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WIREs Syst Biol Med
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Chromatin imaging and new technologies for imaging the nucleome

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Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super‐resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single‐molecule localization microscopy increases the spatial resolution by approximately 10‐fold at the expense of slower acquisition speed. Stimulated emission‐depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to “light up” global and sequence‐specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single‐molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New‐generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus‐specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor–operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator‐like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single‐molecule tracking, these labeling techniques enable direct visualization of intra‐ and inter‐chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging
Advances in imaging techniques and labeling strategies enable visualization of chromatin in space and time. CLEM: correlative light and electron microscopy; CRISPR: clustered regularly interspaced short palindromic repeats; dCas9: dead CRISPR‐associated protein 9; PAINT: point accumulation in imaging nanoscale topology; PALM: photoactivated localization microscopy; SIM: structured illumination microscopy; SMT: single‐molecule tracking; STED: stimulated emission‐depletion microscopy; STORM: stochastic optical reconstruction microscopy; TALE: transcription activator‐like effector; ZFP: zinc finger protein
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