Prof. Jan Lohmann Stem Cell Biology
The department of Stem Cell Biology investigates how a small, self-organising niche of cells at the shoot apex specifies, maintains, and tunes the plant stem cell population that builds every leaf, stem and flower a plant will ever make — and how it does so across days, seasons, and generations. We pursue an integrated programme combining classical and CRISPR genetics, single-cell and spatial transcriptomics, biochemistry, multi-angle confocal live imaging, and computational modelling, using Arabidopsis thaliana as a reference system.
Plant stem cells - founders of life
Plant stem cells reside at the growing points of each individual — the root tip and the shoot apex — and are embedded into specialised structures called meristems, which provide a local environment that regulates the balance between proliferation and differentiation. Because plant cells are surrounded by a rigid cell wall and cannot migrate, growth and morphogenesis depend on the tightly controlled interplay of cell division and cell expansion. Local and mobile signals, including plant hormones, are integrated to produce complex tissues across the plant’s entire life.
Research directions
- WUSCHEL and the architecture of the stem cell niche. How does the homeodomain transcription factor WUSCHEL specify and maintain stem cell identity at the shoot apex — and how does a single short-range signal sustain a population of cells across decades of growth? We map its cell-type-resolved targets, cofactors and chromatin context.
- Decoding context-dependent genetic networks in vivo. Which genetic activities are required in each cell of a developing tissue, and how does that requirement shift as the cell’s state and environment change? Through the ERC Synergy project DECODE, we combine tissue-targeted conditional CRISPR/Cas9 perturbations with single-cell transcriptomics and live imaging in the Arabidopsis root tip.
- Cytokinin, auxin and the whole-plant conversation. Hormonal signals — chiefly cytokinin, auxin and jasmonate — couple meristem behaviour to the developmental, metabolic and defensive state of the whole plant. We map where these pathways intersect the WUS circuit and how their balance is integrated at transcription and protein turnover, including the trade-off between growth and defence in the shoot apex.
- Sensing the world — acclimation, regeneration and growth. Daylength, temperature, light and nutrients all modulate meristem activity. We ask how the niche senses environmental information, how it meets the metabolic hub of TOR-kinase signalling to set growth, and how the same dimensions govern regeneration. As part of the GreenRobust Cluster of Excellence, we map how temperature and autophagy set the limits of regeneration across Marchantia, Arabidopsis and Brachypodium.
Approaches
To address these questions, we employ an integrated approach leveraging classical and CRISPR genetics; GreenGate cloning; bulk and single-cell/nucleus transcriptomics; spatial multi-omics; recombinant protein expression with in vitro DNA-binding and protein–protein interaction studies; multi-angle live confocal imaging; mathematical and AI/ML modelling — in collaboration with the labs of Marciniak-Czochra, Velten, Sinning, and the DECODE partner labs (Boutros, Huber, Stegle).
Group leader
Jan Lohmann is full professor and head of the Department of Stem Cell Biology at COS, and from 2026 Dean of the Faculty of Biosciences, Heidelberg University. From 2013 to 2025 he was Speaker of the Collaborative Research Centre SFB 873. His research has been recognised by the Lautenschläger Research Prize (2025), an ERC Synergy Grant (“DECODE”, 2018), election to EMBO (2015), the Research Prize of Heidelberg University (2014), an ERC Starting Grant (2011), the President’s Medal of the Society for Experimental Biology (2009), the EMBO Young Investigator Award (2005), and an HFSP Career Development Award (2003).
Funding
Our work is supported by funds from a variety of public sources, including the DFG, the ERC and the GreenRobust cluster of excellence.
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