Molecular Basis of Histone H3K4me3 Recognition by ING4

Abstract

The inhibitors of growth (ING) family of tumor suppressors consists of five homologous proteins involved in chromatin remodeling. They form part of different acetylation and deacetylation complexes and are thought to direct them to specific regions of the chromatin, through the recognition of H3K4me3 (trimethylated K4 in the histone 3 tail) by their conserved plant homeodomain (PHD). We have determined the crystal structure of ING4-PHD bound to H3K4me3, which reveals a tight complex stabilized by numerous interactions. NMR shows that there is a reduction in the backbone mobility on the regions of the PHD that participate in the peptide binding, and binding affinities differ depending on histone tail lengths Thermodynamic analysis reveals that the discrimination in favor of methylated lysine is entropydriven, contrary to what has been described for chromodomains. The molecular basis of H3K4me3 recognition by ING4 differs from that of ING2, which is consistent with their different affinities for methylated histone tails. These differences suggest a distinct role in transcriptional regulation for these two ING family members because of the antagonistic effect of the complexes that they recruit onto chromatin. Our results illustrate the versatility of PHD fingers as readers of the histone code.Regulation of chromatin dynamics dictates the outcome of fundamental nuclear processes such as DNA transcription replication and repair (1-3). It is central to cell homeostasis, because alterations in chromatin structure contribute to the development of cancer and other human diseases (4). The ING 6 family of tumor suppressors consists of five homologous proteins implicated in chromatin remodeling, growth arrest, and, in cooperation with p53, senescence and apoptosis (5-7). They are frequently deregulated in different types of cancer (8) and contain a conserved C-terminal PHD finger (9) that is present in many nuclear proteins involved in gene expression regulation and chromatin remodeling (10). They form stable histone acetylation or deacetylation complexes (11) and are thought to direct them to specific regions of the chromatin through binding of their PHD fingers to histone 3 N-terminal tails trimethylated at lysine 4 (12, 13). These binding properties link ING proteins with actively transcribed genes, because H3K4 trimethylation is a hallmark of active genes (14). The recognition of H3K4me3 by ING2 is critical for the occupancy of the mSin3A-HDAC1 complex at the promoter of the cyclin D1 gene, which results in histone deacetylation and transcriptional repression of the active gene in response to DNA damage (15). This result suggests a general active transcriptional repression role for ING2; nonetheless, the biological outcome of the recognition of methylated histone tails by the other ING proteins is still unclear. Different PHD fingers link H3K4me3 recognition with gene activation, such as the PHD of the bromodomain PHD finger transcription factor, which helps to recruit the nucleosome remodeling factor complex to target ...

Inhibitor of growth-4 promotes IκB promoter activation to suppress NF-κB signaling and innate immunity

“…These nuclear proteins have been proposed to play roles in numerous biological functions by interacting with different acetylation and deacetylation complexes involved in chromatin remodeling and gene expression (10,11). In addition, biochemical analysis has indicated that ING4 interacts with methylated histone H3 (12)(13)(14) and with the HB01-JADE-hEAF6 histone acetyltransferase complex (11). This latter complex is responsible for most nucleosomal histone H4 acetylation in eukaryotes, and knockdown experiments indicated that Ing4-HB01 association is required for cells to progress properly through the DNA synthesis (S) phase of the cell cycle (15,16).…”

Citrullination of Inhibitor of Growth 4 (ING4) by Peptidylarginine Deminase 4 (PAD4) Disrupts the Interaction between ING4 and p53

“…ING4 is a native subunit of an HBO1 histone acetyltransferase complex and contains a C-terminal conserved PHD finger that recognizes methylated histone H3 (H3K4me3) (37,38). This interaction between ING4 and H3K4me3 promotes HBO1 acetylation of H3.…”

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

“…Protein solutions (dialysed against PBS, pH 7.0, 2 mM TCEP) were titrated with concentrated peptide stocks prepared by dissolving the lyophilized peptides in the dialysis buffer and adjusting the pH to 7.0 with NaOH, if necessary. The binding isotherms were analysed by non-linear least-squares fitting of the experimental data to a model assuming a single set of equivalent sites 48 . Data analysis employed Microcal Origin (OriginLab) and in-house developed software.…”