The research group led by Prof. Cao Xiaofeng at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, recently unveiled the cooperative roles of photoreceptors, epigenetic modifiers, and transcription factors in light-responsive gene regulation in plant.
Light serves as both the energy source for photosynthesis and a critical environmental signal that regulates various developmental processes in plants, including seed germination, seedling morphogenesis, leaf development, stem elongation, flowering time, circadian rhythms, and shade avoidance. Upon seedling exposure to light from soil, light signals rapidly activate photomorphogenesis, characterized by suppressed hypocotyl elongation, expanded and greened cotyledons, and initiation of photosynthesis—a pivotal phase in early plant development.
Plants have developed sensitive light signaling systems to fine-tune photomorphogenesis in dynamic light environments. Epigenetic modifications, particularly histone covalent modifications, play essential roles in regulating plant growth and environmental responses. Among these, histone H3 lysine 27 trimethylation (H3K27me3) is a key repressive mark that maintains gene silencing, with its dynamic regulation critical for cell fate determination and development in both plants and animals.
CAO’s research group previously identified and characterized REF6/JMJ12, an H3K27me3 demethylase in Arabidopsis, elucidating its targeting mechanism and roles in plant development and ambient temperature responses. In this study, they employed chromatin profiling, transcriptomics, biochemical and genetic approaches to systematically decipher the molecular mechanism by which REF6 participates in red light signaling.
Phenotypic analyses revealed that REF6 loss-of-function mutants exhibited markedly shortened hypocotyls under light, whereas mutants of other H3K27me3 demethylases (JMJ11, JMJ13, JMJ30 and JMJ32) showed no significant phenotypic changes, indicating the dominant role for REF6 in photomorphogenesis.
Further investigations demonstrated that REF6 protein accumulation and H3K27 demethylase activity were significantly enhanced under red light compared to darkness. Red light-activated phytochrome B (phyB-Pfr) physically interacts with REF6, stabilizing REF6 protein and enhancing its chromatin-binding capacity. This interaction facilitated the expression of cell elongation-related genes in open chromatin states. Then, REF6 synergizes with the phyB-PIF4 module to finely regulate hypocotyl growth under continuous light, ensuring proper plant development.
By integrating light signaling with epigenetic regulation, this study expands the multidimensional regulatory framework of photomorphogenesis. It highlights how photoreceptors, epigenetic factors, and transcription factors collaboratively fine-tune hypocotyl growth in fluctuating light environments—a sophisticated strategy critical for plant adaptation.
The work, titled “The Arabidopsis demethylase REF6 physically interacts with phyB to promote hypocotyl elongation under red light”, was published online in Proceedings of the National Academy of Sciences (PNAS) on March 10, 2025 (https://doi.org/10.1073/pnas.2417253122).
This work was supported by grants from the National Natural Science Foundation of China, the Youth Talent Support Project of the China Association for Science and Technology, and the Youth Innovation Promotion Association of the Chinese Academy of Sciences.
T
he histone H3K27 demethylase REF6 regulates plant photomorphogenesis. (Image by IGDB)
Contact:
Dr. CAO Xiaofeng
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Email: xfcao@genetics.ac.cn
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