Chromatin Recognition Protein Modules: The PHD Finger

Abstract

Abstract The structure of chromatin controls the accessibility to deoxyribonucleic acid (DNA) information. Posttranslational modifications (PTMs) of histones modify the architecture of chromatin and provide docking platforms for proteins that control many DNA‐templated processes. The plant homeodomain (PHD) fingers are small protein domains found in nuclear factors that interact with chromatin. Recent studies have characterised two classes among the PHD fingers, which specifically bind to either unmodified or trimethylated K4 histone H3. A number of PHD finger structures in complex with histone peptides reveal the recognition mechanisms. The combination of multiple histone PTMs, the cooperation between different PHD fingers or between PHD fingers and other histone recognition proteins illustrate the plurality and versatility of this protein module. Mutations or translocations in PHD fingers that affect their interaction with histones have been related to immunological diseases, cancer or mental retardation. Key Concepts: Histone modifications form part of the chromatin control of DNA‐templated processes. PHD fingers are small nuclear protein domains that bind two zinc ions in an interlaced topology. Several PHD fingers specifically recognise the di‐ and trimethylated K4 histone H3 tail, and others bind specifically to unmethylated K4 histone H3. Aromatic cages are cavities formed by the side chains of 2–4 aromatic residues used by PHD fingers and by other protein modules for binding to methylated lysines. Alterations of the histone recognition by PHD fingers are related to immunological diseases, cancer and mental retardation.