New publication from the lab! Winter cold doesn't just make plants flower. Long cold also primes them to regenerate🌱❄️. We show cold-induced CBFs recruit HAG1 to switch on key regeneration genes like WOX5. Many congrats to @fu-yu-h.bsky.social! www.cell.com/developmenta...
Many thanks to @keikosugimoto.bsky.social for hosting me and for her support and guidance throughout, to all coauthors and collaborators @johannakrahmer.bsky.social, @deveylderlab.bsky.social, and Mitsuhiro Aida for their contributions.
My postdoc preprint is now online @biorxiv-plants.bsky.social. We established HYDRA, a shoot regeneration assay in Arabidopsis without exogenous hormones, and show that photosynthesis-derived carbon drives regeneration via RBR1 pathway–mediated cell cycle activation. www.biorxiv.org/content/10.6...
Photosynthesis-derived carbon gates cell cycle activation to enable hormone-autonomous shoot regeneration
Shoot regeneration is a powerful model for cell fate reprogramming but how it occurs in nature remains poorly understood because studies in Arabidopsis thaliana conventionally rely on in vitro assays ...
biorxiv.org
Excited to share that I will start my lab this summer as an ECL Unit Leader at RIKEN CSRS! We will study perception by cell-surface receptors across diverse plant species. I’ll be recruiting soon, so please reach out if you’re interested!
🌱✂️ Wounding activates HSFA1 to drive reprogramming. HSFA1 turns on WIND1, PLT3, and ZAT6. SUMOylation keeps it in check #plantscience @theplantcell.bsky.social @duncan-coleman.bsky.social @wigge.bsky.social @deveylderlab.bsky.social @keikosugimoto.bsky.social academic.oup.com/plcell/advan...
Wounding activates the HSFA1 transcription factors to promote cellular reprogramming in Arabidopsis
The HEAT SHOCK FACTOR A1 transcription factors rapidly accumulate in the nucleus after wounding and directly activate regenerative pathways in plants.
academic.oup.com
Huge congratulations to Beverley Glover & Uta Paszkowski on being elected Fellows of the @royalsociety.org - a wonderful recognition of their significant contributions to plant sciences! 🎉 Read more: tinyurl.com/3vetucr4 @beverleycubg.bsky.social @paszkowskilab.bsky.social 🧪
Thrilled to announce our newest preprint on #dedifferentiation in Arabidopsis 🧬🌱. We used scRNA-seq and hormone treatments to track transcriptional reprogramming in diverse somatic cell types and found what we think is some pretty cool biology. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
Fantastic 2 days to discuss plant cell plasticity and latest single cell & spatial technologies at our ASPIRE & GreenTE gathering 🌱🍃🌿! Many thanks to @PaszkowskiLab & @JST_ASPIRE ❤️.
Not sure which scRNA-seq platform to use for 🪴 plant samples? How well do doublet detection algorithms really work in 🌱? How can I optimise sample prep ? Find out in our benchmark study! Led by @carogro.bsky.social and @thomaseekhout.bsky.social. Open access at EMBO Journal: doi.org/10.1038/s443...
Benchmarking plant single cell RNA-sequencing sample processing strategies - The EMBO Journal
The isolation of single plant cells from complex tissues is prone to selective enrichment and sampling biases, which complicates accurate profiling of the large diversity in cell types. Optimizing methodologies for cell enrichment and single-cell transcriptomics is therefore critical for single-cell studies addressing plant cell heterogeneity. Here, we systematically compared protoplast enrichment technologies (including conventional and image-based flow cytometry, as well as magnetic cell sorting) and single-cell RNA sequencing (scRNA-seq) platforms (10X Genomics Chromium, BD Rhapsody) using Arabidopsis roots. Image-based flow cytometry offered increased precision due to customizable gating strategies, while magnetic sorting provided faster processing and enhanced representation of cell size heterogeneity. Both scRNA-seq platforms captured root cell heterogeneity and yielded reproducible gene expression profiles, but showed platform-associated differences in cell type composition. Notably, single-nucleotide polymorphism analysis of a mixed ecotype sample revealed that, among cells identified as doublets by computational algorithms, two-thirds were likely to have been misclassified. These insights identify key biases in plant cell purification and scRNA-seq workflows and provide practical guidance for improving data quality across plant species.
doi.org
Are you an aspiring PI? Interested in Japan? It's application season for our ECL program! 🧪 check out the details here: https://www.riken.jp/en/careers/programs/riken_ecl/call2026/index.html #sciencejobs #STS #STEMjobs
And latest summary on "wound-triggered plasticity in plant regeneration" out in Current Opinion in Genetics and Development. Fun writing with Max Minne www.sciencedirect.com/science/arti...
Wound-triggered plasticity in plant regeneration
Plant regeneration exemplifies the remarkable developmental plasticity of plants, yet how regenerative programs are initiated and spatially restricted…
sciencedirect.com
Our new preprint! Winter-like extended cold primes plants for regeneration🌱❄️! Work by Fu-Yu Hung, now a new PI in Taiwan!
bioRxiv Plant Bio@biorxiv-plants.bsky.social · 4mo agoProlonged cold exposure enhances regeneration potential in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.04.20.719581v1
How do plants respond to wounding? Well it it's not too dissimilar to how they respond to heat. We found that plants utilize the HSFA1 transcription factors to rapidly induce wound-induced regeneration genes after injury. @keikosugimoto.bsky.social @deveylderlab.bsky.social @wigge.bsky.social
Wounding activates the HSFA1 transcription factors to promote cellular reprogramming in Arabidopsis
The HEAT SHOCK FACTOR A1 transcription factors rapidly accumulate in the nucleus after wounding and directly activate regenerative pathways in plants.
doi.org
Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social
Huge congratulations to Ramin & Birnbaum lab🤩! Very happy we are copublishing complementary work with you guys. Grateful to @JST_ASPIRE for supporting our collaborative efforts in plant regeneration research 🌱.
Molecular Plant & Plant Communications@mplantpcom.bsky.social · 5mo agoHistone deacetylases and cell cycle regulators orchestrate cell identity transitions during Arabidopsis root regeneration #research #MolecularPlant cell.com/molecular-pl...
Many congrats to Akira!
Molecular Plant & Plant Communications@mplantpcom.bsky.social · 5mo agoWIND1 controls cell fate transition through coordinately integrating histone acetylation and deacetylation-mediated transcriptional reprogramming during somatic embryogenesis #research #MolecularPlant cell.com/molecular-pl...
We are very excited to share a new resource from our team: spatial subcellular proteome maps in plants! We developed an MS-based method that registers localizations of about 8000 proteins in Arabidopsis roots in a single experiment. (1/9) www.biorxiv.org/cgi/content/...
biorxiv.org
I am organizing a concurrent session “Cellular reprogramming and organ regeneration” at #ICAR2026 together with @charlesmelnyk.bsky.social! Submit your abstract by Feb 22 (for oral) and share your exciting science with us🌿 icar2026.sg
ICAR 2026
icar2026.sg
This is a very special paper for me. I had the idea of combining transcription factor binding with chromatin in 2016/8. It took some time, but thanks to Fred and Vikas, we can finally share the story in @plos.org Genetics looking at chromatin states in Arabidopsis and Marchantia. #PlantScience
Chromatin state architecture governs transcription factor accessibility across plant genomes
Author summary In eukaryotes, DNA is tightly associated with histone proteins. Histone covalent modifications and histones isoforms, also called histone variants provide most of the complexity of chro...
journals.plos.org
It's been a busy time in the Paszkowski lab! First, a pre-print on how rice distinguishes friend (AM fungi)🍄 from foe (pathogens)👾: doi.org/10.1101/2025... And second, a review on single-cell omic approaches to understand the spatially and temporally complex AM symbiosis 🔬: doi.org/10.1093/jxb/...
Defining the pre-symbiotic transcriptional landscape of rice roots
Plants interact with a plethora of organisms in the rhizosphere, with outcomes that range from detrimental to beneficial. Arbuscular mycorrhizal (AM) symbiosis is the most ubiquitous beneficial plant ...
doi.org
Only a few days left to apply! My group is looking for a postdoc to engineer and deploy new tools to precisely manipulate and decode how auxin coordinates plant morphogenesis. @starmorph-syg.bsky.social Research Associate - Reprogramming Development (closes 7 October 2025)
cam.ac.uk
(Part 2) “From my first visit, I was struck by the energy and excitement...It feels like being a graduate student again, chasing curiosity wherever it leads." @hhmi.org Investigator David Stern will join the Stowers Institute in Feb. 2026 from @hhmijanelia.bsky.social. Read more: bit.ly/4np96Fb
(Part 1) Hear from @hhmi_news Investigator David Stern about his research program and what he's uncovering in the lab. Stern will join the Institute in February 2026, bringing his lab and HHMI appointment to Kansas City. @hhmi.org Read more: bit.ly/4np96Fb
How do plants regenerate after wounding? Our new work shows that HSFA1 transcription factors are among the earliest wound-activated regulators of cellular reprogramming in plants!
bioRxiv Plant Bio@biorxiv-plants.bsky.social · 11mo agoWounding activates the HSFA1 transcription factors to promote cellular reprogramming in Arabidopsis https://www.biorxiv.org/content/10.1101/2025.09.29.679115v1
It's official! We are moving to Stowers! Very exciting opportunity to expand our studies of insect-plant interactions. We have many opportunities available in biochemistry, development, behavior, genetics, evolution, genomics, AI, and even pest control. Interested in any of these things? Reach out!
Stowers Institute@stowersinstitute.bsky.social · 11mo agoNEWS🎉 We’re excited to announce @hhmijanelia.bsky.social Investigator David Stern will join the Institute from Janelia Research Campus. His lab studies how aphids transform plants at the genetic level, uncovering secrets of #evolution & new strategies for pest control. @hhmi.org bit.ly/4np96Fb
Please share & RSVP to join the November 25th webinar! Hear from the 2025 Philip N. Benfey Arabidopsis Community Lifetime Achievement Awardees! bit.ly/naascawards @plantevolution.bsky.social
