H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1

Renata Z Jurkowska,Jinrong Min,Ludmila Dombrovski,Wolfram Tempel,Judith Stiefelmaier,Peter Loppnau,Albert Jeltsch,Yanli Liu,Richard Reinhardt,Su Qin,Pavel Bashtrykov,Hong Wu,Tomasz P Jurkowski,Sara Weirich,Srikanth Kudithipudi,Goran Kungulovski,Raluca Tamas

doi:10.1038/s41467-017-02259-9

Abstract

SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.

Highlights

SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation
SETDB1 plays a critical role in gene regulation[11], and it forms a complex with KAP-1 that is required in embryonic stem cells[12,13], primordial germ cells[14], and B lymphocytes[15]
The KAP-1/ SETDB1 complex is required for silencing of LTR retroviruses[12,13,14,15], and it has been connected to H3K9 methylation of LINE elements[14,15,22,23,24]

Summary

Introduction

SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. We show that K9me3/K14ac regions bound by SETDB1 are enriched in LINE elements and propose that 3TD-mediated recruitment of SETDB1 to chromatin-containing active marks (K14ac) contributes to the efficient silencing of these regions. We characterize a reader for the combined K14ac/K9me mark, demonstrate the role of Tudor domains in binding acetyllysine, and identify a pocket switch mechanism in histone reading domains. Future work will show if this modification-dependent conformational change of the substrate triggers any downstream effects in SETDB1 or any of its complex partners

Methods

Results

Discussion

Conclusion