Edge CMT: epigenetic regulation of heat stress memory in photosynthetic cells

The National Science Foundation's Division of Integrative Organismal Systems awarded $1.6M to the Donald Danforth Plant Science Center under the Biological Sciences program (CFDA 47.074) on December 15, 2025, to investigate the epigenetic regulation of heat stress memory (HSM) in photosynthetic cells. The three-year project (through November 30, 2028) focuses on understanding how plants tolerate repeated high temperatures through studying the unicellular green alga Chlamydomonas reinhardtii, which exhibits transgenerational, inheritable heat stress memory for 4–6 stress-free generations. The research aims to identify the mechanisms underlying HSM through epigenetic regulation analysis, with applications for improving crop resilience and agricultural productivity in response to elevated temperatures. The project will also generate computational tools as community resources and develop education and outreach activities to engage researchers studying plant stress responses.

The grant includes collaborative research contributions from two sub-awardees awarded in December 2025 and January 2026. Washington University will conduct systems-wide analysis of chromatin dynamics and histone modifications during heat stress memory induction, maintenance, and termination under the direction of Co-PI Dr. Xuehua Zhong. The University of Missouri System's Cheng Lab will apply bioinformatics and machine learning methods—including differential expression analysis, deep autoencoders, and gene regulatory network modeling tools (GNET2 and GRNFormer)—to integrate transcriptomics, methylation, and histone modification data to identify genes and epigenetic features critical to HSM mechanisms. The sub-awardees will also conduct comparative sequence analysis and phylogenetic studies across plant species to determine evolutionary relationships of HSM proteins.

Abstract

Changing variable environments are causing plants to respond to repeated high temperatures impairing plant growth and reducing crop yields. To engineer crops with improved thermotolerance, IT is crucial to understand how plants tolerate repeated high temperatures. Plants that experience moderate high temperatures can survive subsequent extreme lethal heat. This acquired heat tolerance is critical for plant survival, but its underlying mechanisms are unclear. Photosynthesis, the process by which plants use sunlight to produce food, is one of the most heat sensitive functions in plant cells. Understanding how photosynthesis responds to repeated high temperatures remains largely unexplored. This proposal focuses on the mechanisms controlling short-term stress memory over multiple generations using cultures of green algae, which share similar photosynthetic mechanisms with land plants and model plants grown in soil. The research will help improve crop resilience to environmental stress, drive innovative agricultural solutions in response to elevated temperatures, and engage a broad range of researchers who study stress responses in plant cells. The project will also form the basis of education and outreach activities designed to equip mentees at various levels and implement computational tools as community resources to the scientific community and the public. Unicellular green alga chlamydomonas reinhardtii exhibits transgenerational, inheritable heat stress memory (HSM) for 4-6 stress-free generations but the mechanisms are unknown. IT is hypothesized that the mechanisms underlying HSM may involve epigenetic regulation. Chlamydomonas is an excellent model to determine these generalizable mechanisms because of its fast growth rate, haploid genome, simple gene families, high-throughput phenotyping techniques, and relatedness to land plants. The project has three specific research aims. Aim 1 will employ systems-wide omics approaches (RNA-SEQ, atac-SEQ, histone proteomics, and chip-SEQ) along with computational methods to investigate transcriptional and epigenetic changes associated with HSM to determine the molecular basis of HSM. Aim 2 will dissect the function and mechanism of heat shock FACTOR1 (CRHSF1, the master regulator of heat responses) and FORGETTER1 (CRFGT1, a putative chromatin remodeler) in HSM. Aim 3 will validate the function of HSM candidate genes using quantitative, high-throughput, pooled phenotyping of mutant collections. Highly conserved, novel HSM gene candidates will be selected and functionally verified in dicot and monocot models. This research addresses fundamental biological questions about how plant cells tolerate repeated high temperatures, particularly focusing on photosynthetic processes. The project integrates genomics, machine learning, physiology, and genetics, to build a comprehensive regulatory framework of stress memory in photosynthetic cells. This research is poised to make a substantial impact on our understanding of epigenetic regulation of HSM. Given that the basic mechanisms regulating chromatin dynamics and gene expression are highly conserved the results are expected to provide insights into the memory mechanisms of other stresses. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are planned for this award.