Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions

Abstract

BackgroundHistone posttranslational modifications (PTMs) function to regulate chromatin structure and function in part through the recruitment of effector proteins that harbor specialized “reader” domains. Despite efforts to elucidate reader domain–PTM interactions, the influence of neighboring PTMs and the target specificity of many reader domains is still unclear. The aim of this study was to use a high-throughput histone peptide microarray platform to interrogate 83 known and putative histone reader domains from the chromo and Tudor domain families to identify their interactions and characterize the influence of neighboring PTMs on these interactions. ResultsNearly a quarter of the chromo and Tudor domains screened showed interactions with histone PTMs by peptide microarray, revealing known and several novel methyllysine interactions. Specifically, we found that the CBX/HP1 chromodomains that recognize H3K9me also recognize H3K23me2/3—a poorly understood histone PTM. We also observed that, in addition to their interaction with H3K4me3, Tudor domains of the Spindlin family also recognized H4K20me3—a previously uncharacterized interaction. Several Tudor domains also showed novel interactions with H3K4me as well.ConclusionsThese results provide an important resource for the epigenetics and chromatin community on the interactions of many human chromo and Tudor domains. They also provide the basis for additional studies into the functional significance of the novel interactions that were discovered.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0117-5) contains supplementary material, which is available to authorized users.

Suppressor mutations in Mecp2-null mice reveal that the DNA damage response is key to Rett syndrome pathology

“…The co-repressors Ncor1, transducin (beta)-like 1X-linked receptor 1(Tbl1xr1), Rcor1 and Sin3a are transcriptional repressors that act with MECP2, yet missense mutations in these genes occurred in lines that were not mated, so they are included in Table 2 but are not given Sum designations. Several additional supported genes are particularly intriguing because they are predicted to alter chromatin structure: these include PR domain containing 15 (Prdm15), zinc finger ZZ domain containing 3 (Zzz3), and lysine (K)-specific demethylase 4A (Kdm4a) (Shanle et al 2017). The PR domain proteins, many of which have histone methyltransferase activity and others that recruit methyltransferases to DNA, play roles as molecular switches in many developmental processes (Fog et al 2012;Hohenauer and Moore 2012).…”

“…Spindlin 1 (Spin1) primarily plays a role in meiosis (Chew et al 2013), while its induction in oocytes can trigger the DNA damage response; interestingly, the mutation lies within its third TUDOR-like domain (Supplemental Figure S2), which binds methylated histone H3, a mark associated with the DNA damage response (Choi et al 2017;Shanle et al 2017).…”

Spindlin‐1 recognizes methylations of K20 and R23 of histone H4 tail

“…Spindlin-1 reportedly binds the dual H3K4me3-H3R8me2a methylation pattern that plays an import role in activation of Wnt-signaling pathway [22]. By comparing the complex structure of Spindlin-1-H4 (16)(17)(18)(19)(20)(21)(22)(23)(24)(25) K20me3 with that of Spindlin-1-H3(1-8)K4me3R8-me2a, as well as the sequences of the two peptides, we hypothesized that Spindlin-1 harbors the structural features necessary to recognize methylated H4R23 via domain I either alone or in addition to H4K20me3 recognized by domain II (Fig. S6).…”

“…S3. The F o ÀF c omit map of R17-V21 of H4 (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)K20me3 peptides contoured at 2 sigma is shown in light blue. Fig.…”

“…When we identified Spindlin‐1 as a potential binding protein to H4K20me3 according to CLASPI, Erin et al . classified it as a reader of H4K20me3 using histone peptide microarray screens of the chromo and Tudor domains. Although domain II of Spindlin‐1 was verified as being responsible for H4K20me3 binding via introduction of a Y170A mutation, the details of the interaction between Spindlin‐1 and H4K20me3 remained unclear.…”