Super-Resolution Microscopy of Chromatin

Birk, Udo

doi:10.3390/genes10070493

Cited by 18 publications

(15 citation statements)

References 93 publications

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“…What matters is not always the highest resolution, but the right resolution needed to solve a given biological problem. Other parameters are of equal importance, such as structure integrity of the sample, the choice of fluorophores, optimally suited for the labeling of chosen targets with little fluorophore bleaching, optimal signal, and noise levels recorded by detectors with high quantum efficiency, software for image analysis and 3D reconstructions …”

Section: Support Of the Anc‐inc Model With Super‐resolved Fluorescencmentioning

confidence: 99%

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

et al. 2020

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This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.

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Section: Support Of the Anc‐inc Model With Super‐resolved Fluorescencmentioning

confidence: 99%

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

et al. 2020

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“…The technical ability to visualize the spatial relationships of multiple proteins in tissues at super‐resolution represents a major capability in the field of microscopy. Applications for studying biological structure with super‐resolution microscopy have grown considerably in the last few years (Birk, 2019; Fang et al., 2018; Garcia et al., 2017; Mockl et al., 2014; Schermelleh et al., 2019; Sieben et al., 2018; Sreedharan et al., 2017; Stracy & Kapanidis, 2017; Xu & Liu, 2019) and new advances in the field are predicted to improve our understanding as the potential of the technology is further realized. In the past, studies of microglia in brain tissue were typically conducted using immunocytochemistry in combination with brightfield, epifluorescence widefield, or confocal microscopy (Sarmiento, 2013).…”

Section: Discussionmentioning

confidence: 99%

Ground state depletion microscopy as a tool for studying microglia–synapse interactions

Paasila

Fok

Flores‐Rodriguez

et al. 2021

J of Neuroscience Research

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Advances in microscopy research have facilitated the development of various techniques of super-resolution microscopy which overcome the diffraction limits of light that constrain confocal and two-photon microscopy (Galbraith & Galbraith, 2011). Single molecule localization microscopy (SMLM) techniques perform two basic operations for image reconstruction: (a) the super-localization of single emitters within the nanometer range and (b) the active control of emitters to reduce the concentration of fluorescing molecules at any one time

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“…However, when assessing chromatin conformation within TADs, subTADs, and particular loop domains, one should consider methods of super-resolution fluorescent (SRM) or electron microscopy. In the last decade, stochastic optical reconstruction microscopy (STORM), photoactivated localization microscopy (PALM), structured illumination microscopy (SIM), focused ion beam scanning electron microscopy (FIB-SEM) were applied intensively in the exploration of chromatin domains within individual cells ( Lakadamyali and Cosma, 2015 ; Birk, 2019 ; Szydlowski et al, 2019 ; Shim, 2021 ; Xie and Liu, 2021 ). Highlights and practical guidance for the application of these microscopy tools is beyond the scope of the present review and can be found elsewhere ( Lambert and Waters, 2017 ; Schermelleh et al, 2019 ).…”

Section: Fish As a An Efficient Approach For Chromatin Domain Visualizationmentioning

confidence: 99%

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

Maslova

Krasikova

2021

Front. Cell Dev. Biol.

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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.

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Super-Resolution Microscopy of Chromatin

Cited by 18 publications

References 93 publications

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

Ground state depletion microscopy as a tool for studying microglia–synapse interactions

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

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