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Illuminating the structure and dynamics of chromatin by fluorescence labeling

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Frontiers in Biology

Abstract

Background

Visualization of chromosomal loci location and dynamics is crucial for understanding many fundamental intra-nuclear processes such as DNA transcription, replication, and repair.

Objective

Here, we will describe the development of fluorescence labeling methods for chromatin imaging, including traditional as well as emerging chromatin labeling techniques in both fixed and live cells.We will also discuss current issues and provide a perspective on future developments and applications of the chromatin labeling technology.

Methods

A systematic literature search was performed using the PubMed. Studies published over the past 50 years were considered for review. More than 100 articles were cited in this review.

Results

Taking into account sensitivity, specificity, and spatiotemporal resolution, fluorescence labeling and imaging has been the most prevalent approach for chromatin visualization. Among all the fluorescent labeling tools, the adoption of genome editing tools, such as TALE and CRISPR, have great potential for the labeling and imaging of chromatin.

Conclusion

Although a number of chromatin labeling techniques are available for both fixed and live cells, much more effort is still clearly required to develop fluorescence labeling methods capable of targeting arbitrary sequences non-intrusively to allow long-term, multiplexing, and high-throughput imaging of genomic loci and chromatin structures. The emerging technological advances will outline a next-generation effort toward the comprehensive delineation of chromatin at single-cell level with single-molecule resolution.

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References

  • Abney J R, Cutler B, Fillbach M L, Axelrod D, Scalettar B A (1997). Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J Cell Biol, 137(7): 1459–1468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aizer A, Brody Y, Ler L W, Sonenberg N, Singer R H, Shav-Tal Y (2008). The dynamics of mammalian P body transport, assembly, and disassembly in vivo. Mol Biol Cell, 19(10): 4154–4166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Backlund M P, Joyner R, Weis K, Moerner W E (2014). Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope. Mol Biol Cell, 25(22): 3619–3629

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Badique F, Stamov D R, Davidson P M, Veuillet M, Reiter G, Freund J N, Franz C M, Anselme K (2013). Directing nuclear deformation on micropillared surfaces by substrate geometry and cytoskeleton organization. Biomaterials, 34(12): 2991–3001

    Article  CAS  PubMed  Google Scholar 

  • Beliveau B J, Boettiger A N, Avendaño M S, Jungmann R, McCole R B, Joyce E F, Kim-Kiselak C, Bantignies F, Fonseka C Y, Erceg J, Hannan M A, Hoang H G, Colognori D, Lee J T, Shih W M, Yin P, Zhuang X, Wu C T (2015). Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun, 6: 7147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beliveau B J, Joyce E F, Apostolopoulos N, Yilmaz F, Fonseka C Y, McCole R B, Chang Y, Li J B, Senaratne T N, Williams B R, Rouillard J M, Wu C T (2012). Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci USA, 109(52): 21301–21306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belmont A S (2001). Visualizing chromosome dynamics with GFP. Trends Cell Biol, 11(6): 250–257

    Article  CAS  PubMed  Google Scholar 

  • Bertrand E, Chartrand P, Schaefer M, Shenoy S M, Singer R H, Long R M (1998). Localization of ASH1 mRNA particles in living yeast. Mol Cell, 2(4): 437–445

    Article  CAS  PubMed  Google Scholar 

  • Bick M D, Davidson R L (1974). Total substitution of bromodeoxyuridine for thymidine in the DNA of a bromodeoxyuridine-dependent cell line. Proc Natl Acad Sci USA, 71(5): 2082–2086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A (2013). A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods, 10(2): 122–124

    Article  CAS  PubMed  Google Scholar 

  • Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science, 326(5959): 1509–1512

    Article  CAS  PubMed  Google Scholar 

  • Boettiger A N, Bintu B, Moffitt J R, Wang S, Beliveau B J, Fudenberg G, Imakaev M, Mirny L A, Wu C T, Zhuang X (2016). Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature, 529(7586): 418–422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bohn M, Diesinger P, Kaufmann R, Weiland Y, Müller P, Gunkel M, von Ketteler A, Lemmer P, Hausmann M, Heermann D W, Cremer C (2010). Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. Biophys J, 99(5): 1358–1367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Müller S, Eils R, Cremer C, Speicher M R, Cremer T (2005). Threedimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol, 3(5): e157

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chacón M R, Delivani P, Tolić I M (2016). Meiotic Nuclear Oscillations Are Necessary to Avoid Excessive Chromosome Associations. Cell Reports, 17(6): 1632–1645

    Article  PubMed  CAS  Google Scholar 

  • Chakalova L, Fraser P (2008). Brushed aside and silenced. Dev Cell, 14(4): 461–462

    Article  CAS  PubMed  Google Scholar 

  • Chen B, Gilbert L A, Cimini B A, Schnitzbauer J, Zhang W, Li G W, Park J, Blackburn E H, Weissman J S, Qi L S, Huang B (2013). Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 155(7): 1479–1491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim W A, Huang B (2016). Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res, 44(8): e75

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen B C, Legant W R, Wang K, Shao L, Milkie D E, Davidson M W, Janetopoulos C, Wu X S, Hammer J A 3rd, Liu Z, English B P, Mimori-Kiyosue Y, Romero D P, Ritter A T, Lippincott-Schwartz J, Fritz-Laylin L, Mullins R D, Mitchell D M, Bembenek J N, Reymann A C, Böhme R, Grill S W, Wang J T, Seydoux G, Tulu U S, Kiehart D P, Betzig E (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science, 346(6208): 1257998

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cheng A W, Jillette N, Lee P, Plaskon D, Fujiwara Y, Wang W, Taghbalout A, Wang H (2016). Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling. Cell Res, 26(2): 254–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chuang C H, Carpenter A E, Fuchsova B, Johnson T, de Lanerolle P, Belmont A S (2006). Long-range directional movement of an interphase chromosome site. Curr Biol, 16(8): 825–831

    Article  CAS  PubMed  Google Scholar 

  • Cremer M, Grasser F, Lanctôt C, Müller S, Neusser M, Zinner R, Solovei I, Cremer T (2008). Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol, 463: 205–239

    Article  CAS  PubMed  Google Scholar 

  • Cremer T, Cremer C (2001). Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet, 2(4): 292–301

    Article  CAS  PubMed  Google Scholar 

  • Cremer T, Kreth G, Koester H, Fink R H, Heintzmann R, Cremer M, Solovei I, Zink D, Cremer C (2000). Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr, 10(2): 179–212

    Article  CAS  PubMed  Google Scholar 

  • Daigle N, Ellenberg J (2007). LambdaN-GFP: an RNA reporter system for live-cell imaging. Nat Methods, 4(8): 633–636

    Article  CAS  PubMed  Google Scholar 

  • Dekker J, et al (2017). The 4D Nucleome Project. bio Rxiv

    Google Scholar 

  • Dekker J, Mirny L (2016). The 3D Genome as Moderator of Chromosomal Communication. Cell, 164(6): 1110–1121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng W, Lee J, Wang H, Miller J, Reik A, Gregory P D, Dean A, Blobel G A (2012). Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell, 149(6): 1233–1244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng W, Shi X, Tjian R, Lionnet T, Singer R H (2015). CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci USA, 112(38): 11870–11875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dixon J R, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu J S, Ren B (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(7398): 376–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Esvelt K M, Mali P, Braff J L, Moosburner M, Yaung S J, Church G M (2013). Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods, 10(11): 1116–1121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fabre P J, et al (2016). Visualizing the HoxD Gene Cluster at the Nanoscale Level. Cold Spring Harb Symp Quant Biol

    Google Scholar 

  • Fanucchi S, Shibayama Y, Burd S, Weinberg M S, Mhlanga M M (2013). Chromosomal contact permits transcription between coregulated genes. Cell, 155(3): 606–620

    Article  CAS  PubMed  Google Scholar 

  • Finlan L E, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb J R, Bickmore W A (2008). Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet, 4(3): e1000039

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fujita T, Fujii H (2013). Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochem Biophys Res Commun, 439(1): 132–136

    Article  CAS  PubMed  Google Scholar 

  • Gall J G, Pardue M L (1969). Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA, 63(2): 378–383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gebhardt J C, Suter D M, Roy R, Zhao Z W, Chapman A R, Basu S, Maniatis T, Xie X S (2013). Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods, 10(5): 421–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert W, Müller-Hill B (1966). Isolation of the lac repressor. Proc Natl Acad Sci USA, 56(6): 1891–1898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gratzner H G (1982). Monoclonal antibody to 5-bromo- and 5- iododeoxyuridine: A new reagent for detection of DNA replication. Science, 218(4571): 474–475

    Article  CAS  PubMed  Google Scholar 

  • Grimm J B, English B P, Chen J, Slaughter J P, Zhang Z, Revyakin A, Patel R, Macklin J J, Normanno D, Singer R H, Lionnet T, Lavis L D (2015). A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods, 12(3): 244–250, 3, 250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guan J, Liu H, Shi X, Feng S, Huang B (2017). Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH. Biophys J, 112(6): 1077–1084

    Article  CAS  PubMed  Google Scholar 

  • Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin D U, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang M Q, Ren B, Krainer A R, Maniatis T, Wu Q (2015). CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell, 162(4): 900–910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Held M, Schmitz M H, Fischer B, Walter T, Neumann B, Olma M H, Peter M, Ellenberg J, Gerlich D W (2010). CellCognition: timeresolved phenotype annotation in high-throughput live cell imaging. Nat Methods, 7(9): 747–754

    Article  CAS  PubMed  Google Scholar 

  • Hillen W, Klock G, Kaffenberger I, Wray L V, Reznikoff W S (1982). Purification of the TET repressor and TET operator from the transposon Tn10 and characterization of their interaction. J Biol Chem, 257(11): 6605–6613

    CAS  PubMed  Google Scholar 

  • Horvath P, Barrangou R (2010). CRISPR/Cas, the immune system of bacteria and archaea. Science, 327(5962): 167–170

    Article  CAS  PubMed  Google Scholar 

  • Hsu P D, Lander E S, Zhang F (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6): 1262–1278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu H, Zhang H, Wang S, Ding M, An H, Hou Y, Yang X, Wei W, Sun Y, Tang C (2017). Live visualization of genomic loci with BiFC-TALE. Sci Rep, 7: 40192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hübner M R, Spector D L (2010). Chromatin dynamics. Annu Rev Biophys, 39(1): 471–489

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert L A, Ishikawa H, Leonetti M D, Marshall W F, Weissman J S, Huang B (2016). Versatile protein tagging in cells with split fluorescent protein. Nat Commun, 7: 11046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanda T, Sullivan K F, Wahl G M (1998). Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol, 8(7): 377–385

    Article  CAS  PubMed  Google Scholar 

  • Kapuscinski J (1995). DAPI: a DNA-specific fluorescent probe. Biotech Histochem, 70(5): 220–233

    Article  CAS  PubMed  Google Scholar 

  • Kepten E, Weron A, Bronstein I, Burnecki K, Garini Y (2015). Uniform Contraction-Expansion Description of Relative Centromere and Telomere Motion. Biophys J, 109(7): 1454–1462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries S S, Janssen H, Amendola M, Nolen L D, Bickmore W A, van Steensel B (2013). Single-cell dynamics of genome-nuclear lamina interactions. Cell, 153(1): 178–192

    Article  CAS  PubMed  Google Scholar 

  • Kumaran R I, Spector D L (2008). A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol, 180(1): 51–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumaran R I, Thakar R, Spector D L (2008). Chromatin dynamics and gene positioning. Cell, 132(6): 929–934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langer-Safer P R, Levine M, Ward D C (1982). Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci USA, 79(14): 4381–4385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larson D R, Zenklusen D, Wu B, Chao J A, Singer R H (2011). Realtime observation of transcription initiation and elongation on an endogenous yeast gene. Science, 332(6028): 475–478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levi V, Ruan Q, Plutz M, Belmont A S, Gratton E (2005). Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J, 89(6): 4275–4285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levine M (2014). The contraction of time and space in remote chromosomal interactions. Cell, 158(2): 243–244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levsky J M, Singer R H (2003). Fluorescence in situ hybridization: past, present and future. J Cell Sci, 116(Pt 14): 2833–2838

    Article  CAS  PubMed  Google Scholar 

  • Li D, Shao L, Chen B C, Zhang X, Zhang M, Moses B, Milkie D E, Beach J R, Hammer J A 3rd, Pasham M, Kirchhausen T, Baird M A, Davidson M W, Xu P, Betzig E (2015). ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science, 349(6251): aab3500

    Google Scholar 

  • Li J, Zhang B B, Ren Y G, Gu S Y, Xiang Y H, Du J L (2015). Intron targeting-mediated and endogenous gene integrity-maintaining knockin in zebrafish using the CRISPR/Cas9 system. Cell Res, 25(5): 634–637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindhout B I, Fransz P, Tessadori F, Meckel T, Hooykaas P J, van der Zaal B J (2007). Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins. Nucleic Acids Res, 35(16): e107

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lottersberger F, Karssemeijer R A, Dimitrova N, de Lange T (2015). 53BP1 and the LINC complex promote microtubule-dependent DSB mobility and DNA Repair. Cell, 163(4): 880–893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lucas J S, Zhang Y, Dudko O K, Murre C (2014). 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell, 158(2): 339–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma H, Naseri A, Reyes-Gutierrez P, Wolfe S A, Zhang S, Pederson T (2015). Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci USA, 112(10): 3002–3007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma H, Reyes-Gutierrez P, Pederson T (2013). Visualization of repetitive DNA sequences in human chromosomes with transcription activatorlike effectors. Proc Natl Acad Sci USA, 110(52): 21048–21053

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma H, Tu L C, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016). Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol, 34(5): 528–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mali P, Yang L, Esvelt K M, Aach J, Guell M, DiCarlo J E, Norville J E, Church G M (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121): 823–826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marshall W F, Straight A, Marko J F, Swedlow J, Dernburg A, Belmont A, Murray A W, Agard D A, Sedat J W (1997). Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol, 7(12): 930–939

    Article  CAS  PubMed  Google Scholar 

  • Masui O, Bonnet I, Le Baccon P, Brito I, Pollex T, Murphy N, Hupé P, Barillot E, Belmont A S, Heard E (2011). Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell, 145(3): 447–458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meaburn K J, Misteli T (2007). Cell biology: chromosome territories. Nature, 445(7126): 379–781

    Article  CAS  PubMed  Google Scholar 

  • Meldi L, Brickner J H (2011). Compartmentalization of the nucleus. Trends Cell Biol, 21(12): 701–708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miyanari Y (2014). TAL effector-mediated genome visualization (TGV). Methods, 69(2): 198–204

    Article  CAS  PubMed  Google Scholar 

  • Miyanari Y, Ziegler-Birling C, Torres-Padilla M E (2013). Live visualization of chromatin dynamics with fluorescent TALEs. Nat Struct Mol Biol, 20(11): 1321–1324

    Article  CAS  PubMed  Google Scholar 

  • Nelles D A, Fang MY, O’Connell MR, Xu J L, Markmiller S J, Doudna J A, Yeo G W (2016). Programmable RNA tracking in live cells with CRISPR/Cas9. Cell, 165(2): 488–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D (2011). The dynamic architecture of Hox gene clusters. Science, 334(6053): 222–225

    Article  CAS  PubMed  Google Scholar 

  • Nora E P, Lajoie B R, Schulz E G, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum N L, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 485(7398): 381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Connell M R, Oakes B L, Sternberg S H, East-Seletsky A, Kaplan M, Doudna J A (2014). Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature, 516(7530): 263–266

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ochiai H, Sugawara T, Yamamoto T (2015). Simultaneous live imaging of the transcription and nuclear position of specific genes. Nucleic Acids Res, 43(19): e127

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pederson T (2014). Repeated TALEs: visualizing DNA sequence localization and chromosome dynamics in live cells. Nucleus, 5(1): 28–31

    Article  PubMed  PubMed Central  Google Scholar 

  • Pope B D, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera D L, Wang Y, Hansen R S, Canfield T K, Thurman R E, Cheng Y, Gülsoy G, Dennis J H, Snyder M P, Stamatoyannopoulos J A, Taylor J, Hardison R C, Kahveci T, Ren B, Gilbert D M (2014). Topologically associating domains are stable units of replication-timing regulation. Nature, 515(7527): 402–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M (2017). Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Nat Commun, 8: 14725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ran F A, Cong L, Yan W X, Scott D A, Gootenberg J S, Kriz A J, Zetsche B, Shalem O, Wu X, Makarova K S, Koonin E V, Sharp P A, Zhang F (2015). In vivo genome editing using Staphylococcus aureus Cas9. Nature, 520(7546): 186–191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reddy K L, Zullo J M, Bertolino E, Singh H (2008). Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature, 452(7184): 243–247

    Article  CAS  PubMed  Google Scholar 

  • Ren R, Deng L, Xue Y, Suzuki K, Zhang W, Yu Y, Wu J, Sun L, Gong X, Luan H, Yang F, Ju Z, Ren X, Wang S, Tang H, Geng L, Zhang W, Li J, Qiao J, Xu T, Qu J, Liu G H (2017). Visualization of agingassociated chromatin alterations with an engineered TALE system. Cell Res, 27(4): 483–504

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ricci M A, Manzo C, García-Parajo M F, Lakadamyali M, Cosma M P (2015). Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell, 160(6): 1145–1158

    Article  CAS  PubMed  Google Scholar 

  • Ried T, Schröck E, Ning Y, Wienberg J (1998). Chromosome painting: a useful art. Hum Mol Genet, 7(10): 1619–1626

    Article  CAS  PubMed  Google Scholar 

  • Robinett C C, Straight A, Li G, Willhelm C, Sudlow G, Murray A, Belmont A S (1996). In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol, 135(6 Pt 2): 1685–1700

    Article  CAS  PubMed  Google Scholar 

  • Roukos V, Voss T C, Schmidt C K, Lee S, Wangsa D, Misteli T (2013). Spatial dynamics of chromosome translocations in living cells. Science, 341(6146): 660–664

    Article  CAS  PubMed  Google Scholar 

  • Saad H, Gallardo F, Dalvai M, Tanguy-le-Gac N, Lane D, Bystricky K (2014). DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells. PLoS Genet, 10(3): e1004187

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Salic A, Mitchison T J (2008). A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc Natl Acad Sci USA, 105(7): 2415–2420

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schermelleh L, Carlton P M, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso M C, Agard D A, Gustafsson M G, Leonhardt H, Sedat J W (2008). Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science, 320(5881): 1332–1336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Segal D J, Dreier B, Beerli R R, Barbas C F 3rd (1999). Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc Natl Acad Sci USA, 96(6): 2758–2763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shachar S, Voss T C, Pegoraro G, Sciascia N, Misteli T (2015). Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping. Cell, 162(4): 911–923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shalem O, Sanjana N E, Zhang F (2015). High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet, 16(5): 299–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shao S, et al (2017). Multiplexed sgRNA Expression Allows Versatile Single Non-repetitive DNA Labeling and Endogenous Gene Regulation. bioRxiv

    Google Scholar 

  • Shao S, Zhang W, Hu H, Xue B, Qin J, Sun C, Sun Y, Wei W, Sun Y (2016). Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res, 44(9): e86

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shechner D M, Hacisuleyman E, Younger S T, Rinn J L (2015). Multiplexable, locus-specific targeting of long RNAs with CRISPRDisplay. Nat Methods, 12(7): 664–670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006). Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet, 38(11): 1348–1354

    Article  CAS  PubMed  Google Scholar 

  • Smeets D, Markaki Y, Schmid V J, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M (2014). Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin, 7(1): 8

    Article  PubMed  PubMed Central  Google Scholar 

  • Solovei I, Cremer M (2010). 3D-FISH on cultured cells combined with immunostaining. Methods Mol Biol, 659: 117–126

    Article  CAS  PubMed  Google Scholar 

  • Soutoglou E, Dorn J F, Sengupta K, Jasin M, Nussenzweig A, Ried T, Danuser G, Misteli T (2007). Positional stability of single doublestrand breaks in mammalian cells. Nat Cell Biol, 9(6): 675–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strack R L, Disney M D, Jaffrey S R (2013). A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods, 10(12): 1219–1224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tagarro I, Fernández-Peralta A M, González-Aguilera J J (1994). Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes. Hum Genet, 93(4): 383–388

    Article  CAS  PubMed  Google Scholar 

  • Takei Y, Shah S, Harvey S, Qi L S, Cai L (2017). Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH. Biophy J, 112(9): 1773–1776

    Article  CAS  Google Scholar 

  • Tanenbaum ME, Gilbert L A, Qi L S, Weissman J S, Vale R D (2014). A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell, 159(3): 635–646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang Z, Luo O J, Li X, Zheng M, Zhu J J, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian S Z, Penrad-Mobayed M, Sachs L M, Ruan X, Wei C L, Liu E T, Wilczynski G M, Plewczynski D, Li G, Ruan Y (2015). CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell, 163(7): 1611–1627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thanisch K, Schneider K, Morbitzer R, Solovei I, Lahaye T, Bultmann S, Leonhardt H (2014). Targeting and tracing of specific DNA sequences with dTALEs in living cells. Nucleic Acids Res, 42(6): e38

    Article  CAS  PubMed  Google Scholar 

  • Therizols P, Illingworth R S, Courilleau C, Boyle S, Wood A J, Bickmore W A (2014). Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells. Science, 346(6214): 1238–1242

    Article  CAS  PubMed  Google Scholar 

  • Tsukamoto T, Hashiguchi N, Janicki S M, Tumbar T, Belmont A S, Spector D L (2000). Visualization of gene activity in living cells. Nat Cell Biol, 2(12): 871–878

    Article  CAS  PubMed  Google Scholar 

  • Verdaasdonk J S, Vasquez P A, Barry R M, Barry T, Goodwin S, Forest M G, Bloom K (2013). Centromere tethering confines chromosome domains. Mol Cell, 52(6): 819–831

    Article  CAS  PubMed  Google Scholar 

  • Viollier P H, Thanbichler M, McGrath P T, West L, Meewan M, McAdams H H, Shapiro L (2004). Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci USA, 101(25): 9257–9262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vogel M J, Peric-Hupkes D, van Steensel B (2007). Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc, 2(6): 1467–1478

    Article  CAS  PubMed  Google Scholar 

  • Wäldchen S, Lehmann J, Klein T, van de Linde S, Sauer M (2015). Light-induced cell damage in live-cell super-resolution microscopy. Sci Rep, 5: 15348

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Waldman F M, Chew K, Ljung B M, Goodson W, Hom J, Duarte L A, Smith H S, Mayall B (1991). A comparison between bromodeoxyuridine and 3H thymidine labeling in human breast tumors. Mod Pathol, 4(6): 718–722

    CAS  PubMed  Google Scholar 

  • Wan H, Feng C, Teng F, Yang S, Hu B, Niu Y, Xiang A P, Fang W, Ji W, Li W, Zhao X, Zhou Q (2015). One-step generation of p53 gene biallelic mutant Cynomolgus monkey via the CRISPR/Cas system. Cell Res, 25(2): 258–261

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Su J H, Beliveau B J, Bintu B, Moffitt J R, Wu C T, Zhuang X (2016). Spatial organization of chromatin domains and compartments in single chromosomes. Science, 353(6299): 598–602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang W, Li G W, Chen C, Xie X S, Zhuang X (2011). Chromosome organization by a nucleoid-associated protein in live bacteria. Science, 333(6048): 1445–1449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wijchers P J, Krijger P H, Geeven G, Zhu Y, Denker A, Verstegen M J, Valdes-Quezada C, Vermeulen C, Janssen M, Teunissen H, Anink- Groenen L C, Verschure P J, de Laat W (2016). Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments. Mol Cell, 61(3): 461–473

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Y, Zhou H, Fan X, Zhang Y, Zhang M, Wang Y, Xie Z, Bai M, Yin Q, Liang D, Tang W, Liao J, Zhou C, Liu W, Zhu P, Guo H, Pan H, Wu C, Shi H, Wu L, Tang F, Li J (2015). Correction of a genetic disease by CRISPR-Cas9-mediated gene editing in mouse spermatogonial stem cells. Cell Res, 25(1): 67–79

    Article  CAS  PubMed  Google Scholar 

  • Zalatan J G, Lee ME, Almeida R, Gilbert L A, Whitehead E H, La Russa M, Tsai J C, Weissman J S, Dueber J E, Qi L S, Lim W A (2015). Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell, 160(1-2): 339–350

    Article  CAS  PubMed  Google Scholar 

  • Zhou Y, Wang P, Tian F, Gao G, Huang L, Wei W, Xie X S (2017). Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res, 27(2): 298–301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zuleger N, Boyle S, Kelly D A, de las Heras J I, Lazou V, Korfali N, Batrakou D G, Randles K N, Morris G E, Harrison D J, Bickmore W A, Schirmer E C (2013). Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery. Genome Biol, 14(2): R14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgments

This work is supported by grants from the National Science Foundation of China 21573013, 21390412, 31271423, and 31327901, 863 Program SS2015AA020406 and CAS Interdisciplinary Innovation Team for Y.S.

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  1. State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China

    Shipeng Shao, Lei Chang, Yingping Hou & Yujie Sun

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  1. Shipeng Shao
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  2. Lei Chang
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Correspondence to Yujie Sun.

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Shao, S., Chang, L., Hou, Y. et al. Illuminating the structure and dynamics of chromatin by fluorescence labeling. Front. Biol. 12, 241–257 (2017). https://doi.org/10.1007/s11515-017-1454-2

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