Abstract
Chromatin organization play a vital role in gene regulation and genome maintenance in normal biological processes and in response to environmental insults. Disruption of chromatin organization imposes a significant effect on many cellular processes and is often associated with a range of pathological processes such as aging and cancer. Extensive attention has been attracted to understand the structural and functional studies of chromatin architecture. Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture. Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at nanometer resolution in the intact cells or tissue. In this review, we will first discuss the recent technical advantages and challenges of using SMLM to image chromatin architecture. Next, we will focus on the recent applications of SMLM for structural and functional studies to probe chromatin architecture in key cellular processes. Finally, we will provide our perspectives on the recent development and potential applications of super-resolution imaging of chromatin architecture in improving our understanding in diseases.
Highlights
In eukaryotic cells, chromatin is composed of DNA wrapped around histone proteins, forming the basic building block of nucleosomes assuming “beads-on-a-string” structure
The nucleosomes are further compacted into higher-order chromatin architecture, organized into condensed compartments or heterochromatin domain and open compartments or euchromatin domain (Figure 1)
Chromatin architecture has been traditionally probed by biochemical assays such as chromatin immunoprecipitation (ChIP) and chromosome conformation capture (3C) based techniques (Lieberman-Aiden et al, 2009), coupled with various molecular biology techniques, next-generation sequencing and bioinformatics analysis
Summary
Chromatin is composed of DNA wrapped around histone proteins, forming the basic building block of nucleosomes assuming “beads-on-a-string” structure. Chromatin architecture has been traditionally probed by biochemical assays such as chromatin immunoprecipitation (ChIP) and chromosome conformation capture (3C) based techniques (Lieberman-Aiden et al, 2009), coupled with various molecular biology techniques, next-generation sequencing and bioinformatics analysis. These tools have significantly advanced our understanding of chromatin organization. Chromatin conformation capture techniques identified the presence of chromatin domains, designated as topologically associating domains (TADs), as the key building blocks of chromatin organization, through genomescale analysis of contact frequencies between DNA sequences (Dixon et al, 2012, 2016) These biochemical methods remain the mainstream techniques for probing chromatin architecture, but with several limitations.
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