Regulation of the DNA repair system under abiotic stress
Lucas Gabriel Machain
Collaborators: All members of the EU-HeatDDR consortia
Background: Securing sustainable food production for a growing world population under changing climates is a global challenge for agricultural crop production. Farmers are confronted with dynamic environmental stresses that impair plant growth and negatively impact crop yield. Fortunately, plants have adaptive resilience strategies to handle environmental changes and to survive these challenges. Heat and drought are two major abiotic stresses that reduce crop yield, with heat attracting increasing attention due to global warming and the growing occurrence of extreme temperature events. From a biological perspective, mechanisms that enable plants to cope with heat stress are not fully understood. Thus, leveraging adaptive heat stress mechanisms could help developing crops with superior development and yield performance under increasingly harsh conditions.
Project: Heat stress triggers DNA breaks in plant genomes with potentially fatal consequences for cell survival and, particularly, for cell division in meristematic tissues. We will conduct single-cell RNA sequencing to identify points of convergence between DNA damage and heat stress responses in underlying gene regulatory networks. These analyses will rely on established gene network analysis pipelines to dissect regulatory hubs at cell age and cell type resolutions and to eventually establish a gene network atlas of DNA damages and heat stress responses at single cell resolution.
Lab tools / techniques: Cell type-specific and single-cell RNA-seq/transcriptomics, gene network analyses, bioinformatic promoter prediction, cell cycle/growth assays, CLSM, Comet assay
Relevant publications:
Rich-Griffin, C., Eichmann, R., Reitz, M. U., Hermann, S., Woolley-Allen, K., Brown, P. E., Wiwatdirekkul, K., Esteban, E., Pasha, A., Kogel, K. H., Provart, N. J., Ott, S., & Schäfer, P. (2020) Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots. Plant Cell 32: 2742–2762.
Rich-Griffin, C., Stechemesser, A.H., Finch, J., Lucas, E.S., Ott, S., Schäfer, P. (2020) Single-cell transcriptomics - a high-resolution avenue for plant functional genomics. Trends in Plant Science 25:186-197.
Huang, Y., An, J., Sircar, S. et al. HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions. Nat Commun14, 469 (2023). https://doi.org/10.1038/s41467-023-36227-3
Kaduchová K, Šály P, Kashkan I and Pecinka A (2025) Heat stress suppresses DNA replication and mitosis in barley root apical meristems. Front. Plant Sci. 16:1679234. doi: 10.3389/fpls.2025.1679234