The tumor suppressor inhibitor of growth 4 binds double‐stranded DNA through its disordered central region

Abstract

The tumor suppressor inhibitor of growth 4 (ING4) regulates chromatin structure by recruiting the histone acetyl transferase complex HBO1 to sites with histone H3 trimethylated at K4. ING4 dimerizes through its N-terminal domain and recognizes H3K4me3 by the C-terminal plant homeodomain (PHD). The central region of ING4 is disordered and contains the nuclear localization signal. Here, utilizing electrophoresis and nuclear magnetic resonance, we show that ING4 binds double-stranded DNA through its central region with micromolar affinity. Our findings suggest that the cooperativity arising from the presence of two DNA-binding regions in the ING4 dimer, as well as two H3K4me3-binding PHD fingers, may strengthen nucleosome binding and HBO1 complex recruitment.

DisorderING promotes epigenetic order

“…As also pointed out by the authors , isoforms of ING4 lacking the PHD have been described and the biological activities of ING2 in promoting muscle differentiation appear to be independent of the PHD . This suggests that the interaction of the IDR/NLS of the INGs with DNA may impart biological functions to the ING family of proteins beyond their suspected role of strengthening nucleosome binding.…”

“…Having previously shown that interacting amino termini of ING4 proteins promote formation of homodimers that are capable of targeting carboxyl ING4 PHDs to adjacent histones, the Blanco group has explored the function of the disordered central region of ING4 that was previously identified as a nuclear localization sequence (NLS) containing nucleolar‐targeting signals . As shown in Fig.…”

“…As shown in Fig. , ING4 dimers, and most likely other ING protein homo‐ and heterodimers given their sequence conservation in this region , can form dimers through their amino termini, leaving their PHDs free to interact with nearby H3K4Me3 residues of nucleosomes . While multiple interactions would clearly promote local epigenetic modification by the acetylation complexes that associate with the INGs , how such complexes might favour modification of histones within the same or nearby nucleosomes is unclear.…”

“…The recent observations by Ormaza et al . suggest that intranucleosomal modification might be favoured as a consequence of the IDR/NLS of ING4 binding DNA. The ~ 85 amino acids of the ING4 IDR/NLS contains 20 basic (Lys, Arg) residues that could promote electrostatic interaction with DNA, as well as 26 residues that are secondary structure breakers (Gly, Pro, Asp, Asn, Ser).…”

Inhibitor of growth protein 4 interacts with Beclin 1 and represses autophagy

“…It appears intriguing that ING4, which is generally viewed as a transcription-regulatory factor interacting with methylated histones (in particular H3K4me3) [ 48 ] and DNA [ 49 ] has major cytoplasmic functions as well. However, ING4 reportedly acts on NF-κB as an E3 ubiquitin ligase [ 36 ], and at least a fraction of ING4 is located in the cytoplasm [ 24 ], supporting the possibility that it exerts important extranuclear functions.…”