Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions

Abstract

The reader ability of PHD fingers is largely limited to the recognition of the histone H3 N-terminal tail. Distinct subsets of PHDs bind either H3K4me3 (a transcriptional activator mark) or H3K4me0 (a transcriptional repressor state). Structural studies have identified common features among the different H3K4me3 effector PHDs, including 1) removal of the initiator methionine residue of H3 to prevent steric interference, 2) a groove where arginine-2 binds, and 3) an aromatic cage that engages methylated lysine-4. We hypothesize that PHDs have the ability to engage with non-histone ligands, as long as they adhere to these three rules. A search of the human proteome revealed an enrichment of chromatin-binding proteins that met these criteria, which we termed H3 N-terminal mimicry proteins (H3TMs). Seven H3TMs were selected, and used to screen a protein domain microarray for potential effector domains, and they all had the ability to bind H3K4me3-interacting effector domains. Furthermore, the binding affinity between the VRK1 peptide and the PHD domain of PHF2 is ~3-fold stronger than that of PHF2 and H3K4me3 interaction. The crystal structure of PHF2 PHD finger bound with VRK1 K4me3 peptide provides a molecular basis for stronger binding of VRK1 peptide. In addition, a number of the H3TMs peptides, in their unmethylated form, interact with NuRD transcriptional repressor complex. Our findings provide in vitro evidence that methylation of H3TMs can promote interactions with PHD and Tudor domain-containing proteins and potentially block interactions with the NuRD complex. We propose that these interactions can occur in vivo as well.

Molecular convergence by differential domain acquisition is a hallmark of chromosomal passenger complex evolution

“…( A ) Multiple sequence alignment of the H3 N terminus in different species showing conservation of threonine 3 and 11 (T3, T11). Histone H3 polypeptides are typically numbered with omission of the N-terminal methionine, since it is likely removed cotranslationally ( 58 , 59 ). Therefore, the initiator Met has not been included in the peptides used in the in vitro assays in C .…”

A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2

“…In contrast to PHF8 and KIAA1718, PHF2 is enzymatically inactive in vitro (based on mass spectrometry– and fluorescence-based demethylase assays on peptide substrates) ( 28 ) and remains inactive until it is phosphorylated by protein kinase A ( 29 ). In addition to its histone substrates, PHF2 also binds to methylated nonhistone proteins that mimic the histone H3 N-terminal tail sequence ( 30 ) including vaccinia-related kinase 1 (VRK1), a serine/threonine protein kinase ( 31 ). PHF2 forms a complex with the DNA-interacting protein ARID5B, resulting in both demethylation of ARID5B by PHF2 ( 29 ) and subsequent recruitment of the PHF2–ARID5B complex to select H3K9me2-marked promoters of specific genes regulated by transcription factor Sox9 ( 32 ) or the lipogenic transcription factor ChREBP (carbohydrate-responsive element binding protein) ( 27 ).…”

Histone mimics: more tales to read

“…The study led by Chen et al was set out to determine whether in the human proteome there are proteins that have an H3-like N-terminal motif and whether they interact with known H3K4me3-reader proteins in a methylation-dependent manner [4]. A systematic analysis of ∼20 000 annotated human proteins identified 257 candidate proteins that were named as the H3 N-terminal mimicry proteins (H3TMs).…”

“…Importantly, these interactions were validated by individual peptide pulldowns using both recombinant protein domains and full-length proteins from whole-cell extracts. In addition, these H3TMs can be modified in vitro by the histone H3K4 methyltransferases, including SET7/9, MLL4, and PRDM9, suggesting potential crosstalk in cells [4].…”

“…For example, compared with the H3K4me3 peptide, methyl-VRK1 showed a three folds higher binding affinity to the PHF2 PHD finger. The crystal structure of PHF2 PHD finger in complex with the methyl-VRK1 peptide revealed extensive interactions between PHF2 and the first seven residues of VRK1 involving electrostatic, hydrogen bonds, aromatic cage, and van der Waals contacts, accounting for the high binding affinity [4]. PHF2 belongs to the KDM7 histone demethylase family and contains a PHD finger and a Jumonji-C ( JMJC) domain.…”