MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes.

Chang-Hui Shen,James Allan

doi:10.3390/cells10092239

Abstract

The compact nucleosomal structure limits DNA accessibility and regulates DNA-dependent cellular activities. Linker histones bind to nucleosomes and compact nucleosomal arrays into a higher-order chromatin structure. Recent developments in high throughput technologies and structural computational studies provide nucleosome positioning at a high resolution and contribute to the information of linker histone location within a chromatosome. However, the precise linker histone location within the chromatin fibre remains unclear. Using monomer extension, we mapped core particle and chromatosomal positions over a core histone-reconstituted, 1.5 kb stretch of DNA from the chicken adult β-globin gene, after titration with linker histones and linker histone globular domains. Our results show that, although linker histone globular domains and linker histones display a wide variation in their binding affinity for different positioned nucleosomes, they do not alter nucleosome positions or generate new nucleosome positions. Furthermore, the extra ~20 bp of DNA protected in a chromatosome is usually symmetrically distributed at each end of the core particle, suggesting linker histones or linker histone globular domains are located close to the nucleosomal dyad axis.

Highlights

Published: 29 August 2021In the eukaryotic genome, DNA is packaged inside nuclei by association with histone proteins to form chromatin
Monomer extension is an approach that can be used to compare the translational positions adopted by core histone octamers and chromatosomes and, to determine the extra linker DNA protected by the linker histones or linker histone globular domains
Since the higher-order chromatin structure imposes a constraint on nucleosome positioning, linker histone could in principle at least indirectly affect positioning as it is the agent of higher-order folding

Summary

Introduction

Published: 29 August 2021In the eukaryotic genome, DNA is packaged inside nuclei by association with histone proteins to form chromatin. Gene activation and transcription are often accompanied by the removal of nucleosomes from the transcription factor binding region. Nucleosome positioning with respect to the underlying DNA is crucial for chromatin dynamics during gene activation. In addition to the core histones, present as an octameric unit, linker histones are invariably associated with nucleosomes. These histones bind to the nucleosome, interacting with an extra 20 bp of linker DNA, to form chromatosomes [7,8,9]. Chromatosomal arrays are hierarchically folded into higher-order structures which can modulate nucleosome positioning [10]. Linker histones can be considered as epigenetic regulators as they bind reversibly to nucleosomes and alter chromatin structures and dynamics. The removal of linker histones from chromatin can lead to the migration of the histone octamer

Methods

Results

Conclusion