody as well as the 3D architecture of the nucleus, and on the other hand, to allow the penetration of the DNA probe to detect gene loci or chromosome territories (1-5). Here we provide a protocol that combines visualization of chromatin modifications with genomic loci in 3D preserved nuclei.
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Affiliation(s)
- Julie Chaumeil
- Department of Pathology, New York University School of Medicine, NY, USA
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48
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A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods 2012; 10:122-124. [PMID: 23263692 DOI: 10.1038/nmeth.2306] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/14/2012] [Indexed: 11/08/2022]
Abstract
We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.
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49
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Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays 2012; 34:412-26. [PMID: 22508100 DOI: 10.1002/bies.201100176] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.
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Affiliation(s)
- Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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50
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Gandhi M, Evdokimova VN, T.Cuenco K, Nikiforova MN, Kelly LM, Stringer JR, Bakkenist CJ, Nikiforov YE. Homologous chromosomes make contact at the sites of double-strand breaks in genes in somatic G0/G1-phase human cells. Proc Natl Acad Sci U S A 2012; 109:9454-9. [PMID: 22645362 PMCID: PMC3386068 DOI: 10.1073/pnas.1205759109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Double-strand DNA breaks (DSBs) are continuously induced in cells by endogenously generated free radicals and exogenous genotoxic agents such as ionizing radiation. DSBs activate the kinase activity in sensor proteins such as ATM and DNA-PK, initiating a complex DNA damage response that coordinates various DNA repair pathways to restore genomic integrity. In this study, we report the unexpected finding that homologous chromosomes contact each other at the sites of DSBs induced by either radiation or the endonuclease I-PpoI in human somatic cells. Contact involves short segments of homologous chromosomes and is centered on a DSB in active genes but does not occur at I-PpoI sites in intergenic DNA. I-PpoI-induced contact between homologous genes is abrogated by the transcriptional inhibitors actinomycin D and α-amanitin and requires the kinase activity of ATM but not DNA-PK. Our findings provide documentation of a common transcription-related and ATM kinase-dependent mechanism that induces contact between allelic regions of homologous chromosomes at sites of DSBs in human somatic cells.
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Affiliation(s)
- Manoj Gandhi
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Viktoria N. Evdokimova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Karen T.Cuenco
- Department of Oral Biology, School of Dental Medicine and
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219
| | - Marina N. Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Lindsey M. Kelly
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - James R. Stringer
- Department of Molecular Genetics, University of Cincinnati, Cincinnati, OH 45267; and
| | - Christopher J. Bakkenist
- Department of Molecular Genetics, University of Cincinnati, Cincinnati, OH 45267; and
- Departments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213
| | - Yuri E. Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
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