H3K4 Methylation Readers in Plants: Recognition Mechanisms and Biological Functions

Methylation of histone H3 at lysine 4 (H3K4me) is a key epigenetic mark in plants, governing transcriptional regulation, development, and stress adaptation. While the enzymes that deposit and remove this mark are well studied, how H3K4me signals are interpreted by reader proteins remains less understood. This review synthesizes recent advances in the molecular recognition of H3K4me states by plant reader domains, including PHD, BAH, CW, Tudor, and chromodomain modules. Unlike prior reviews that focused on writers and erasers or on stress-specific responses, we systematically examine the reader-side mechanisms, with particular emphasis on how distinct methylation states, including trimethylated (H3K4me3), dimethylated (H3K4me2), monomethylated (H3K4me1), and unmethylated H3K4, are discriminated and translated into chromatin-based outputs. These readers function as signaling hubs, integrating environmental and hormonal cues to regulate flowering, DNA repair, and stress memory, with implications for crop performance. However, fundamental gaps remain, including the identification of H3K4me1-specific readers, the structural basis for combinatorial histone mark recognition, and the evolutionary divergence of reader pathways between monocots and dicots. Our review provides a framework for understanding H3K4me reader biology and explores its potential for application in plant breeding.