POLE3-POLE4 Is a Histone H3-H4 Chaperone that Maintains Chromatin Integrity during DNA Replication

Roberto Bellelli,Ondrej Belan,Valerie E Pye,Camille Clement,Sarah L Maslen,J Mark Skehel,Peter Cherepanov,Genevieve Almouzni,Simon J Boulton

doi:10.1016/j.molcel.2018.08.043

Roberto Bellelli, Ondrej Belan + Show 7 more

Open Access

https://doi.org/10.1016/j.molcel.2018.08.043

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Abstract

SummaryMaintenance of epigenetic integrity relies on coordinated recycling and partitioning of parental histones and deposition of newly synthesized histones during DNA replication. This process depends upon a poorly characterized network of histone chaperones, remodelers, and binding proteins. Here we implicate the POLE3-POLE4 subcomplex of the leading-strand polymerase, Polε, in replication-coupled nucleosome assembly through its ability to selectively bind to histones H3-H4. Using hydrogen/deuterium exchange mass spectrometry and physical mapping, we define minimal domains necessary for interaction between POLE3-POLE4 and histones H3-H4. Biochemical analyses establish that POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. In cells, POLE3-POLE4 binds both newly synthesized and parental histones, and its depletion hinders helicase unwinding and chromatin PCNA unloading and compromises coordinated parental histone retention and new histone deposition. Collectively, our study reveals that POLE3-POLE4 possesses intrinsic H3-H4 chaperone activity, which facilitates faithful nucleosome dynamics at the replication fork.

Highlights

During S phase of the cell cycle, accurate and processive replication of genomic DNA has to be coupled to duplication of the epigenetic information encoded in histones and their post-translational modifications (Kouzarides, 2007)
We recently showed that cells lacking POLE4 display reduced levels of the Polε complex components POLE1 and POLE2, which we attributed to defective origin activation (Bellelli et al, 2018)
H/D exchange experiments, carried out in 300 mM concentrations, suggested an increased exposure of the central region of H3, which points to a conformational change of histones H3 and H4 upon engagement of H4 by POLE3-POLE4, which is different from that observed with histone chaperones known to bind histone dimers such as NAP1 and DAXX (D’Arcy et al, 2013; DeNizio et al, 2014)

Summary

Introduction

During S phase of the cell cycle, accurate and processive replication of genomic DNA has to be coupled to duplication of the epigenetic information encoded in histones and their post-translational modifications (Kouzarides, 2007) For this to happen, chromatin must be disrupted ahead of the replication fork and restored in a timely and regulated fashion on sister chromatids, a process known as replication-coupled nucleosome assembly This process relies on two different but interlocked mechanisms involving the recycling of parental histones and the deposition of newly synthesized ones. Changes in chromatin composition and structure impact on aging (Feser et al, 2010; O’Sullivan et al, 2010)

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