Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
Highlights
OVERVIEW OF THE TOOLKITS FOR CHROMATIN DOMAIN IMAGINGThe term “chromatin” was coined by Walther Flemming at the end of the 19th century to designate structures stained by aniline dyes and confined within the cell nucleus (Paweletz, 2001)
We focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains
Complex detection schemes with activator and photoswitchable reporter dyes should be taken into consideration during design of the Oligopaint libraries for high-resolution imaging of small-scale genomic targets by single-molecule localization microscopy (SMLM) methods, like stochastic optical reconstruction microscopy (STORM) (Figure 4C.III) or DNA point accumulation for imaging of nanoscale topography (DNA-PAINT; Figure 4C.IV; Boettiger et al, 2016; Beliveau et al, 2017; Bintu et al, 2018; Nir et al, 2018)
Summary
OVERVIEW OF THE TOOLKITS FOR CHROMATIN DOMAIN IMAGINGThe term “chromatin” was coined by Walther Flemming at the end of the 19th century to designate structures stained by aniline dyes and confined within the cell nucleus (Paweletz, 2001). Complex detection schemes with activator and photoswitchable reporter dyes should be taken into consideration during design of the Oligopaint libraries for high-resolution imaging of small-scale genomic targets by single-molecule localization microscopy (SMLM) methods, like STORM (Figure 4C.III) or DNA point accumulation for imaging of nanoscale topography (DNA-PAINT; Figure 4C.IV; Boettiger et al, 2016; Beliveau et al, 2017; Bintu et al, 2018; Nir et al, 2018).
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