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

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.

Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver

“…We propose a model where first close residues H3K9 and H3K14 are acetylated by the same histone acetyltransferase (HAT), then H3K9 is deacetylated by Hdac3, allowing for subsequent triple methylation of H3K9 by Setdb1/Kap1 and establishment of the bivalent region (Figure ). Our model is consistent with a prior study reporting that, first, established H3K14ac mark is recognized by the Tudor domain of Setdb1, followed by triple methylation of H3K9 by the SET domain of Setdb1 (Jurkowska et al, ).…”

“…Additional functional analysis using EnrichR (Kuleshov et al, ) identified Kap1 binding sites (ChIP‐Seq, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31183) as significantly overrepresented among both regions identified as dually marked in both young and old livers ( p ‐values < 7.55E‐10 and < 2.90E‐11, respectively, Figure e). Kap1 interacts with Setdb1 (Schultz, Ayyanathan, Negorev, Maul, & Rauscher, ), a chromatin regulator that is associated with H3K9me3/H3K14ac dually marked regions in mESCs (Jurkowska et al, ). Our analysis suggests that Setdb1 in complex with Kap1 is also associated with H3K9me3/H3K14ac bivalent regions in young and old livers.…”

“…The resolution of sequential ChIP can identify bivalent nucleosomes but is not sufficient to pinpoint dually marked single histone tails. However, since we identified Setdb1 ChIP‐Seq signal in sequential ChIP‐Seq regions, a subset of reChIP sites corresponds to dually modified single histone tails because Setdb1 has been shown to recognize and be recruited to dually modified H3K9me3/H3K14ac peptides (Jurkowska et al, ). Hence, our results show a correlation between H3K9me3/H3K14ac bulk bivalent regions, bivalent nucleosomes, and dually marked single histone tails.…”

“…The role of bivalent domains in differentiated tissues is less clear. Presence of another bivalent mark, consisting of H3K9me3 and H3K14ac modifications, has been recently reported in mESCs where the authors demonstrate that the Tudor domain of Setdb1 recognized H3K14ac, whereas the SET domain of Setdb1 methylated H3K9me3 (Jurkowska et al, ). This study linked Setdb1 binding at these bivalent domains to silencing of LINE elements.…”

Essential roles of Windei and nuclear monoubiquitination of Eggless/ SETDB 1 in transposon silencing

“…The domain structures and predicted Egg post‐translational modification sites are summarized in Fig C. We first immunoisolated Egg from OSCs and probed with anti‐ubiquitin (Ub) antibodies.…”