Uriel Urquiza-García
I build synthetic plant chromosomes — DNA molecules that never existed before — and test whether they can function as autonomous, heritable units inside living cells. The central question is whether a complex gene regulatory network, the plant circadian clock, can be modularised and reconstructed on a synthetic neochromosome in Physcomitrium patens. Answering this requires solving the full stack of chromosome engineering: telomere acquisition, centromere boot-up, replication, and faithful segregation.
Research
The programme establishes plant synthetic genomics as a constructive discipline. We do not recode existing chromosomes — we build new ones from scratch and ask whether they can boot up inside a plant cell. The organising biological question, whether the circadian clock depends on its native genomic context or is modular and portable, was conceived during my PhD and is now testable because the synthetic chromosome platform makes it so.
Synthetic neochromosome assembly
We assemble large synthetic DNA directly in P. patens using an iterative integration system based on alternating selectable markers, allowing successive rounds of assembly without marker exhaustion. The current 42 kb construct was assembled as three fragments in a single transformation, demonstrating that the moss HDR machinery can handle multi-fragment knock-ins at scale.
RepTiles HDR P. patensCentromere boot-up
A chromosome without a centromere is just a DNA fragment — it cannot segregate. Based on centromere seeding strategies published for animals and plants we are attempting this centromere booting up, an active area of research in the group.
CENH3 neocentromere optogeneticsChromosome liberation & maintenance
Once the neochromosome body carries functional centromere and telomere elements, it must be excised and maintained as an episomal unit. The liberation strategy uses nuclease cutting at flanking sites, enzymatic exposure of pre-seeded telomeric ends. Replication origin strategy and segregation fidelity measurement remain active areas of development.
telomere seeding chromosome liberation counter-selectionCircadian clock relocation
The highest-risk, highest-reward component of the programme. The plant circadian clock is a gene regulatory network scattered across the genome — at least 20 genes on multiple chromosomes, interacting through transcriptional feedback loops. We will reconstruct it on the synthetic neochromosome and ask: does it tick? If it does, the clock is modular with respect to genomic context. If it doesn't, we learn which dependencies are hardwired into chromosomal architecture. The quantitative readout system — NanoLUC-based absolute protein quantification, developed in my MSB 2025 paper — is already built and validated.
clock modularity NanoLUC gene regulatory network JTF grantBiodesign automation & plant optogenetics
RepTiles provides automated hierarchical assembly design for generating large synthetic DNA from community-standard Golden Braid parts. PolyGEN enables multiplexed CRISPR using polycistronic tRNA-gRNA (PTG) arrays. A plant optogenetic system enables light-controlled gene expression in stable transgenic plants. These tools are integrated into the synthetic chromosome platform for programmable control of biological functions.
RepTiles Golden Braid PolyGEN plant optogeneticsWhy Physcomitrium patens?
The choice of chassis came from direct experimental failure. After two years of attempting yeast-based TAR cloning for large plant DNA assemblies, I recognised that the standard intermediary approach was a bottleneck, not a solution. P. patens has the highest native homologous recombination efficiency of any land plant, is haploid (simplifying genotyping), and regenerates from single cells — enabling clonal analysis of engineered lines in weeks rather than months. This insight preceded the broader community's recognition of moss as a synthetic genomics chassis and was arrived at independently, from first principles.
Selected publications
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Abundant clock proteins point to missing molecular regulation in the plant circadian clockMolecular Systems Biology (2025)
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Gearing up Golden Braid assembly for plant synthetic genomics with RepTilesbioRxiv (2025) — preprint · doi
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Cryptochrome 1 promotes photomorphogenesis in Arabidopsis by displacing substrates from the COP1 ubiquitin ligaseThe Plant Journal (2025)
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Testing the inferred transcription rates of a dynamic, gene network model in absolute unitsin silico Plants (2021)
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Expanding the bioluminescent reporter toolkit for plant science with NanoLUCPlant Methods (2019)
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Better research by efficient sharing: evaluation of free management platforms for synthetic biology designsSynthetic Biology (2019)
Full list on Google Scholar.
Funding
John Templeton Foundation — "Bottling Time"
Grant ID 63576. Reconstructing a moss's inner clock through synthetic genomics. Testing whether the circadian clock is modular and genetically portable — whether its function depends on native genomic architecture or can be reconstituted on a synthetic neochromosome.
HHU Strategic Research Fund (SFF)
Expansion of the neochromosome technology platform and biomedical peptide production applications.
CEPLAS Seed Fund
Establishing the plant synthetic genomics research line within the Cluster of Excellence on Plant Sciences. Awarded November 2022 — the founding grant of the programme.
CEPLAS Collaborative Research Support
Collaboration with Dr Emily Wheeler on artificial origins of replication, and publication support.
Group
Dr Uriel Urquiza-García — Group Leader
Technician
MSc Student
MSc Student
Key collaborators: Dr André Marques (MPI Plant Breeding Research / CEPLAS — chromosome biology) · Prof Björn Usadel (FZ Jülich / HHU / CEPLAS — computational plant biology, embedded in JTF grant) · Prof Matias Zurbriggen (HHU — synthetic biology) · Dr Emily Wheeler (artificial origins of replication)
Teaching & supervision
I teach MSc course M2209 in Synthetic Biology and Biotechnology at HHU Düsseldorf. Student theses span two pillars: molecular control (optogenetics, CRISPR, programmable gene regulation) and chromosome engineering (DNA assembly, centromere targeting, telomere strategy). Seven BSc theses in the synthetic genomics pillar collectively address every essential structural component of the plant artificial chromosome — three of these students are co-authors on the RepTiles preprint, with a BSc student (V. Petrova) as first author.
A central aim is to train the first generation of plant synthetic genomics researchers in Germany — students with hands-on experience in chromosome engineering, quantitative biology, and biodesign automation.
Trajectory
I trained at the National Autonomous University of Mexico (UNAM) in the Genomic Sciences programme, where I participated in iGEM 2009 and won a travel grant for an oral presentation at the Synthetic Biology Conference at Stanford. I completed my MSc and PhD at the University of Edinburgh on competitive international scholarships, working on quantitative models of the plant circadian clock with Andrew Millar at SynthSys. The question that now organises the programme — whether the clock is modular with respect to genomic context — crystallised during the PhD, but answering it required a synthetic chromosome. That requirement drove everything that followed.
My doctoral work with Andrew at Edinburgh produced the MSB 2025 paper on absolute protein quantification of clock transcription factors — the first such measurement in any plant system — which provides the quantitative readout infrastructure now embedded in the JTF experimental logic. The NanoLUC approach, the ODE model refactoring, and the sequence-to-affinity pipeline all trace back to this period.
I entered Photobiology with Karen Halliday in my first postdoctoral period in Edinburgh. After which I relocated to Düsseldorf to join Matias Zurbriggen as CEPLAS postdocotral researcher working in plant optogenetics, reconstruction biology and in general plant synthetic biology.
Since 2023, I have led the Plant Synthetic Genomics group at HHU Düsseldorf, embedded in CEPLAS and the Institute of Synthetic Biology. The programme was built through a deliberate escalation of competitive support — from CEPLAS seed funding (November 2022), through the HHU Strategic Research Fund, to international competitive funding from the John Templeton Foundation — and is now preparing applications for competitive funding at the European level.
Contact
Institute of Synthetic Biology
Heinrich Heine University Düsseldorf
Building 26.24, Room 00.068
Düsseldorf, Germany
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