The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail

Tyler M Weaver,Katelyn E Connelly,Katayoun Varzavand,Jiachen Liu,Chris Coble,Catherine A Musselman,Emily C Dykhuizen

doi:10.1038/s41598-018-37699-w

Tyler M Weaver, Katelyn E Connelly + Show 5 more

Open Access

https://doi.org/10.1038/s41598-018-37699-w

Copy DOI

Abstract

SANT domains are found in a number of chromatin regulators. They contain approximately 50 amino acids and have high similarity to the DNA binding domain of Myb related proteins. Though some SANT domains associate with DNA others have been found to bind unmodified histone tails. There are two SANT domains in Enhancer of Zeste 2 (EZH2), the catalytic subunit of the Polycomb Repressive Complex 2 (PRC2), of unknown function. Here we show that the first SANT domain (SANT1) of EZH2 is a histone binding domain with specificity for the histone H4 N-terminal tail. Using NMR spectroscopy, mutagenesis, and molecular modeling we structurally characterize the SANT1 domain and determine the molecular mechanism of binding to the H4 tail. Though not important for histone binding, we find that the adjacent stimulation response motif (SRM) stabilizes SANT1 and transiently samples its active form in solution. Acetylation of H4K16 (H4K16ac) or acetylation or methylation of H4K20 (H4K20ac and H4K20me3) are seen to abrogate binding of SANT1 to H4, which is consistent with these modifications being anti-correlated with H3K27me3 in-vivo. Our results provide significant insight into this important regulatory region of EZH2 and the first characterization of the molecular mechanism of SANT domain histone binding.

Highlights

Histone proteins are dynamically post-translationally modified during all DNA-templated processes in the eukaryotic cell, and are thought to be one of the main mechanisms by which chromatin structure is regulated in response to cellular signals[1,2]
Our results suggest that the SANT1 domain of Enhancer of Zeste Homologue 2 (EZH2) can associate with the H4 N-terminal tail and provide sensitivity to its modification state
Our results suggest that EZH2 SANT1 provides sensitivity to the modification state of H4K16 and H4K20

Summary

Introduction

Histone proteins are dynamically post-translationally modified during all DNA-templated processes in the eukaryotic cell, and are thought to be one of the main mechanisms by which chromatin structure is regulated in response to cellular signals[1,2]. Histone post-translational modifications (PTMs) have been shown to either alter chromatin structure directly, or recruit or regulate the function of chromatin regulatory proteins and complexes[1] The latter is mediated through the action of histone binding subdomains known as reader domains, that allow for specific recognition of the histone proteins and their modification state[3,4,5]. Though some SANT domains have been shown to interact with DNA, another subset has been found to bind to unmodified histone tails, which is important for regulating the activity of their respective chromatin modifying complexes[21,22,23,24,25,26,27]. Our results provide valuable insight into this regulatory region of PRC2 and uncover an additional mechanism by which PRC2 can sense the local chromatin landscape via the SANT1 domain

Methods

Results

Conclusion