Meristemania · Lohmann Lab
Research programme — Stem cell biology

How a handful of cells
builds an entire plant.

Plants grow throughout their lives from small populations of stem cells held in shoot and root meristems. We work out how those populations are specified, maintained, and tuned — in space, in time, and in changing environments.

3D confocal rendering of an Arabidopsis shoot apical meristem with the WUSCHEL organising centre in green and CLV3-expressing stem cells in red at the apex.
Shoot apical meristem of Arabidopsis · WUS organising centre (green), CLV3 stem cells (red).

At the tip of every shoot, a self-organising niche of stem cells supplies the cells that will become stems, leaves and flowers — for the lifetime of the plant.

We dissect the regulatory logic of this niche — from single transcription factor–DNA contacts to whole-meristem dynamics — and ask what makes it robust.

Four lines of inquiry

01 — 04
Axis 01 — transcriptional core

WUSCHEL and the architecture of the stem cell niche

The homeodomain transcription factor WUSCHEL is necessary and sufficient to specify stem cell identity in the shoot apex. We dissect WUS function mechanistically — mapping direct and indirect targets in a cell-type-resolved way, characterising the cofactors and chromatin states it depends on, and asking how a single short-range signal sustains a population of cells across decades of growth.

WUSCHELCLAVATAprotein movementcis-regulation

Foundational · Lohmann et al., Cell 2001 · Leibfried et al., Nature 2005 · Busch et al., Dev Cell 2010 · Daum et al., PNAS 2014 · Fuchs et al., bioRxiv 2024

Axis 02 — context-dependent networks

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, with the labs of Boutros, Huber and Stegle, we combine tissue-targeted, conditional CRISPR/Cas9 perturbations with single-cell transcriptomics and live imaging in the Arabidopsis root tip and the Drosophila gut, then infer the direct, cell-state-specific networks that underwrite tissue robustness and plasticity.

conditional CRISPRsingle-cell RNA-seqgene×gene interactionscausal inferencenetwork plasticity

Foundational · Gaillochet et al., eLife 2017 · Liu et al., Mol Plant 2021 · Zeng et al., Nat Commun 2023 · Grones et al., Plant Cell 2024 · Wang et al., Nature 2025

Axis 03 — hormonal integration

Cytokinin, auxin and the whole-plant conversation

The stem cell niche does not act alone. 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 at protein turnover, including the trade-off between growth and defence in the shoot apex.

cytokininauxinjasmonategrowth vs. defencesignal integration

Foundational · Leibfried et al., Nature 2005 · Zhao et al., Nature 2010 · Schuster et al., Dev Cell 2014 · Gaillochet et al., eLife 2017 · Ma et al., Nat Commun 2019 · Fan et al., bioRxiv 2026

Axis 04 — environment, adaptation & regeneration

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 short-term acclimation converges with long-term adaptation across natural Arabidopsis variation. The same dimensions govern regeneration: in RegenerateRobust (GreenRobust Cluster of Excellence, with the Marciniak-Czochra and Dagdas labs), we map how temperature and autophagy set its limits across Marchantia, Arabidopsis and Brachypodium.

temperaturelight & sugar signallingnatural variationregenerationautophagycross-species comparison

Foundational · Wigge et al., Science 2005 · Pfeiffer et al., eLife 2016 · Pfeiffer et al., Curr Opin Plant Biol 2017 · Janocha et al., bioRxiv 2024 · Baulies et al., Nat Plants 2025

Methods & mindset

An integrated programme — from base-pairs to whole plants.

Top row: three genetically identical Arabidopsis thaliana plants grown under different conditions — short day 23 °C, long day 23 °C, long day 17 °C. Bottom row: rosettes of genetically diverse Arabidopsis accessions grown under identical conditions.
Arabidopsis thaliana — top row: genetically identical plants grown under diverse conditions (short day 23 °C; long day 23 °C; long day 17 °C). Bottom row: genetically diverse accessions grown under identical conditions. Two faces of the same question: how does one genome read many environments, and how do many genomes meet one environment.
Why Arabidopsis

A reference plant — and a conceptual system.

We use Arabidopsis thaliana for its unmatched experimental toolkit — dense genetic resources, fast transformation, a community-curated genome, and mature reporter and imaging systems. But the questions are not specific to one species: the principles that emerge allow conclusions about stem cell control across the tree of life.