A comprehensive understanding of heterosis has long been out of reach. Led by super postdoc Luguang Jiang, we applied scifi-ATAC-seq to three 🌽 inbred lines and their recip hybrids, and identified a widespread loss of cell-type-specific ACRs in hybrid genomes 🧬 1/10 www.biorxiv.org/content/10.6...
So proud to share our latest publication @CellCellPress! Yue Rui reveals that the same enzyme that makes the wall, cellulose synthase complex (CESA), also tethers the plasma membrane to the wall during water-deficit stress, providing resilience. sciencedirect.com/science/articl…
New preprint! The same TFs can drive distinct regulatory programs depending on where they bind. TSS → rapid stress responses Intronic & upstream → cell-type programs Enhancer-like CRMs → embryo/meristem programs Coding-sequence binding → repression www.biorxiv.org/content/10.6...
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
Absolutely delighted that our paper on epigenetic dynamics during plant aging is out today in Science! www.science.org/doi/10.1126/...
Aging drives a program of DNA methylation decay in plant organs
Plants display a wide range of life spans and aging rates. Although dynamic changes to DNA methylation are a hallmark of aging in mammals, it is unclear whether similar molecular signatures reflect ra...
science.org
Given the described activators of cambium growth, we reasoned repressors were needed to balance the system. Here they are! www.biorxiv.org/content/10.6... Discovery: Xing, Jingyi, Emma, Riikka, Anne-Maarit, Julia, Qing, Hanan, Raluca, Joanna, Yuqi, Wiki #plantscience #plantdev
biorxiv.org
Our paper is out in MBE! doi.org/10.1093/molb... We tracked TF binding site evolution across 589 grass species, and found that while binding preferences are pretty stable over 80 million years of evolution, individual binding sites have turned over a lot. Thread here: bsky.app/profile/char...
Charlie Hale@charleshale.bsky.social · last yr.New preprint from my PhD! How cis-regulatory evolution shaped grass diversification worldwide www.biorxiv.org/content/10.1... We looked across 589 (!) grass species to ask: — What regulatory changes enabled grasses to adapt? — How can this inform crop breeding for resilience? Here’s what we found:
Targeting T-DNA to a specific locus using CRISPR From: onlinelibrary.wiley.com/doi/full/10....
Versatile Applications of CRISPR‐Based Programmable T‐DNA Integration in Plants
Agrobacterium-mediated T-DNA integration into plant genomes represents a cornerstone for transgenic expression in plant basic research and synthetic biology. However, random T-DNA integration can dis...
onlinelibrary.wiley.com
Thank you to everyone who attended the 1st Great Lakes Plant Science Conference and helped make it a success! This inaugural meeting brought together 416 registrants from 55 institutions. Together, we’ve built momentum for the future of #plantscience in the Great Lakes region and beyond! #GLPSC2025
MSU is great place to do plant science research. My lab will be a great place to develop new expertise in genomics and plant molecular biology. Application instruction and link: careers.msu.edu/jobs/researc... Please email me if you have any questions.
Research Associate-Fixed Term - East Lansing, Michigan, United States
Position Summary The Li lab in the Department of Plant Biology is recruiting a postdoctoral research associate to work on project(s) in plant molecular biology, biochemistry, and/or genomics. The idea...
careers.msu.edu
Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe. Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Plant cells are totipotent, meaning individual cells have the potential to develop into a full organism, a property unique to the zygote for animals. However, in most species for most cells, plant cells are not spontaneously totipotent, since they must be treated with specific hormone combinations to unlock their totipotency. Species within the Kalanchoe genus is unique as they spontaneously develop foliar embryos that are fully realized plantlets with shoot and root from notches along the edges of leaves. We speculate that the progenitor cells that give rise to these foliar embryos are totipotent, and we are using single cell techniques to identify & characterize them. In addition to being a fundamental process for plant biology, we foresee unlocking totipotency has many biotechnological applications, such as faciliating genetic transformation and the development of synthetic organs of biomanufacturing.
cxli233.github.io
Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com: Drought recovery in plants triggers a cell-state-specific immune activation. doi.org/10.1038/s414... Read thread below 👇
Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications
Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.
doi.org
delighted to share work from my postdoc @cshlnews.bsky.social - here, we use TurboID in maize meristems to be able to resolve CLV receptor interactions, unlocking its potential to resolve in vivo receptor interactions important for meristem signaling.
bioRxiv Plant Bio@biorxiv-plants.bsky.social · last yr.Antagonistic interactions between CLAVATA receptors shape maize ear development https://www.biorxiv.org/content/10.1101/2025.08.04.667500v1
Single-cell-level response to drought in Sorghum bicolor reveals novel targets for improving water use efficiency https://www.biorxiv.org/content/10.1101/2025.08.28.671794v1
Our new Nature Plants paper is out (and we’re on the cover 😁)!👉 bit.ly/4lS8sOB By combining scRNA-seq with conserved TF binding (multiDAP) we define gene regulatory networks for 65 cell types across 4 tissues in a wide range of flowering plants!
A great example of how comparative genomics across the full range of vascular plant lineages can be used as a catalyst for gene discovery! Exciting new single cell datasets for gymnosperms, ferns and lycophytes! The scale of this study is really amazing! www.cell.com/cell/fulltex...
A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery
A cross-species single-cell atlas highlights a core subset of cell-type foundational genes associated with major vascular plant cell types, enabling the identification of hidden cell types and the dev...
cell.com
The August issue is now fully online, with a beautiful cover that might be a nostalgia trigger for some of us (young people can find an explanation in the Editorial): www.nature.com/nplants/volu...
This project was a huge team effort with five(!) co-first authors, including JGI scientists @leobaumgart.bsky.social, @abmora.bsky.social, Peng Wang, and Yu Zhang each playing crucial roles, and @omalley-regulome.bsky.social at the helm. An amazing group!
