Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation

Saurabh K Bhardwaj,Blaine Bartholomew,Jim Persinger,Solomon G Hailu,Lola Olufemi,Swetansu K Hota,Sandipan Brahma,Soumyadipta Kundu

doi:10.1038/s41467-020-19700-1

Abstract

Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a’s dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.

Highlights

Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome
Yeast ISW1a is the first from a large superfamily of ATPdependent chromatin remodelers to recognize the simplest element of higher-order chromatin organization, namely dinucleosomes
The only other subunit that ISW1a has besides the catalytic subunit is the Ioc[3] accessory subunit and Ioc[3] is the key factor contributing to ISW1a’s unique characteristics

Summary

Introduction

Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. Ioc[3] binding to nucleosomal DNA at the dyad axis is lifted when binding dinucleosomes compared to mononucleosomes These conformational changes are associated with ISW1a mobilizing dinucleosomes an order of magnitude more efficiently than mononucleosomes, even though the rate of ATP hydrolysis is equivalent for both substrates. We dissect these properties further by mutational analysis of Ioc[3] and find its DNA binding domain is critical for these differences and show that it is required both in vitro and in vivo for ISW1a remodeling

Methods

Results

Conclusion