Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2

Abstract

Four papers in this issue tackle the hot topic of chromatin remodelling, specifically, how methyl marks on chromatin are 'read' by the proteins that interact with them. Two report on BPTF (bromodomain and PHD domain transcription factor), a subunit of NURF, the nucleosome remodelling factor. It contains a domain known as a PHD finger, which is shown to bind to histone H3 trimethylated at lysine 4 (H3K4) and to maintain proper activity at developmentally critical HOX genes. The accompanying structural study of the complex explains how the site specificity for H3K4 is achieved. The two other papers reveal that the PHD domain of tumour suppressor ING2 also recognizes trimethylated H3K4, and link the histone mark to repression of transcription. The four papers together establish certain PHD finger domains as previously unrecognized chromatin-binding modules. In a News and Views piece, Peter B. Becker discusses what these papers tell us about the function of the chemical modifications of histone tails. One of four papers establishing certain PHD domains as effectors of trimethylated histone H3K4, a chromatin mark generally associated with active transcription. This paper describes the structure of the PHD finger from the tumour suppressor ING2 complexed with H3K4me3. Covalent modifications of histone tails have a key role in regulating chromatin structure and controlling transcriptional activity. In eukaryotes, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with active chromatin and gene expression1,2,3,4. We recently found that plant homeodomain (PHD) finger of tumour suppressor ING2 (inhibitor of growth 2) binds H3K4me3 and represents a new family of modules that target this epigenetic mark5. The molecular mechanism of H3K4me3 recognition, however, remains unknown. Here we report a 2.0 Å resolution structure of the mouse ING2 PHD finger in complex with a histone H3 peptide trimethylated at lysine 4. The H3K4me3 tail is bound in an extended conformation in a deep and extensive binding site consisting of elements that are conserved among the ING family of proteins. The trimethylammonium group of Lys 4 is recognized by the aromatic side chains of Y215 and W238 residues, whereas the intermolecular hydrogen-bonding and complementary surface interactions, involving Ala 1, Arg 2, Thr 3 and Thr 6 of the peptide, account for the PHD finger's high specificity and affinity. Substitution of the binding site residues disrupts H3K4me3 interaction in vitro and impairs the ability of ING2 to induce apoptosis in vivo. Strong binding of other ING and YNG PHD fingers suggests that the recognition of H3K4me3 histone code is a general feature of the ING/YNG proteins. Elucidation of the mechanisms underlying this novel function of PHD fingers provides a basis for deciphering the role of the ING family of tumour suppressors in chromatin regulation and signalling.