Single-Molecule Techniques to Study Chromatin.

Anna Chanou,Stephan Hamperl

doi:10.3389/fcell.2021.699771

Anna Chanou, Stephan Hamperl

Open Access

https://doi.org/10.3389/fcell.2021.699771

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Abstract

Besides the basic organization in nucleosome core particles (NCPs), eukaryotic chromatin is further packed through interactions with numerous protein complexes including transcription factors, chromatin remodeling and modifying enzymes. This nucleoprotein complex provides the template for many important biological processes, such as DNA replication, transcription, and DNA repair. Thus, to understand the molecular basis of these DNA transactions, it is critical to define individual changes of the chromatin structure at precise genomic regions where these machineries assemble and drive biological reactions. Single-molecule approaches provide the only possible solution to overcome the heterogenous nature of chromatin and monitor the behavior of individual chromatin transactions in real-time. In this review, we will give an overview of currently available single-molecule methods to obtain mechanistic insights into nucleosome positioning, histone modifications and DNA replication and transcription analysis—previously unattainable with population-based assays.

Highlights

The remarkable length and complexity of eukaryotic genomes poses several challenges to the cell
The nucleosome is the basic unit of chromatin, each occupying 147 bp of DNA wrapped around histone octamers
Apart from intrinsically favorable or unfavorable DNA sequences for nucleosome formation (Travers et al, 2010), other cellular components, such as transcription factors and ATP-dependent chromatin remodeling machines contribute to the chromatin landscape in vivo (Dou and Gorovsky, 2000; Jenuwein, 2001; Lusser and Kadonaga, 2003; Heintzman et al, 2009; Bell et al, 2011)

Summary

Introduction

The remarkable length and complexity of eukaryotic genomes poses several challenges to the cell. We will give an overview of currently available single-molecule methods that provide mechanistic insight into chromatin structure and processes, such as chromatin accessibility, histone modifications, replication and transcription (Supplementary Table 1).

Results

Conclusion