In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin.

Ben C Tilly,Gillian E Chalkley,Yuri M Moshkin,Jeroen Aa Demmers,Jan A Van Der Knaap,Dick Hw Dekkers,Tsung Wai Kan,C Peter Verrijzer

doi:10.7554/elife.69424

Abstract

ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of Drosophila polytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.

Highlights

ATP-dependent chromatin remodeling enzymes alter the structure and organization of nucleosomes, the basic building blocks of eukaryotic chromatin (Becker and Workman, 2013; Bracken et al, 2019; Clapier et al, 2017; Jungblut et al, 2020; Sundaramoorthy and Owen-Hughes, 2020)
Loss of ATP-binding enhances BRM chromatin retention and clustering in Schneider 2 (S2) cells To study the in vivo dynamics of BRM, we generated S2 cell lines that express either BRM that is tagged at its amino-terminus with enhanced green fluorescent protein (GFP-BRM) or a catalytically inactive ATP-binding mutant, GFP-BRM-K804R (Elfring et al, 1998)
At the height of E74 and E75 transcription, a substantial portion of RNA polymerase II (RNAPII) is locally recycled in what Lis and colleagues named a transcription compartment (Yao et al, 2007)

Summary

Introduction

ATP-dependent chromatin remodeling enzymes (remodelers) alter the structure and organization of nucleosomes, the basic building blocks of eukaryotic chromatin (Becker and Workman, 2013; Bracken et al, 2019; Clapier et al, 2017; Jungblut et al, 2020; Sundaramoorthy and Owen-Hughes, 2020). Remodelers are large, multi-subunit complexes that harbor a Snf2-class ATPase motor (Clapier et al, 2017; Jungblut et al, 2020; Sundaramoorthy and Owen-Hughes, 2020). Nucleosome remodeling is the result of ATP-dependent DNA translocation by the ATPase, which is locked onto the nucleosome through binding additional DNA- and histone sites. Different classes of remodelers, defined by their ATPase and unique sets of accessory subunits, are dedicated to distinct chromatin regulatory functions

Methods

Results

Conclusion