An analysis of the PHD‐finger domain in arabidopsis and rice using bioinformatics, functional genomics and biochemistry

The Plant HomeoDomain (PHD) zinc finger was first identified in plants, though its presence is nearly ubiquitous in eukaryotes. It consists of a zinc‐binding Cys4‐His‐Cys3 motif. Recent reports have determined that conserved residues within some PHD fingers allow binding to trimethylated Lys4 of histone H3 (H3K4me3), an important chromatin modification associated with transcriptional activity. In addition, some PHD fingers have been shown to bind to specific phosphatidylinositol phosphates (PtdInsPs), which may be important for nuclear membrane localization. We have undertaken a bioinformatic analysis of the PHD finger in plants. In Arabidopsis, 76 separate PHD finger domains were identified in 66 different proteins. Most of these proteins also contained a domain annotated as functioning in chromatin remodeling, suggesting a major role for PHD containing proteins in this process. From this analysis we predict that only a small group of PHD fingers from plants bind to H3K4me3. In contrast, we predict that many plant PHD fingers have the ability to bind PtdInsPs. To test the prevalence of PtdInsP binding by plant PHD fingers, we cloned and expressed a group of plant PHD proteins and have demonstrated that they are able to bind to PtdInsPs. To begin to understand the function of the plant PHD domain, we have identified and characterized an Arabidopsis loss‐of‐function mutant in the plant ortholog of the mammalian ING2. NSF award to G.G. MCB# 0316705