Functional Dissection and Mechanism of Action of Plant PHD-Finger Proteins: A Research Progress Review

Abstract The PHD (Plant Homeodomain) finger is a class of zinc finger domain that is widely conserved across eukaryotes. This domain not only mediates protein–protein interactions but also recognizes specific histone methylation marks, thereby modulating the structural state of chromatin at target gene loci and influencing gene expression. Based on the domain composition features, this review proposes a classification framework for plant PHD-finger proteins and provides a systematic account of the biological functions and mechanisms of action of representative members, including Alfin-like, VIN3-like, and MS1 proteins. Acting as transcription factors, these proteins play critical regulatory roles in plant growth, development, and stress responses through diverse mechanisms, such as regulating gene expression, remodeling chromatin architecture, and participating in SUMOylation modifications. Finally, this review discusses future perspectives and key research directions concerning the PHD finger domain in plants. Among the classified subfamilies, Ehd3 and MMD1 both belong to Class I single-PHD-only proteins without extra auxiliary domains, which is clearly defined in our domain-based classification framework.