Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing.

Ross T. Fennessy,Tom Owen-Hughes

doi:10.1093/nar/gkw331

Abstract

Nucleosomes, the fundamental subunits of eukaryotic chromatin, are organized with respect to transcriptional start sites. A major challenge to the persistence of this organization is the disassembly of nucleosomes during DNA replication. Here, we use complimentary approaches to map the locations of nucleosomes on recently replicated DNA. We find that nucleosomes are substantially realigned with promoters during the minutes following DNA replication. As a result, the nucleosomal landscape is largely re-established before newly replicated chromosomes are partitioned into daughter cells and can serve as a platform for the re-establishment of gene expression programmes. When the supply of histones is disrupted through mutation of the chaperone Caf1, a promoter-based architecture is generated, but with increased inter-nucleosomal spacing. This indicates that the chromatin remodelling enzymes responsible for spacing nucleosomes are capable of organizing nucleosomes with a range of different linker DNA lengths.

Highlights

The genomes of eukaryotes exist as chromatin
To ensure that ethynyl-2 -deoxy-uridine (EdU) was available for rapid incorporation we used a strain in which five copies of the herpes simplex thymidine kinase were expressed from GDP1 promoters [40] and the human equilabrative transporter 1 (ENT1) gene was expressed from the ADH1 promoter [41,42]
The enrichment for nascent chromatin was c6-fold using the CsCl approach in comparison to 20-fold using EdU meaning that we could not enrich for chromatin at very early time points

Summary

Introduction

The genomes of eukaryotes exist as chromatin. The fundamental subunit of chromatin, the nucleosome is not a static structure, but can be reconfigured dynamically. Variant histones can be incorporated into nucleosomes and the histone polypeptides themselves subject to extensive post-translational modification. In combination, such changes have led to the identification of distinct chromatin states [1,2,3]. Chromatin states are often conserved through cell divisions, and recent studies have shown that different types of histone modification are restored at different rates [4,5]. The processes that underlie this are poorly understood

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Conclusion