1
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He X, Tan Y, Feng Y, Sun Y, Ma H. Tracking pairwise genomic loci by the ParB-ParS and Noc-NBS systems in living cells. Nucleic Acids Res 2024; 52:4922-4934. [PMID: 38412314 PMCID: PMC11109969 DOI: 10.1093/nar/gkae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
The dynamics of genomic loci pairs and their interactions are essential for transcriptional regulation and genome organization. However, a robust method for tracking pairwise genomic loci in living cells is lacking. Here we developed a multicolor DNA labeling system, mParSpot (multicolor ParSpot), to track pairs of genomic loci and their interactions in living cells. The mParSpot system is derived from the ParB/ParS in the parABS system and Noc/NBS in its paralogous nucleoid occlusion system. The insertion of 16 base-pair palindromic ParSs or NBSs into the genomic locus allows the cognate binding protein ParB or Noc to spread kilobases of DNA around ParSs or NBSs for loci-specific visualization. We tracked two loci with a genomic distance of 53 kilobases and measured their spatial distance over time. Using the mParSpot system, we labeled the promoter and terminator of the MSI2 gene span 423 kb and measured their spatial distance. We also tracked the promoter and terminator dynamics of the MUC4 gene in living cells. In sum, the mParSpot is a robust and sensitive DNA labeling system for tracking genomic interactions in space and time under physiological or pathological contexts.
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Affiliation(s)
- Xiaohui He
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuxi Tan
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Feng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hanhui Ma
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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2
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Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
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Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
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3
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Vanderperre S, Merabet S. Visualization of the Association of Dimeric Protein Complexes on Specific Enhancers in the Salivary Gland Nuclei of Drosophila Larva. Cells 2024; 13:613. [PMID: 38607052 PMCID: PMC11012150 DOI: 10.3390/cells13070613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by recognizing specific target enhancers in the genome. The DNA-binding and regulatory activity of TFs depend on the presence of additional protein partners, leading to the formation of versatile and dynamic multimeric protein complexes. Visualizing these protein-protein interactions (PPIs) in the nucleus is key for decrypting the molecular cues underlying TF specificity in vivo. Over the last few years, Bimolecular Fluorescence Complementation (BiFC) has been developed in several model systems and applied in the analysis of different types of PPIs. In particular, BiFC has been applied when analyzing PPIs with hundreds of TFs in the nucleus of live Drosophila embryos. However, the visualization of PPIs at the level of specific target enhancers or genomic regions of interest awaits the advent of DNA-labelling methods that can be coupled with BiFC. Here, we present a novel experimental strategy that we have called BiFOR and that is based on the coupling of BiFC with the bacterial ANCHOR DNA-labelling system. We demonstrate that BiFOR enables the precise quantification of the enrichment of specific dimeric protein complexes on target enhancers in Drosophila salivary gland nuclei. Given its versatility and sensitivity, BiFOR could be applied more widely to other tissues during Drosophila development. Our work sets up the experimental basis for future applications of this strategy.
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Affiliation(s)
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR5242, Ecole Normale Supérieure de Lyon (ENSL), CNRS, Université de Lyon, 69007 Lyon, France;
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4
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Sexton T, Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort M, Meabum K, Taylor T, Shchuka V, Kocanova S, Oliveira G, Mitchell J, Soutoglou E, Lenstra T, Molina N, Papantonis A, Bystricky K. Competition between transcription and loop extrusion modulates promoter and enhancer dynamics. RESEARCH SQUARE 2023:rs.3.rs-3164817. [PMID: 37645793 PMCID: PMC10462181 DOI: 10.21203/rs.3.rs-3164817/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the spatiotemporal arrangement of the Sox2 gene and its enhancer, in response to a battery of perturbations. We find a close link between chromatin mobility and transcriptional status: active elements display more constrained mobility, consistent with confinement within specialized nuclear sites, and alterations in enhancer mobility distinguish poised from transcribing alleles. Strikingly, we find that whereas loop extrusion and transcription factor-mediated clustering contribute to promoter-enhancer proximity, they have antagonistic effects on chromatin dynamics. This provides an experimental framework for the underappreciated role of chromatin dynamics in genome regulation.
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Affiliation(s)
- Tom Sexton
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
| | | | - Cathie Erb
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nacho Molina
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
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5
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van Staalduinen J, van Staveren T, Grosveld F, Wendt KS. Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics. Epigenetics Chromatin 2023; 16:27. [PMID: 37349773 PMCID: PMC10288748 DOI: 10.1186/s13072-023-00503-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution techniques based on next-generation sequencing as well as optical imaging that can investigate chromatin conformations down to the single cell level have revealed that chromatin structure is highly heterogeneous at the level of the individual allele. While TAD boundaries and enhancer-promoter pairs emerge as hotspots of 3D proximity, the spatiotemporal dynamics of these different types of chromatin contacts remain largely unexplored. Investigation of chromatin contacts in live single cells is necessary to close this knowledge gap and further enhance the current models of 3D genome organization and enhancer-promoter communication. In this review, we first discuss the potential of single locus labeling to study architectural and enhancer-promoter contacts and provide an overview of the available single locus labeling techniques such as FROS, TALE, CRISPR-dCas9 and ANCHOR, and discuss the latest developments and applications of these systems.
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Affiliation(s)
- Jente van Staalduinen
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.
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6
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Lu S, Hou Y, Zhang XE, Gao Y. Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques. Front Cell Dev Biol 2023; 11:1216232. [PMID: 37342234 PMCID: PMC10277805 DOI: 10.3389/fcell.2023.1216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.
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Affiliation(s)
- Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yu Hou
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
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7
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Dahal L, Walther N, Tjian R, Darzacq X, Graham TG. Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 PMCID: PMC10212543 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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Affiliation(s)
- Liza Dahal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, U.S.A
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, U.S.A
| | - Nike Walther
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, U.S.A
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, U.S.A
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, U.S.A
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, U.S.A
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, U.S.A
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, U.S.A
| | - Thomas G.W. Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, U.S.A
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, Berkeley, U.S.A
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8
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Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort MAC, Meaburn K, Taylor T, Shchuka VM, Kocanova S, Oliveira GM, Mitchell JA, Soutoglou E, Lenstra TL, Molina N, Papantonis A, Bystricky K, Sexton T. Competition between transcription and loop extrusion modulates promoter and enhancer dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538222. [PMID: 37162887 PMCID: PMC10168261 DOI: 10.1101/2023.04.25.538222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the 4D arrangement of the Sox2 gene and its enhancer, in response to a battery of perturbations. We find that alterations in chromatin mobility, not promoter-enhancer distance, is more informative about transcriptional status. Active elements display more constrained mobility, consistent with confinement within specialized nuclear sites, and alterations in enhancer mobility distinguish poised from transcribing alleles. Strikingly, we find that whereas loop extrusion and transcription factor-mediated clustering contribute to promoter-enhancer proximity, they have antagonistic effects on chromatin dynamics. This provides an experimental framework for the underappreciated role of chromatin dynamics in genome regulation.
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Affiliation(s)
- Angeliki Platania
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Cathie Erb
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Mariano Barbieri
- Translational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Bastien Molcrette
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Erwan Grandgirard
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Marit AC de Kort
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Karen Meaburn
- Genome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK
| | - Tiegh Taylor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Virlana M Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Silvia Kocanova
- Molecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France
| | - Guilherme Monteiro Oliveira
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Evi Soutoglou
- Genome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Nacho Molina
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Argyris Papantonis
- Translational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Kerstin Bystricky
- Molecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France
- Institut Universitaire de France (IUF)
| | - Tom Sexton
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
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9
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Cosma MP, Neguembor MV. The magic of unraveling genome architecture and function. Cell Rep 2023; 42:112361. [PMID: 37059093 DOI: 10.1016/j.celrep.2023.112361] [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] [Received: 12/06/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Over the last decades, technological breakthroughs in super-resolution microscopy have allowed us to reach molecular resolution and design experiments of unprecedented complexity. Investigating how chromatin is folded in 3D, from the nucleosome level up to the entire genome, is becoming possible by "magic" (imaging genomic), i.e., the combination of imaging and genomic approaches. This offers endless opportunities to delve into the relationship between genome structure and function. Here, we review recently achieved objectives and the conceptual and technical challenges the field of genome architecture is currently undertaking. We discuss what we have learned so far and where we are heading. We elucidate how the different super-resolution microscopy approaches and, more specifically, live-cell imaging have contributed to the understanding of genome folding. Moreover, we discuss how future technical developments could address remaining open questions.
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Affiliation(s)
- Maria Pia Cosma
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu District, 510080 Guangzhou, China; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.
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10
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Pecori F, Torres-Padilla ME. Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. Dev Cell 2023; 58:435-449. [PMID: 36977375 PMCID: PMC10062924 DOI: 10.1016/j.devcel.2023.02.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/29/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Nuclear organization has emerged as a potential key regulator of genome function. During development, the deployment of transcriptional programs must be tightly coordinated with cell division and is often accompanied by major changes in the repertoire of expressed genes. These transcriptional and developmental events are paralleled by changes in the chromatin landscape. Numerous studies have revealed the dynamics of nuclear organization underlying them. In addition, advances in live-imaging-based methodologies enable the study of nuclear organization with high spatial and temporal resolution. In this Review, we summarize the current knowledge of the changes in nuclear architecture in the early embryogenesis of various model systems. Furthermore, to highlight the importance of integrating fixed-cell and live approaches, we discuss how different live-imaging techniques can be applied to examine nuclear processes and their contribution to our understanding of transcription and chromatin dynamics in early development. Finally, we provide future avenues for outstanding questions in this field.
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Affiliation(s)
- Federico Pecori
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany; Faculty of Biology, Ludwig Maximilians University, Munich, Germany.
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11
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Viushkov VS, Lomov NA, Rubtsov MA, Vassetzky YS. Visualizing the Genome: Experimental Approaches for Live-Cell Chromatin Imaging. Cells 2022; 11:cells11244086. [PMID: 36552850 PMCID: PMC9776900 DOI: 10.3390/cells11244086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming "four-dimensional": our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, "programmed" proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods.
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Affiliation(s)
- Vladimir S. Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikolai A. Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Yegor S. Vassetzky
- CNRS UMR9018, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Correspondence:
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12
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Shodhan A, Xaver M, Wheeler D, Lichten M. Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae. Genetics 2022; 222:iyac106. [PMID: 35876814 PMCID: PMC9434160 DOI: 10.1093/genetics/iyac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
The DNA double-strand breaks that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for double-strand break formation; double-strand break levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with double-strand break levels. How axis protein levels influence double-strand break formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased double-strand breaks and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in double-strand breaks did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote double-strand break formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local double-strand break levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
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Affiliation(s)
- Anura Shodhan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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13
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Tišma M, Panoukidou M, Antar H, Soh YM, Barth R, Pradhan B, Barth A, van der Torre J, Michieletto D, Gruber S, Dekker C. ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment. SCIENCE ADVANCES 2022; 8:eabn3299. [PMID: 35767606 PMCID: PMC9242446 DOI: 10.1126/sciadv.abn3299] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in vitro single-molecule fluorescence imaging, we show that ParB from Bacillus subtilis can load onto DNA distantly of parS, as loaded ParB molecules themselves are found to be able to recruit additional ParB proteins from bulk. Notably, this recruitment can occur in cis but also in trans, where, at low tensions within the DNA, newly recruited ParB can bypass roadblocks as it gets loaded to spatially proximal but genomically distant DNA regions. The data are supported by molecular dynamics simulations, which show that cooperative ParB-ParB recruitment can enhance spreading. ParS-independent recruitment explains how ParB can cover substantial genomic distance during chromosome segregation, which is vital for the bacterial cell cycle.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Maria Panoukidou
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Young-Min Soh
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Biswajit Pradhan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
- Corresponding author.
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14
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Ide S, Tamura S, Maeshima K. Chromatin behavior in living cells: Lessons from single‐nucleosome imaging and tracking. Bioessays 2022; 44:e2200043. [DOI: 10.1002/bies.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
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15
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Nollmann M, Bennabi I, Götz M, Gregor T. The Impact of Space and Time on the Functional Output of the Genome. Cold Spring Harb Perspect Biol 2022; 14:a040378. [PMID: 34230036 PMCID: PMC8733053 DOI: 10.1101/cshperspect.a040378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Over the past two decades, it has become clear that the multiscale spatial and temporal organization of the genome has important implications for nuclear function. This review centers on insights gained from recent advances in light microscopy on our understanding of transcription. We discuss spatial and temporal aspects that shape nuclear order and their consequences on regulatory components, focusing on genomic scales most relevant to function. The emerging picture is that spatiotemporal constraints increase the complexity in transcriptional regulation, highlighting new challenges, such as uncertainty about how information travels from molecular factors through the genome and space to generate a functional output.
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Affiliation(s)
- Marcelo Nollmann
- Centre de Biologie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Isma Bennabi
- Department of Stem Cell and Developmental Biology, CNRS UMR3738, Institut Pasteur, 75015 Paris, France
| | - Markus Götz
- Centre de Biologie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Thomas Gregor
- Department of Stem Cell and Developmental Biology, CNRS UMR3738, Institut Pasteur, 75015 Paris, France
- Joseph Henry Laboratory of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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16
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Delker RK, Munce RH, Hu M, Mann RS. Fluorescent labeling of genomic loci in Drosophila imaginal discs with heterologous DNA-binding proteins. CELL REPORTS METHODS 2022; 2:100175. [PMID: 35475221 PMCID: PMC9017127 DOI: 10.1016/j.crmeth.2022.100175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Using the Drosophila melanogaster Hox gene Ultrabithorax (Ubx) as an example, we demonstrate the use of three heterologous DNA-binding protein systems-LacI/LacO, ParB1/ParS1, and ParB2/ParS2-to label genomic loci in imaginal discs with the insertion of a small DNA tag. We compare each system, considering the impact of labeling in genomic regions (1) inside versus outside of a transcribed gene body and (2) with varying chromatin accessibility. We demonstrate the value of this system by interrogating the relationship between gene expression level and enhancer-promoter distance, as well as inter-allelic distance at the Ubx locus. We find that the distance between an essential intronic cis-regulatory element, anterobithorax (abx), and the promoter does not vary with expression level. In contrast, inter-allelic distance correlates with Ubx expression level.
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Affiliation(s)
- Rebecca K. Delker
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Ross H. Munce
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Michelle Hu
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neuroscience, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
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17
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Vines AJ, Cox K, Leland BA, King MC. Homology-directed repair involves multiple strand invasion cycles in fission yeast. Mol Biol Cell 2022; 33:ar30. [PMID: 35080989 PMCID: PMC9250353 DOI: 10.1091/mbc.e20-07-0433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Homology-directed repair of DNA double-strand breaks (DSBs) represents a highly faithful pathway. Non–crossover repair dominates in mitotically growing cells, likely through a preference for synthesis-dependent strand annealing (SDSA). How homology-directed repair mechanism choice is orchestrated in time and space is not well understood. Here, we develop a microscopy-based assay in living fission yeast to determine the dynamics and kinetics of an engineered, site-specific interhomologue repair event. We observe highly efficient homology search and homology-directed repair in this system. Surprisingly, the initial distance between the DSB and the donor sequence does not correlate with the duration of repair. Instead, we observe that repair often involves multiple site-specific and Rad51-dependent colocalization events between the DSB and donor sequence. Upon loss of the RecQ helicase Rqh1 (BLM in humans) we observe rapid repair possibly involving a single strand invasion event, suggesting that multiple strand invasion cycles antagonized by Rqh1 could reflect ongoing SDSA. However, failure to colocalize with the donor sequence and execute repair is also more likely in rqh1Δ cells, possibly reflecting erroneous strand invasion. This work has implications for the molecular etiology of Bloom syndrome, caused by mutations in BLM and characterized by aberrant sister chromatid crossovers and inefficient repair.
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Affiliation(s)
- Amanda J Vines
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut, USA, 06520
| | - Kenneth Cox
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut, USA, 06520
| | - Bryan A Leland
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut, USA, 06520
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut, USA, 06520
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18
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García Fernández F, Fabre E. The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks. Genes (Basel) 2022; 13:genes13020215. [PMID: 35205260 PMCID: PMC8872016 DOI: 10.3390/genes13020215] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).
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Affiliation(s)
- Fabiola García Fernández
- Institut Curie, CNRS UMR3664, Sorbonne Université, F-75005 Paris, France
- Correspondence: (F.G.F.); (E.F.)
| | - Emmanuelle Fabre
- Génomes Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Université de Paris, F-75010 Paris, France
- Correspondence: (F.G.F.); (E.F.)
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19
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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20
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Oliveira GM, Oravecz A, Kobi D, Maroquenne M, Bystricky K, Sexton T, Molina N. Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes. Nat Commun 2021; 12:6184. [PMID: 34702821 PMCID: PMC8548522 DOI: 10.1038/s41467-021-26466-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022] Open
Abstract
The spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes, it is essential to go beyond static viewpoints of chromosome structures, to accurately characterize chromatin's diffusion properties. We present GP-FBM: a computational framework based on Gaussian processes and fractional Brownian motion to extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM uses higher-order temporal correlations present in the data, therefore, outperforming existing methods. Furthermore, GP-FBM allows to interpolate incomplete trajectories and account for substrate movement when two or more particles are present. Using our method, we show that average chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. We observe surprising heterogeneity in local chromatin dynamics, correlating with potential regulatory activity. We also present GP-Tool, a user-friendly graphical interface to facilitate usage of GP-FBM by the research community.
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Affiliation(s)
- Guilherme M Oliveira
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France.
| | - Attila Oravecz
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | - Dominique Kobi
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | - Manon Maroquenne
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | - Kerstin Bystricky
- Molecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) UPS, CNRS, Toulouse, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France.
| | - Nacho Molina
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) CNRS UMR7104, INSERM U1258, University of Strasbourg, Illkirch, France.
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21
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Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Dev Cell 2021; 56:2649-2663.e6. [PMID: 34529940 PMCID: PMC8629127 DOI: 10.1016/j.devcel.2021.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023]
Abstract
The nuclear lamina is typically associated with transcriptional silencing, and peripheral relocation of genes highly correlates with repression. However, the DNA sequences and proteins regulating gene-lamina interactions are largely unknown. Exploiting the developmentally timed hunchback gene movement to the lamina in Drosophila neuroblasts, we identified a 250 bp intronic element (IE) both necessary and sufficient for relocation. The IE can target a reporter transgene to the lamina and silence it. Endogenously, however, hunchback is already repressed prior to relocation. Instead, IE-mediated relocation confers a heritably silenced gene state refractory to activation in descendent neurons, which terminates neuroblast competence to specify early-born identity. Surprisingly, we found that the Polycomb group chromatin factors bind the IE and are required for lamina relocation, revealing a nuclear architectural role distinct from their well-known function in transcriptional repression. Together, our results uncover in vivo mechanisms underlying neuroblast competence and lamina association in heritable gene silencing. In Drosophila neuroblasts, relocation of the hunchback gene locus to the nuclear lamina confers heritable silencing in daughter neurons. Lucas et al. identify a genomic element necessary and sufficient for hunchback gene movement in vivo. Polycomb proteins target this element for lamina relocation, thereby regulating competence, but not hunchback expression.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Terry L Hafer
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Harrison G Zhang
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Natalia Molotkova
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
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22
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Yang B, Borgeaud AC, Buřičová M, Aeschbach L, Rodríguez-Lima O, Ruiz Buendía GA, Cinesi C, Taylor AS, Baubec T, Dion V. Expanded CAG/CTG repeats resist gene silencing mediated by targeted Epigenome editing. Hum Mol Genet 2021; 31:386-398. [PMID: 34494094 PMCID: PMC8825355 DOI: 10.1093/hmg/ddab255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/08/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Expanded CAG/CTG repeat disorders affect over 1 in 2500 individuals worldwide. Potential therapeutic avenues include gene silencing and modulation of repeat instability. However, there are major mechanistic gaps in our understanding of these processes, which prevent the rational design of an efficient treatment. To address this, we developed a novel system, ParB/ANCHOR-mediated Inducible Targeting (PInT), in which any protein can be recruited at will to a GFP reporter containing an expanded CAG/CTG repeat. Previous studies have implicated the histone deacetylase HDAC5 and the DNA methyltransferase DNMT1 as modulators of repeat instability via mechanisms that are not fully understood. Using PInT, we found no evidence that HDAC5 or DNMT1 modulate repeat instability upon targeting to the expanded repeat, suggesting that their effect is independent of local chromatin structure. Unexpectedly, we found that expanded CAG/CTG repeats reduce the effectiveness of gene silencing mediated by targeting HDAC5 and DNMT1. The repeat-length effect in gene silencing by HDAC5 was abolished by a small molecule inhibitor of HDAC3. Our results have important implications on the design of epigenome editing approaches for expanded CAG/CTG repeat disorders. PInT is a versatile synthetic system to study the effect of any sequence of interest on epigenome editing.
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Affiliation(s)
- Bin Yang
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Alicia C Borgeaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.,UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Marcela Buřičová
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Lorène Aeschbach
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Oscar Rodríguez-Lima
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Gustavo A Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Cinzia Cinesi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Alysha S Taylor
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
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23
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Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, Stasevich TJ, Kimura H. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Genes Cells 2021; 26:905-926. [PMID: 34465007 PMCID: PMC8893316 DOI: 10.1111/gtc.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022]
Abstract
In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG- and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously see the dynamics of the two loci in single living cells. This shows a close association between the two loci in the majority of cells, but the loci markedly separate from the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof of principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.
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Affiliation(s)
- Yang Liu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, SOKENDAI, Mishima, Japan
| | - Yotaro Yamamoto
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yoshifusa Sadamura
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
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24
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Sato Y, Nakao M, Kimura H. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics. Microscopy (Oxf) 2021; 70:415-422. [PMID: 34329472 PMCID: PMC8491620 DOI: 10.1093/jmicro/dfab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized by both small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind weakly to specific modifications, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformational changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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25
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Quentin-Froignant C, Kappler-Gratias S, Top S, Bertagnoli S, Gallardo F. ANCHOR-tagged equine herpesvirus 1: A new tool for monitoring viral infection and discovering new antiviral compounds. J Virol Methods 2021; 294:114194. [PMID: 34022301 DOI: 10.1016/j.jviromet.2021.114194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022]
Abstract
Equine herpesvirus 1 (EHV-1) is a causative agent of respiratory disorders, abortion and myeloencephalopathy in horses and has an important impact on equine health and economy. Several bacterial artificial chromosomes have already been developed and enabled identification and functional characterization of EHV-1 genes. Unfortunately, little is known about its replication. Here, the ANCHOR system was inserted by targeted homologous recombination into the equine herpesvirus genome. This insertion led to the conversion of EHV-1 DNA to auto-fluorescent spots easily detectable by fluorescence microscopy, and enabled production of an auto-fluorescent EHV-1 ANCHORGFP with tropism and replication kinetic like the parental strain. High resolution imaging allowed first visualization of EHV-1 replication from apparition of first viral genome to large replicative centers, in single cells or inside syncytia. Combined with high content microscopy, EHV-1 ANCHORGFP leads to identification of auranofin and azacytidine-5 as new potential antivirals to treat EHV-1 infection.
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Affiliation(s)
- Charlotte Quentin-Froignant
- NeoVirTech SAS, Centre Pierre Potier, Toulouse, France; IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France.
| | | | - Sokunthea Top
- NeoVirTech SAS, Centre Pierre Potier, Toulouse, France.
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26
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Müller TG, Zila V, Peters K, Schifferdecker S, Stanic M, Lucic B, Laketa V, Lusic M, Müller B, Kräusslich HG. HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells. eLife 2021; 10:64776. [PMID: 33904396 PMCID: PMC8169111 DOI: 10.7554/elife.64776] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization, and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Nuclear cDNA initially co-localized with a fluorescent integrase fusion (IN-FP) and the viral CA (capsid) protein, but cDNA-punctae separated from IN-FP/CA over time. This phenotype was conserved in primary HIV-1 target cells, with nuclear HIV-1 complexes exhibiting strong CA-signals in all cell types. CLEM revealed cone-shaped HIV-1 capsid-like structures and apparently broken capsid-remnants at the position of IN-FP signals and elongated chromatin-like structures in the position of viral cDNA punctae lacking IN-FP. Our data argue for nuclear uncoating by physical disruption rather than cooperative disassembly of the CA-lattice, followed by physical separation from the pre-integration complex.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kyra Peters
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Schifferdecker
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mia Stanic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bojana Lucic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
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27
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Mackenroth B, Alani E. Collaborations between chromatin and nuclear architecture to optimize DNA repair fidelity. DNA Repair (Amst) 2021; 97:103018. [PMID: 33285474 PMCID: PMC8486310 DOI: 10.1016/j.dnarep.2020.103018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023]
Abstract
Homologous recombination (HR), considered the highest fidelity DNA double-strand break (DSB) repair pathway that a cell possesses, is capable of repairing multiple DSBs without altering genetic information. However, in "last resort" scenarios, HR can be directed to low fidelity subpathways which often use non-allelic donor templates. Such repair mechanisms are often highly mutagenic and can also yield chromosomal rearrangements and/or deletions. While the choice between HR and its less precise counterpart, non-homologous end joining (NHEJ), has received much attention, less is known about how cells manage and prioritize HR subpathways. In this review, we describe work focused on how chromatin and nuclear architecture orchestrate subpathway choice and repair template usage to maintain genome integrity without sacrificing cell survival. Understanding the relationships between nuclear architecture and recombination mechanics will be critical to understand these cellular repair decisions.
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Affiliation(s)
- Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States.
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28
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Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S, Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F. ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta. FRONTIERS IN PLANT SCIENCE 2021; 12:677849. [PMID: 34295343 PMCID: PMC8290188 DOI: 10.3389/fpls.2021.677849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/09/2021] [Indexed: 05/05/2023]
Abstract
Together with local chromatin structure, gene accessibility, and the presence of transcription factors, gene positioning is implicated in gene expression regulation. Although the basic mechanisms are expected to be conserved in eukaryotes, less is known about the role of gene positioning in plant cells, mainly due to the lack of a highly resolutive approach. In this study, we adapted the use of the ANCHOR system to perform real-time single locus detection in planta. ANCHOR is a DNA-labeling tool derived from the chromosome partitioning system found in many bacterial species. We demonstrated its suitability to monitor a single locus in planta and used this approach to track chromatin mobility during cell differentiation in Arabidopsis thaliana root epidermal cells. Finally, we discussed the potential of this approach to investigate the role of gene positioning during transcription and DNA repair in plants.
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Affiliation(s)
- Anis Meschichi
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Claire Picart
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Marie Mirouze
- Université de Montpellier, DIADE, Montpellier, France
- Institut de Recherche pour le Développement, DIADE, Montpellier, France
| | - Sophie Desset
- iGReD, CNRS UMR 6293, Université Clermont Auvergne, INSERM U1103, Clermont–Ferrand, France
| | | | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Nathalie Picault
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
- *Correspondence: Frédéric Pontvianne
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29
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Brouwer I, Patel HP, Meeussen JVW, Pomp W, Lenstra TL. Single-Molecule Fluorescence Imaging in Living Saccharomyces cerevisiae Cells. STAR Protoc 2020; 1:100142. [PMID: 33377036 PMCID: PMC7757289 DOI: 10.1016/j.xpro.2020.100142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This protocol describes how to image fluorescently tagged proteins, RNA, or DNA inside living Saccharomyces cerevisiae cells at the single-molecule level. Imaging inside living cells, as opposed to fixed materials, gives access to real-time kinetic information. Although various single-molecule imaging applications are discussed, we focus on imaging of gene transcription at the single-RNA level. To obtain the best possible results, it is important that both imaging parameters and yeast culture conditions are optimized. Here, both aspects are described. For complete details on the use and execution of this protocol, please refer to Lenstra et al. (2015) and Donovan et al. (2019).
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Affiliation(s)
- Ineke Brouwer
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Heta Piyush Patel
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | | | - Wim Pomp
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tineke Laura Lenstra
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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30
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Gallardo F, Schmitt D, Brandely R, Brua C, Silvestre N, Findeli A, Foloppe J, Top S, Kappler-Gratias S, Quentin-Froignant C, Morin R, Lagarde JM, Bystricky K, Bertagnoli S, Erbs P. Fluorescent Tagged Vaccinia Virus Genome Allows Rapid and Efficient Measurement of Oncolytic Potential and Discovery of Oncolytic Modulators. Biomedicines 2020; 8:biomedicines8120543. [PMID: 33256205 PMCID: PMC7760631 DOI: 10.3390/biomedicines8120543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
As a live biologic agent, oncolytic vaccinia virus has the ability to target and selectively amplify at tumor sites. We have previously reported that deletion of thymidine kinase and ribonucleotide reductase genes in vaccinia virus can increase the safety and efficacy of the virus. Here, to allow direct visualization of the viral genome in living cells, we incorporated the ANCH target sequence and the OR3-Santaka gene in the double-deleted vaccinia virus. Infection of human tumor cells with ANCHOR3-tagged vaccinia virus enables visualization and quantification of viral genome dynamics in living cells. The results show that the ANCHOR technology permits the measurement of the oncolytic potential of the double deleted vaccinia virus. Quantitative analysis of infection kinetics and of viral DNA replication allow rapid and efficient identification of inhibitors and activators of oncolytic activity. Our results highlight the potential application of the ANCHOR technology to track vaccinia virus and virtually any kind of poxvirus in living cells.
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Affiliation(s)
- Franck Gallardo
- NeoVirTech SAS, 31106 Toulouse, France; (S.T.); (S.K.-G.); (C.Q.-F.)
- Correspondence: (F.G.); (P.E.)
| | - Doris Schmitt
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Renée Brandely
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Catherine Brua
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Nathalie Silvestre
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Annie Findeli
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Johann Foloppe
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
| | - Sokunthea Top
- NeoVirTech SAS, 31106 Toulouse, France; (S.T.); (S.K.-G.); (C.Q.-F.)
| | | | | | - Renaud Morin
- Imactiv-3D SAS, 31106 Toulouse, France; (R.M.); (J.-M.L.)
| | | | - Kerstin Bystricky
- Centre de Biologie Intégrative (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), University of Toulouse, UPS, CNRS, 31400 Toulouse, France;
- Institut Universitaire de France (IUF), 75231 Paris, France
| | | | - Philippe Erbs
- Transgene SA, 67405 Illkirch-Graffenstaden, France; (D.S.); (R.B.); (C.B.); (N.S.); (A.F.); (J.F.)
- Correspondence: (F.G.); (P.E.)
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31
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Shaban HA, Barth R, Bystricky K. Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription. Genome Biol 2020; 21:278. [PMID: 33203432 PMCID: PMC7670612 DOI: 10.1186/s13059-020-02185-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
The eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber at appropriate sites in a timely manner. We describe how recent advances in quantitative imaging techniques overcome caveats of sequencing-based methods (Hi-C and related) by enabling direct visualization of transcription factors and chromatin at high resolution, from single genes to the whole nucleus. We discuss the contribution of fluorescence imaging to deciphering the principles underlying this coordination within the crowded nuclear space in living cells and discuss challenges ahead.
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Affiliation(s)
- Haitham A Shaban
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, Cairo, 12622, Egypt.
- Current Address: Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
- Institut Universitaire de France (IUF), Paris, France.
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32
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Cheblal A, Challa K, Seeber A, Shimada K, Yoshida H, Ferreira HC, Amitai A, Gasser SM. DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement. Mol Cell 2020; 80:311-326.e4. [PMID: 32970994 DOI: 10.1016/j.molcel.2020.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/02/2023]
Abstract
To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR. The loss of nucleosome remodeler INO80-C did the opposite. To see whether enhanced HDR depends on DSB mobility or the global chromatin response, we tested the ubiquitin ligase mutant uls1Δ, which selectively impairs local but not global movement in response to a DSB. Strand invasion occurs in uls1Δ cells with wild-type kinetics, arguing that global histone depletion rather than DSB movement is rate limiting for HDR. Impaired break movement in uls1Δ correlates with elevated MRX and cohesin loading, despite normal resection and checkpoint activation.
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Affiliation(s)
- Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Present address: Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA 02138, USA
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Haruka Yoshida
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland.
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33
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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34
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Khosravi S, Schindele P, Gladilin E, Dunemann F, Rutten T, Puchta H, Houben A. Application of Aptamers Improves CRISPR-Based Live Imaging of Plant Telomeres. FRONTIERS IN PLANT SCIENCE 2020; 11:1254. [PMID: 32973827 PMCID: PMC7468473 DOI: 10.3389/fpls.2020.01254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/30/2020] [Indexed: 06/01/2023]
Abstract
Development of live imaging techniques for providing information how chromatin is organized in living cells is pivotal to decipher the regulation of biological processes. Here, we demonstrate the improvement of a live imaging technique based on CRISPR/Cas9. In this approach, the sgRNA scaffold is fused to RNA aptamers including MS2 and PP7. When the dead Cas9 (dCas9) is co-expressed with chimeric sgRNA, the fluorescent coat protein-tagged for MS2 and PP7 aptamers (tdMCP-FP and tdPCP-FP) are recruited to the targeted sequence. Compared to previous work with dCas9:GFP, we show that the quality of telomere labeling was improved in transiently transformed Nicotiana benthamiana using aptamer-based CRISPR-imaging constructs. Labeling is influenced by the copy number of aptamers and less by the promoter types. The same constructs were not applicable for labeling of repeats in stably transformed plants and roots. The constant interaction of the RNP complex with its target DNA might interfere with cellular processes.
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Affiliation(s)
- Solmaz Khosravi
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Evgeny Gladilin
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Frank Dunemann
- Institute for Breeding Research on Horticultural Crops, Julius Kühn-Institut (JKI), Quedlinburg, Germany
| | - Twan Rutten
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andreas Houben
- Department for Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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35
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Shaban HA, Seeber A. Monitoring global chromatin dynamics in response to DNA damage. Mutat Res 2020; 821:111707. [PMID: 32505939 DOI: 10.1016/j.mrfmmm.2020.111707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023]
Abstract
DNA damage induced global chromatin motion has been observed in yeast and mammalian cells. Currently, it is unclear what mechanisms may be driving these changes in whole genome dynamics. Recent advances in live-cell microscopy now enable chromatin motion to be quantified throughout the whole nucleus. In addition, much work has improved quantification of single particle trajectories. This topic is particularly important to the field of DNA repair as there are a large number of unanswered questions that can be tackled by monitoring global chromatin movement. Foremost, is how local DNA repair mechanisms interact and change global chromatin structure and whether this impacts repair pathway choice or efficiency. In this review, we describe methodologies to monitor global chromatin movement putting them into context with the DNA repair field highlighting how these techniques can drive new discoveries.
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Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA; Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
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36
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Lawrimore CJ, Lawrimore J, He Y, Chavez S, Bloom K. Polymer perspective of genome mobilization. Mutat Res 2020; 821:111706. [PMID: 32516654 DOI: 10.1016/j.mrfmmm.2020.111706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Chromosome motion is an intrinsic feature of all DNA-based metabolic processes and is a particularly well-documented response to both DNA damage and repair. By using both biological and polymer physics approaches, many of the contributing factors of chromatin motility have been elucidated. These include the intrinsic properties of chromatin, such as stiffness, as well as the loop modulators condensin and cohesin. Various biological factors such as external tethering to nuclear domains, ATP-dependent processes, and nucleofilaments further impact chromatin motion. DNA damaging agents that induce double-stranded breaks also cause increased chromatin motion that is modulated by recruitment of repair and checkpoint proteins. Approaches that integrate biological experimentation in conjunction with models from polymer physics provide mechanistic insights into the role of chromatin dynamics in biological function. In this review we discuss the polymer models and the effects of both DNA damage and repair on chromatin motion as well as mechanisms that may underlie these effects.
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Affiliation(s)
- Colleen J Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Josh Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Yunyan He
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Sergio Chavez
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Kerry Bloom
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States.
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37
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Bucher L, Kappler-Gratias S, Desbois N, Bystricky K, Gallardo F, Gros CP. A 3- and A 2B-nitrocorroles: synthesis and antiviral activity evaluation against human cytomegalovirus infection. RSC Med Chem 2020; 11:771-782. [PMID: 33479674 DOI: 10.1039/d0md00034e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Human cytomegalovirus (hCMV) is responsible for several pathologies impacting immunocompromised patients and can trigger life-threatening infection. Several antivirals are available and are used in the clinic, but hCMV resistant strains have appeared and patients have encountered therapeutic failure. Hence, there is a constant need for new best in class or first in class antiviral molecules. We have previously shown that nitrocorroles could be used as a potent anti-hCMV agent without acute toxicity in mice. They therefore represent an excellent platform to perform structure-activity relationship (SAR) studies and to increase efficiency or reduce toxicity. We have generated original A2B- and A3-substituted nitrocorroles and have discovered optimized compounds with selectivity indices above 200. These compounds are easily synthesized in only one to two-step reactions; they are up-scalable and cost efficient. They are therefore excellent candidates for hCMV therapies and they pave the way for a new generation of molecules.
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Affiliation(s)
- Léo Bucher
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB) , UMR CNRS 6302 , Université Bourgogne Franche-Comté , 9 avenue Alain Savary, BP 47870 , 21078 Dijon Cedex , France .
| | | | - Nicolas Desbois
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB) , UMR CNRS 6302 , Université Bourgogne Franche-Comté , 9 avenue Alain Savary, BP 47870 , 21078 Dijon Cedex , France .
| | - Kerstin Bystricky
- Centre de Biologie Intégrative (CBI) , Laboratoire de Biologie Moléculaire Eucaryote (LBME) , University of Toulouse , UPS , CNRS , Route de Narbonne , F-31062 Toulouse , France.,Institut Universitaire de France (IUF) , France
| | - Franck Gallardo
- NeoVirTech , SAS , 1 place Pierre Potier, Oncopole , 31106 Toulouse , France .
| | - Claude P Gros
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB) , UMR CNRS 6302 , Université Bourgogne Franche-Comté , 9 avenue Alain Savary, BP 47870 , 21078 Dijon Cedex , France .
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Remodeling of the Core Leads HIV-1 Preintegration Complex into the Nucleus of Human Lymphocytes. J Virol 2020; 94:JVI.00135-20. [PMID: 32238582 PMCID: PMC7269431 DOI: 10.1128/jvi.00135-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/24/2020] [Indexed: 02/08/2023] Open
Abstract
How the reverse-transcribed genome reaches the host nucleus remains a main open question related to the infectious cycle of HIV-1. The HIV-1 core has a size of ∼100 nm, largely exceeding that of the NPC channel (∼39 nm). Thus, a rearrangement of the viral CA protein organization is required to achieve an effective nuclear translocation. The mechanism of this process remains undefined due to the lack of a technology capable of visualizing potential CA subcomplexes in association with the viral DNA in the nucleus of HIV-1-infected cells. By the means of state-of-the-art technologies (HIV-1 ANCHOR system combined with CLEM), our study shows that remodeled viral complexes retain multiple CA proteins but not an intact core or only a single CA monomer. These viral CA complexes associated with the retrotranscribed DNA can be observed inside the nucleus, and they represent a potential PIC. Thus, our study shed light on critical early steps characterizing HIV-1 infection, thereby revealing novel, therapeutically exploitable points of intervention. Furthermore, we developed and provided a powerful tool enabling direct, specific, and high-resolution visualization of intracellular and intranuclear HIV-1 subviral structures. Retroviral replication proceeds through obligate integration of the viral DNA into the host genome. In particular, for the HIV-1 genome to enter the nucleus, it must be led through the nuclear pore complex (NPC). During the HIV-1 cytoplasmic journey, the viral core acts as a shell to protect the viral genetic material from antiviral sensors and ensure an adequate environment for reverse transcription. However, the relatively narrow size of the nuclear pore channel requires that the HIV-1 core is reshaped into a structure that fits the pore. On the other hand, the organization of the viral CA proteins that remain associated with the preintegration complex (PIC) during and after nuclear translocation is still enigmatic. In this study, we analyzed the progressive organizational changes of viral CA proteins within the cytoplasm and the nucleus by immunogold labeling. Furthermore, we set up a novel technology, HIV-1 ANCHOR, which enables the specific detection of the retrotranscribed DNA by fluorescence microscopy, thereby offering the opportunity to uncover the architecture of the potential HIV-1 PIC. Thus, we combined the immunoelectron microscopy and ANCHOR technologies to reveal the presence of DNA- and CA-positive complexes by correlated light and electron microscopy (CLEM). During and after nuclear translocation, HIV-1 appears as a complex of viral DNA decorated by multiple viral CA proteins remodeled in a pearl necklace-like shape. Thus, we could describe how CA proteins are reshaped around the viral DNA to permit the entrance of the HIV-1 in the nucleus. This particular CA protein complex composed of the integrase and the retrotranscribed DNA leads the HIV-1 genome inside the host nucleus. Our findings contribute to the understanding of the early steps of HIV-1 infection and provide new insights into the organization of HIV-1 CA proteins during and after viral nuclear entry. Of note, we are now able to visualize the viral DNA in viral complexes, opening up new perspectives for future studies on virus’s fate in the cell nucleus. IMPORTANCE How the reverse-transcribed genome reaches the host nucleus remains a main open question related to the infectious cycle of HIV-1. The HIV-1 core has a size of ∼100 nm, largely exceeding that of the NPC channel (∼39 nm). Thus, a rearrangement of the viral CA protein organization is required to achieve an effective nuclear translocation. The mechanism of this process remains undefined due to the lack of a technology capable of visualizing potential CA subcomplexes in association with the viral DNA in the nucleus of HIV-1-infected cells. By the means of state-of-the-art technologies (HIV-1 ANCHOR system combined with CLEM), our study shows that remodeled viral complexes retain multiple CA proteins but not an intact core or only a single CA monomer. These viral CA complexes associated with the retrotranscribed DNA can be observed inside the nucleus, and they represent a potential PIC. Thus, our study shed light on critical early steps characterizing HIV-1 infection, thereby revealing novel, therapeutically exploitable points of intervention. Furthermore, we developed and provided a powerful tool enabling direct, specific, and high-resolution visualization of intracellular and intranuclear HIV-1 subviral structures.
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Addressing the role of centromere sites in activation of ParB proteins for partition complex assembly. PLoS One 2020; 15:e0226472. [PMID: 32379828 PMCID: PMC7205306 DOI: 10.1371/journal.pone.0226472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The ParB-parS partition complexes that bacterial replicons use to ensure their faithful inheritance also find employment in visualization of DNA loci, as less intrusive alternatives to fluorescent repressor-operator systems. The ability of ParB molecules to interact via their N-terminal domains and to bind to non-specific DNA enables expansion of the initial complex to a size both functional in partition and, via fusion to fluorescent peptides, visible by light microscopy. We have investigated whether it is possible to dispense with the need to insert parS in the genomic locus of interest, by determining whether ParB fused to proteins that bind specifically to natural DNA sequences can still assemble visible complexes. In yeast cells, coproduction of fusions of ParB to a fluorescent peptide and to a TALE protein targeting an endogenous sequence did not yield visible foci; nor did any of several variants of these components. In E.coli, coproduction of fusions of SopB (F plasmid ParB) to fluorescent peptide, and to dCas9 together with specific guide RNAs, likewise yielded no foci. The result of coproducing analogous fusions of SopB proteins with distinct binding specificities was also negative. Our observations imply that in order to assemble higher order partition complexes, ParB proteins need specific activation through binding to their cognate parS sites.
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40
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Shaban HA, Seeber A. Monitoring the spatio-temporal organization and dynamics of the genome. Nucleic Acids Res 2020; 48:3423-3434. [PMID: 32123910 PMCID: PMC7144944 DOI: 10.1093/nar/gkaa135] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/17/2020] [Accepted: 02/23/2020] [Indexed: 12/22/2022] Open
Abstract
The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixed snapshots as a result of techniques like FISH and Hi-C, little is known about chromatin dynamics in living cells. The rapid development of flexible genomic loci imaging approaches can address fundamental questions on chromatin dynamics in a range of model organisms. Moreover, it is now possible to visualize not only single genomic loci but the whole genome simultaneously. These advances have opened many doors leading to insight into several nuclear processes including transcription and DNA repair. In this review, we discuss new chromatin imaging methods and how they have been applied to study transcription.
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Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
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41
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Maeshima K, Tamura S, Hansen JC, Itoh Y. Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol 2020; 64:77-89. [PMID: 32283330 DOI: 10.1016/j.ceb.2020.02.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/16/2020] [Accepted: 02/22/2020] [Indexed: 12/23/2022]
Abstract
Eukaryotic chromatin is a negatively charged polymer consisting of genomic DNA, histones, and various nonhistone proteins. Because of its highly charged character, the structure of chromatin varies greatly depending on the surrounding environment (i.e. cations etc.): from an extended 10-nm fiber, to a folded 30-nm fiber, to chromatin condensates/liquid-droplets. Over the last ten years, newly developed technologies have drastically shifted our view on chromatin from a static regular structure to a more irregular and dynamic one, locally like a fluid. Since no single imaging (or genomics) method can tell us everything and beautiful images (or models) can fool our minds, comprehensive analyses based on many technical approaches are important to capture actual chromatin organization inside the cell. Here we critically discuss our current view on chromatin and methodology used to support the view.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
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42
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McCord RP, Kaplan N, Giorgetti L. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. Mol Cell 2020; 77:688-708. [PMID: 32001106 PMCID: PMC7134573 DOI: 10.1016/j.molcel.2019.12.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapidly developing technologies have recently fueled an exciting era of discovery in the field of chromosome structure and nuclear organization. In addition to chromosome conformation capture (3C) methods, new alternative techniques have emerged to study genome architecture and biological processes in the nucleus, often in single or living cells. This sets an unprecedented stage for exploring the mechanisms that link chromosome structure and biological function. Here we review popular as well as emerging approaches to study chromosome organization, focusing on the contribution of complementary methodologies to our understanding of structures revealed by 3C methods and their biological implications, and discuss the next technical and conceptual frontiers.
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Affiliation(s)
- Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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43
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Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, Freeman BC. Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation. Dev Cell 2020; 52:309-320.e5. [PMID: 31902656 PMCID: PMC7108666 DOI: 10.1016/j.devcel.2019.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022]
Abstract
Movement of chromosome sites within interphase cells is critical for numerous pathways including RNA transcription and genome organization. Yet, a mechanism for reorganizing chromatin in response to these events had not been reported. Here, we delineate a molecular chaperone-dependent pathway for relocating activated gene loci in yeast. Our presented data support a model in which a two-authentication system mobilizes a gene promoter through a dynamic network of polymeric nuclear actin. Transcription factor-dependent nucleation of a myosin motor propels the gene locus through the actin matrix, and fidelity of the actin association was ensured by ARP-containing chromatin remodelers. Motor activity of nuclear myosin was dependent on the Hsp90 chaperone. Hsp90 further contributed by biasing the remodeler-actin interaction toward nucleosomes with the non-canonical histone H2A.Z, thereby focusing the pathway on select sites such as transcriptionally active genes. Together, the system provides a rapid and effective means to broadly yet selectively mobilize chromatin sites.
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Affiliation(s)
- Anqi Wang
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Janhavi A Kolhe
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nate Gioacchini
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Imke Baade
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William M Brieher
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian C Freeman
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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Oshidari R, Mekhail K, Seeber A. Mobility and Repair of Damaged DNA: Random or Directed? Trends Cell Biol 2020; 30:144-156. [DOI: 10.1016/j.tcb.2019.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
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45
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Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M. Nat Protoc 2020; 15:840-876. [PMID: 31969721 DOI: 10.1038/s41596-019-0269-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
Simultaneous observation of 3D chromatin organization and transcription at the single-cell level and with high spatial resolution may hold the key to unveiling the mechanisms regulating embryonic development, cell differentiation and even disease. We recently developed Hi-M, a technology that enables the sequential labeling, 3D imaging and localization of multiple genomic DNA loci, together with RNA expression, in single cells within whole, intact Drosophila embryos. Importantly, Hi-M enables simultaneous detection of RNA expression and chromosome organization without requiring sample unmounting and primary probe rehybridization. Here, we provide a step-by-step protocol describing the design of probes, the preparation of samples, the stable immobilization of embryos in microfluidic chambers, and the complete procedure for image acquisition. The combined RNA/DNA fluorescence in situ hybridization procedure takes 4-5 d, including embryo collection. In addition, we describe image analysis software to segment nuclei, detect genomic spots, correct for drift and produce Hi-M matrices. A typical Hi-M experiment takes 1-2 d to complete all rounds of labeling and imaging and 4 additional days for image analysis. This technology can be easily expanded to investigate cell differentiation in cultured cells or organization of chromatin within complex tissues.
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Hinsberger A, Graillot B, Blachère Lopez C, Juliant S, Cerutti M, King LA, Possee RD, Gallardo F, Lopez Ferber M. Tracing Baculovirus AcMNPV Infection Using a Real-Time Method Based on ANCHOR TM DNA Labeling Technology. Viruses 2020; 12:E50. [PMID: 31906433 PMCID: PMC7019957 DOI: 10.3390/v12010050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 12/12/2022] Open
Abstract
Many steps in the baculovirus life cycle, from initial ingestion to the subsequent infection of all larval cells, remain largely unknown; primarily because it has hitherto not been possible to follow individual genomes and their lineages. Use of ANCHORTM technology allows a high intensity fluorescent labelling of DNA. When applied to a virus genome, it is possible to follow individual particles, and the overall course of infection. This technology has been adapted to enable labelling of the baculovirus Autographa californica Multiple NucleoPolyhedroVirus genome, as a first step to its application to other baculoviruses. AcMNPV was modified by inserting the two components of ANCHORTM: a specific DNA-binding protein fused to a fluorescent reporter, and the corresponding DNA recognition sequence. The resulting modified virus was stable, infectious, and replicated correctly in Spodoptera frugiperda 9 (Sf9) cells and in vivo. Both budded viruses and occlusion bodies were clearly distinguishable, and infecting cells or larvae allowed the infection process to be monitored in living cells or tissues. The level of fluorescence in the culture medium of infected cells in vitro showed a good correlation with the number of infectious budded viruses. A cassette that can be used in other baculoviruses has been designed. Altogether our results introduce for the first time the generation of autofluorescent baculovirus and their application to follow infection dynamics directly in living cells or tissues.
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Affiliation(s)
- Aurélie Hinsberger
- LGEI, IMT Mines Alès, Institut Mines-Télécom et Université de Montpellier Sud de France, 6 Avenue de Clavières, 30100 Alès, France; (A.H.); (B.G.); (C.B.L.)
| | - Benoît Graillot
- LGEI, IMT Mines Alès, Institut Mines-Télécom et Université de Montpellier Sud de France, 6 Avenue de Clavières, 30100 Alès, France; (A.H.); (B.G.); (C.B.L.)
| | - Christine Blachère Lopez
- LGEI, IMT Mines Alès, Institut Mines-Télécom et Université de Montpellier Sud de France, 6 Avenue de Clavières, 30100 Alès, France; (A.H.); (B.G.); (C.B.L.)
- INRA, SPE, 400 route des Chappes BP 167, 06903 Sophia-Antipolis CEDEX, France
| | - Sylvie Juliant
- CNRS UPS3044 Baculovirus et Thérapie, LabEx-53, 30380 Saint Christol lèz Alès, France; (S.J.); (M.C.)
| | - Martine Cerutti
- CNRS UPS3044 Baculovirus et Thérapie, LabEx-53, 30380 Saint Christol lèz Alès, France; (S.J.); (M.C.)
| | - Linda A. King
- Department of Biological & Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK;
| | - Robert D. Possee
- Oxford Expression Technologies Ltd. BioInnovation Hub, Oxford OX3 0BP, UK;
| | - Franck Gallardo
- NeoVirTech SAS, 1 Place Pierre Potier, 31000 Toulouse, France
- Institute for Advanced Life Science Technology; ITAV USR3505, 1 Place Pierre Potier, 31000 Toulouse, France
| | - Miguel Lopez Ferber
- LGEI, IMT Mines Alès, Institut Mines-Télécom et Université de Montpellier Sud de France, 6 Avenue de Clavières, 30100 Alès, France; (A.H.); (B.G.); (C.B.L.)
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47
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Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Methods Mol Biol 2020; 2166:373-384. [PMID: 32710421 PMCID: PMC8130451 DOI: 10.1007/978-1-0716-0712-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Elucidating the biological implications of higher order chromatin architectures in animal development requires simultaneous, quantitative measurements of chromatin dynamics and transcriptional activity in living specimen. Here we describe a multicolor labeling and live imaging approach in embryos of the fruit fly Drosophila melanogaster. The method allows simultaneous measurement of movements of specific loci and their transcriptional activity for developmental genes, enabling new approaches to probe the interaction between 3D chromatin architecture and regulation of gene expression in development.
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Affiliation(s)
- Hongtao Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA.
- Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, Paris, France.
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48
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Cinesi C, Yang B, Dion V. GFP Reporters to Monitor Instability and Expression of Expanded CAG/CTG Repeats. Methods Mol Biol 2020; 2056:255-268. [PMID: 31586353 DOI: 10.1007/978-1-4939-9784-8_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Expanded CAG/CTG repeats are genetically unstable and, upon expression, cause neurological and neuromuscular diseases. The molecular mechanisms of repeat instability and expression remain poorly understood despite their importance for the pathogenesis of a family of 14 devastating human diseases. This is in part because conventional assays are tedious and time-consuming. Recently, however, GFP-based reporters have been designed to provide a rapid and reliable means of assessing these parameters. Here we provide protocols for quantifying repeat instability and expression using a GFP-based chromosomal reporter and the newly developed ParB/ANCHOR-mediated Inducible Targeting (PInT) and how to validate the results.
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Affiliation(s)
- Cinzia Cinesi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Bin Yang
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Vincent Dion
- Dementia Research Institute, Cardiff University, Cardiff, UK.
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49
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Pied N, Wodrich H. Imaging the adenovirus infection cycle. FEBS Lett 2019; 593:3419-3448. [PMID: 31758703 DOI: 10.1002/1873-3468.13690] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Incoming adenoviruses seize control of cytosolic transport mechanisms to relocate their genome from the cell periphery to specialized sites in the nucleoplasm. The nucleus is the site for viral gene expression, genome replication, and the production of progeny for the next round of infection. By taking control of the cell, adenoviruses also suppress cell-autonomous immunity responses. To succeed in their production cycle, adenoviruses rely on well-coordinated steps, facilitated by interactions between viral proteins and cellular factors. Interactions between virus and host can impose remarkable morphological changes in the infected cell. Imaging adenoviruses has tremendously influenced how we delineate individual steps in the viral life cycle, because it allowed the development of specific optical markers to label these morphological changes in space and time. As technology advances, innovative imaging techniques and novel tools for specimen labeling keep uncovering previously unseen facets of adenovirus biology emphasizing why imaging adenoviruses is as attractive today as it was in the past. This review will summarize past achievements and present developments in adenovirus imaging centered on fluorescence microscopy approaches.
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Affiliation(s)
- Noémie Pied
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
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50
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Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells. Chromosome Res 2019; 28:7-17. [PMID: 31792795 DOI: 10.1007/s10577-019-09622-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 02/08/2023]
Abstract
The 3D organization of chromatin plays an important role in genome stability and many other pivotal biological programs. Therefore, the establishment of imaging methods, which enable us to study the dynamics of chromatin in living cells, is necessary. Although primary live cell imaging methods were a breakthrough, there is a need to develop more specific labeling techniques. With the discovery of programmable DNA binding proteins, such zinc finger proteins (ZFP), transcription activator-like effectors (TALE), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), a major leap forward was made. Here, we review the applications and potential of fluorescent repressor-operator systems, programmable DNA binding proteins with an emphasis on CRISPR-based chromatin imaging in living and fixed cells, and their potential application in plant science.
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