Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2

Abstract

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 expression. 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 mark. The molecular mechanism of H3K4me3 recognition, however, remains unknown. Here we report a 2.0 A 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.

Detection of novel mRNA splice variants of human ING4 tumor suppressor gene

“…The NLS1 domain is responsible for ING4 nuclear localization and interaction with p53 Zhang et al, 2005). The PHD domain, a zinc finger motif present in many nuclear proteins (Bienz, 2006), is involved in interaction with HPH-2 (Ozer et al, 2005) and H3K4me2/3 (Pena et al, 2006;Shi et al, 2006), thus linking ING4 to regulation of gene expression. A deletion mutant lacking the C-terminal 40 amino acids, including the PHD domain, is unable to interact with p65, thus abrogating the inhibitory effect of ING4 on NF-kB activity (Garkavtsev et al, 2004).…”

“…Our data are in keeping with previous study showing that the deletion of the last 40 amino acids abrogates the effect of ING4 on NF-kB activa tion. Interestingly, the region lacking in ING4-DEx6A contains the PHD domain, involved in the binding to HPH-2, and H3K4me2/3 (Ozer et al, 2005;Pena et al, 2006;Shi et al, 2006). Thus, alternative splicing producing ING4-DEx6 variants could impair some important functions of ING4 and modulate its contribution to specific pathways.…”

“…In a recent report the ING PHD domain has been shown capable to interact with histone H3 di-or tri-methylated at lysine 4 (H3K4me2/3). In particular, with respect to ING2, such interaction results in gene repression (Pena et al, 2006;Shi et al, 2006).…”

“…More recently, ING4 has been shown to interact with HIF-associated prolyl hydroxylase (HPH)-2, and to regulate the activity of the hypoxia-inducible factor (HIF)-1a transcription factor, thus suppressing the expression of HIF-1a responsive genes under hypoxic conditions (Ozer et al, 2005). The interaction with HPH-2 requires the ING4 PHD domain; interestingly, such domain has been recently shown involved in the association with histone H3K4me2/3 (Pena et al, 2006;Shi et al, 2006).…”

MOZ and MORF, two large MYSTic HATs in normal and cancer stem cells

“…PHD fingers may also function as methyl-lysine-binding modules. One PHD finger of NURF recognizes trimethyl lysine 4 of histone H3 to couple ATP-dependent chromatin remodeling to histone methylation Wysocka et al, 2006), and the PHD finger of ING2 binds to the same mark to stimulate methylation-dependent deacetylation (Pena et al, 2006;Shi et al, 2006). Moreover, methylation of histone H3 at lysine 4 promotes association with yeast Yng1, a subunit of the NuA3 acetyltransferase complex (Martin et al, 2006;Taverna et al, 2006).…”