The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma

Matthew J Mcbride,Martin Filipovski,Jacob D Jaffe,Nazar Mashtalir,Sirano Dhe-Paganon,Roodolph St Pierre,Alfredo M Valencia,Cigall Kadoch,Evan B Winter,Tom W Muir,Kristin Qian,Andrew R D’Avino,Neil T Umbreit,Hayley J Zullow,Hyuk-Soo Seo,Hai T Dao

doi:10.1038/s41594-020-0466-9

Abstract

Interactions between chromatin-associated proteins and the histone landscape play major roles in dictating genome topology and gene expression. Cancer-specific fusion oncoproteins, which display unique chromatin localization patterns, often lack classical DNA-binding domains, presenting challenges in identifying mechanisms governing their site-specific chromatin targeting and function. Here we identify a minimal region of the human SS18-SSX fusion oncoprotein (the hallmark driver of synovial sarcoma) that mediates a direct interaction between the mSWI/SNF complex and the nucleosome acidic patch. This binding results in altered mSWI/SNF composition and nucleosome engagement, driving cancer-specific mSWI/SNF complex targeting and gene expression. Furthermore, the C-terminal region of SSX confers preferential affinity to repressed, H2AK119Ub-marked nucleosomes, underlying the selective targeting to polycomb-marked genomic regions and synovial sarcoma–specific dependency on PRC1 function. Together, our results describe a functional interplay between a key nucleosome binding hub and a histone modification that underlies the disease-specific recruitment of a major chromatin remodeling complex.

Highlights

It has remained elusive, how nuclear fusion oncoproteins that lack canonical TF DNA-binding or recognizable chromatin reader domains yield altered, region-specific targeting of chromatin regulatory proteins and protein complexes
SS18-SSX purifications most substantially enriched for ATPase subunits SMARCA4 and SMARCA2, BCL7A, ACTL6A and β-actin, consistent with the fact that SS18 is part of the ATPase module of mSWI/SNF complexes[23], while core module components, SMARCB1, were less enriched compared to WT SS18 purifications (Fig. 1b, Extended Data Fig. 1c,d and Supplementary Table 1)
We have identified an unexpected set of functionally critical properties of the fusion oncoprotein, SS18-SSX, the oncogenic driver of human synovial sarcoma (SS) (Fig. 5)

Summary

Introduction

How nuclear fusion oncoproteins that lack canonical TF DNA-binding or recognizable chromatin reader domains yield altered, region-specific targeting of chromatin regulatory proteins and protein complexes. Some studies have suggested SSX interactions with chromatin-associated factors[22], the mechanism by which the site-specific binding and unique biochemical properties are achieved remains largely unknown. We elucidate the mechanism by which the SS18-SSX oncogenic fusion protein engages with chromatin and directs BAF chromatin remodeling complexes to specialized target sites. We find that SSX contains a basic region that directly binds the nucleosome acidic patch, altering BAF complex subunit configuration and activity. Articles (H2AK119Ub) on nucleosomes, preferential recognition of which requires a second, conserved region of SSX. These dual reader-like features of SSX underlie the highly disease-specific chromatin remodeling complex targeting, gene expression and functional dependencies in SS. Our studies reveal a novel mechanism of chromatin localization with important implications in both disease biology and therapeutic discovery

Methods

Results

Conclusion