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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Shaban HA, Friman ET, Deluz C, Tollenaere A, Katanayeva N, Suter DM. Individual transcription factors modulate both the micromovement of chromatin and its long-range structure. Proc Natl Acad Sci U S A 2024; 121:e2311374121. [PMID: 38648478 PMCID: PMC11067044 DOI: 10.1073/pnas.2311374121] [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: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.
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Affiliation(s)
- Haitham A. Shaban
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
- Spectroscopy Department, Institute of Physics Research, National Research Centre, Cairo12622, Egypt
| | - Elias T. Friman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Armelle Tollenaere
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
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3
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Purshouse K, Pollard SM, Bickmore WA. Imaging extrachromosomal DNA (ecDNA) in cancer. Histochem Cell Biol 2024:10.1007/s00418-024-02280-2. [PMID: 38625562 DOI: 10.1007/s00418-024-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Extrachromosomal DNA (ecDNA) are circular regions of DNA that are found in many cancers. They are an important means of oncogene amplification, and correlate with treatment resistance and poor prognosis. Consequently, there is great interest in exploring and targeting ecDNA vulnerabilities as potential new therapeutic targets for cancer treatment. However, the biological significance of ecDNA and their associated regulatory control remains unclear. Light microscopy has been a central tool in the identification and characterisation of ecDNA. In this review we describe the different cellular models available to study ecDNA, and the imaging tools used to characterise ecDNA and their regulation. The insights gained from quantitative imaging are discussed in comparison with genome sequencing and computational approaches. We suggest that there is a crucial need for ongoing innovation using imaging if we are to achieve a full understanding of the dynamic regulation and organisation of ecDNA and their role in tumourigenesis.
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Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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4
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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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5
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Yavuz S, Kabbech H, van Staalduinen J, Linder S, van Cappellen W, Nigg A, Abraham T, Slotman J, Quevedo M, Poot R, Zwart W, van Royen M, Grosveld F, Smal I, Houtsmuller A. Compartmentalization of androgen receptors at endogenous genes in living cells. Nucleic Acids Res 2023; 51:10992-11009. [PMID: 37791849 PMCID: PMC10639085 DOI: 10.1093/nar/gkad803] [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: 04/14/2023] [Revised: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.
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Affiliation(s)
- Selçuk Yavuz
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hélène Kabbech
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex L Nigg
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan A Slotman
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marti Quevedo
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ihor Smal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
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6
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Saxton MN, Morisaki T, Krapf D, Kimura H, Stasevich TJ. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. SCIENCE ADVANCES 2023; 9:eadh4819. [PMID: 37792937 PMCID: PMC10550241 DOI: 10.1126/sciadv.adh4819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Histone acetylation and RNA polymerase II phosphorylation are associated with transcriptionally active chromatin, but their spatiotemporal relationship in live cells remains poorly understood. To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). Our analysis reveals that chromatin enriched with these two modifications is generally separate. In these separated sites, we show that the two modifications are inversely correlated with one another on the minutes time scale and that single nucleosomes within each region display distinct and opposing dynamics on the subsecond time scale. While nucleosomes diffuse ~15% faster in chromatin enriched with H3K27ac, they diffuse ~15% slower in chromatin enriched with RNAP2-Ser5ph. These results argue that high levels of H3K27ac and RNAP2-Ser5ph are not often present together at the same place and time, but rather each marks distinct transcriptionally poised or active sites, respectively.
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Affiliation(s)
- Matthew N. Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Hiroshi Kimura
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
- 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
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7
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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: 0] [Impact Index Per Article: 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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8
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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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9
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Ye H, Jiang C, Li L, Li H, Rong Z, Lin Y. Live-cell imaging of genomic loci with Cas9 variants. Biotechnol J 2022; 17:e2100381. [PMID: 36058644 DOI: 10.1002/biot.202100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/14/2022] [Accepted: 08/22/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Endonuclease-deactivated clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease (dCas9) has been repurposed for live-cell imaging of genomic loci. Engineered or evolved dCas9 variants have been developed to increase the applicability of the CRISPR/dCas9 system. However, there have been no systematic comparisons of these dCas9 variants in terms of their performance in the visualization of genomic loci. MAIN METHODS AND MAJOR RESULTS Here we demonstrate that dSpCas9 and its variants deSpCas9(1.1), dSpCas9-HF1, devoCas9, and dxCas9(3.7) can be used for CRISPR-based live-cell genomic imaging. dSpCas9 had the greatest utility, with a high labeling efficiency of repetitive sequences-including those with a low number of repeats-and good compatibility with target RNA sequences at the MUC4 locus that varied in length from 13 to 23 nucleotides. We combined CRISPR-Tag with the dSpCas9 imaging system to observe the dynamics of the Tet promoter and found that its movement was restricted when it was active. CONCLUSIONS AND IMPLICATIONS These novel Cas9 variants provide a new set of tools for investigating the spatiotemporal regulation of gene expression through live imaging of genomic sites.
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Affiliation(s)
- Huiying Ye
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Chao Jiang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Hui Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Systems Science, Beijing Normal University, Beijing, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.,Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China
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10
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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; 222:6649696. [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] [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 (DSBs) 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 DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB 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 DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB 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 DSB 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, Maryland 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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11
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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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12
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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13
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Sabaté T, Zimmer C, Bertrand E. Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells. Methods Mol Biol 2022; 2532:275-290. [PMID: 35867254 DOI: 10.1007/978-1-0716-2497-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hi-C and related sequencing-based techniques have brought a detailed understanding of the 3D genome architecture and the discovery of novel structures such as topologically associating domains (TADs) and chromatin loops, which emerge from cohesin-mediated DNA extrusion. However, these techniques require cell fixation, which precludes assessment of chromatin structure dynamics, and are generally restricted to population averages, thus masking cell-to-cell heterogeneity. By contrast, live-cell imaging allows to characterize and quantify the temporal dynamics of chromatin, potentially including TADs and loops in single cells. Specific chromatin loci can be visualized at high temporal and spatial resolution by inserting a repeat array from bacterial operator sequences bound by fluorescent tags. Using two different types of repeats allows to tag both anchors of a loop in different colors, thus enabling to track them separately even when they are in close vicinity. Here, we describe a versatile cloning method for generating many repeat array repair cassettes in parallel and inserting them by CRISPR-Cas9 into the human genome. This method should be instrumental to studying chromatin loop dynamics in single human cells.
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Affiliation(s)
- Thomas Sabaté
- Imaging and Modeling Unit, Institut Pasteur, UMR 3691 CNRS, IP CNRS, Paris, France.
- IGH, University of Montpellier, CNRS, Montpellier, France.
- Sorbonne Université, Collège Doctoral, Paris, France.
| | - Christophe Zimmer
- Imaging and Modeling Unit, Institut Pasteur, UMR 3691 CNRS, IP CNRS, Paris, France
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14
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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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15
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Li J, Pertsinidis A. New insights into promoter-enhancer communication mechanisms revealed by dynamic single-molecule imaging. Biochem Soc Trans 2021; 49:1299-1309. [PMID: 34060610 PMCID: PMC8325597 DOI: 10.1042/bst20200963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/10/2023]
Abstract
Establishing cell-type-specific gene expression programs relies on the action of distal enhancers, cis-regulatory elements that can activate target genes over large genomic distances - up to Mega-bases away. How distal enhancers physically relay regulatory information to target promoters has remained a mystery. Here, we review the latest developments and insights into promoter-enhancer communication mechanisms revealed by live-cell, real-time single-molecule imaging approaches.
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Affiliation(s)
- Jieru Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065, USA
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16
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Shim SH. Super-resolution microscopy of genome organization. Genes Genomics 2021; 43:281-287. [PMID: 33630271 DOI: 10.1007/s13258-021-01044-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 12/31/2022]
Abstract
Recent advancements in sequencing and imaging technologies are providing new perspectives in solving the mystery of three-dimensional folding of genome in a nucleus. Chromosome conformation capture sequencing has discovered new chromatin structures such as topologically associated domains and loops in hundreds of kilobases. Super-resolution fluorescence microscopy with nanometer resolutions, in particular multiplexed approaches with sequence-specificity, has visualized chromatin structures from the rough folds of whole chromosomes to the fine loops of cis-regulatory elements in intact individual nuclei. Here, recent advancements in genome visualization tools with highly multiplexed labeling and reading are introduced. These imaging technologies have found ensemble behavior consistent to sequencing results, while unveiling single-cell variations. But, they also generated contradictory results on the roles of architectural proteins (like cohesion and CTCF) and enhancer-promoter interactions. Live-cell labeling methods for imaging specific genomic loci, especially the CRISPR/dCas9 system, are reviewed in order to give perspectives in the emergence of tools for visualizing genome structural dynamics.
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Affiliation(s)
- Sang-Hee Shim
- Department of Chemistry, Korea University, Seoul, 02481, Korea.
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17
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Birnie A, Dekker C. Genome-in-a-Box: Building a Chromosome from the Bottom Up. ACS NANO 2021; 15:111-124. [PMID: 33347266 PMCID: PMC7844827 DOI: 10.1021/acsnano.0c07397] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box" (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.
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Affiliation(s)
- Anthony Birnie
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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18
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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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19
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Abstract
Proper chromosome segregation during cell division is essential in all domains of life. In the majority of bacterial species, faithful chromosome segregation is mediated by the tripartite ParABS system, consisting of an ATPase protein ParA, a CTPase and DNA-binding protein ParB, and a centromere-like parS site. The parS site is most often located near the origin of replication and is segregated first after chromosome replication. ParB nucleates on parS before binding to adjacent non-specific DNA to form a multimeric nucleoprotein complex. ParA interacts with ParB to drive the higher-order ParB–DNA complex, and hence the replicating chromosomes, to each daughter cell. Here, we review the various models for the formation of the ParABS complex and describe its role in segregating the origin-proximal region of the chromosome. Additionally, we discuss outstanding questions and challenges in understanding bacterial chromosome segregation.
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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20
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Lakadamyali M, Cosma MP. Visualizing the genome in high resolution challenges our textbook understanding. Nat Methods 2020; 17:371-379. [DOI: 10.1038/s41592-020-0758-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/22/2020] [Indexed: 12/29/2022]
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21
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Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2019; 21:207-226. [PMID: 31848476 DOI: 10.1038/s41576-019-0195-2] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.
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Affiliation(s)
- Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
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22
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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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23
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