Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers https://www.biorxiv.org/content/10.64898/2026.05.21.726779v1

New preprint from the Vecchiarelli Lab! 🧵 Congratulations to first author Dr. Claire Dudley! @claire-dudley.bsky.social Claire uncovered a critical player in the organization for the photosynthetic cytoplasm of cyanobacteria - polyphosphate! #polyP www.biorxiv.org/content/10.6...

Plants are unique in that single somatic cells have the remarkable potential to dedifferentiate and regenerate entirely new plants. However, the cell types and regulatory dynamics enabling dedifferentiation competence have not been fully explored... until now ⬇️ (1/12)

#dedifferentiation depends on cell type. This is what happens when you make protoplasts 👌

How do cells break symmetry to generate new shape and form? Using the apical hook as a model, we @joeecker.bsky.social applied spatial and single-cell multiomics, and identify a regulatory hotspot in a transient cell niche that drives this U-shaped structure 1/8 bsky.app/profile/bior...

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...

New OA Resource: "A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination" rdcu.be/fj8H2 Single-nucleus RNAseq profiling of early Arabidopsis seed development. #PlantScience

Excited to share that I will be opening my lab this fall at the @weizmanninstitute.bsky.social in the Department of Plant & Environmental Sciences! I am looking for postdocs interested in plant biology, stress biology, and single-cell technologies. #PlantBiology #SingleCell #Epigenomics #Postdoc

I would encourage plant genomics folks to attend -- organizers are interested in more plant people, and while you have to listen to weird things like cancer, there's lot of technologies and ideas that plant folks could benefit from hearing.

We are very happy and proud to present a study led by @jorgehg.bsky.social (now PI in Madrid – keep an eye on him!) in our team @bic-wur.bsky.social. In this work, we discover how auxin-regulated ARF transcription factors learned to activate transcription. A 🧵…(1/17) www.biorxiv.org/content/10.6...

A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵

This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...

📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...

The maize community is so privileged to have the amazing support of @maizegdb.bsky.social. I don’t think we could do most of what we do without them. Check out their most recent work including large dna model prediction of effects here academic.oup.com/genetics/art...

Thank you, Vanessa, Mike and all involved! So many cool findings described in this work, including parallel evolution of leaf shape and the rapid radiation of Scalesia after genome doubling and Galápagos arrival.

Fantastic paper led by Matthew Davis from @grey-monroe.bsky.social, on genome degradation in long-term walnut tissue culture: Somatic embryogenesis increases mutation rates >30x, with aneuploidy, large deletions, somatic recombination, and elevated #TE activity. www.pnas.org/doi/10.1073/...

Latest paper from the lab with several collaborators: We've built a four-dimensional spatial transcriptome atlas of barley grain development and germination, allowing detailed interrogation of where and when genes are expressed academic.oup.com/plcell/artic...

We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

FYI: New online! Gene regulatory networks: from correlative models to causal explanations

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

Our first study on how the leaf succulent Kalanchoë laxiflora makes stomatal subsidiary cells is finally peer-reviewed & out - and it made the cover! 🌵 🧬 🔬 doi.org/10.1126/scia... Despite 150 years of evolution, grasses and Crassulacean succulents use the SAME gene to make subsidiary cells! 🤯

🌱💚🎉 Sharing (again 😁) my review on regulation of chloroplast biogenesis. First work of my emerging research group at @cbgpmadrid.bsky.social

🔥Fantastic paper!🔥 TE with a role in vegetative phase change and gametogenesis, mediated by 24-nt siRNAs acting in trans to a wide range of genes. Found by GWAS in A. thaliana 🌱. Congratulations to the authors! 👏🏻👏🏻👏🏻 #epigenetics #plantscience www.pnas.org/doi/10.1073/...

#TansleyInsight: Masters of perception: phosphorylation-dependent signaling in plants Mark Roosjen, Justin W. Walley & Dolf Weijers 👇 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... #LatestIssue #PlantScience

Faculty position in Plant Molecular Biology (Associate Professor or Tenure-Track Assistant Professor) at Aarhus University, Denmark mbg.au.dk/aktuelt/ledi...

🪴Postdoc position - UT Austin, TX, USA - Developmental Mechanisms of Adaptation to Underwater Environment/Genome Editing🪴 Do you love amphibious/aquatic plants? Then consider applying to the position! See the attached ads. utaustin.wd1.myworkdayjobs.com/UTstaff/job/...

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

DNA replication globally disrupts the epigenome. But does this create a chromatin-access opportunity for TF binding to facilitate cell identity change? Now 𝐫𝐞𝐩𝐥𝐢-𝐀𝐓𝐀𝐂-𝐬𝐞𝐪 shows 𝘥𝘦 𝘯𝘰𝘷𝘰 chromatin opening & TF binding occurs specifically post-replication, in cellular differentiation & reprogramming!

Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.

🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneT

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain https://www.biorxiv.org/content/10.64898/2026.02.07.704075v1

New paper! From Sam Snodgrass and @genomeofforrest.bsky.social, w/ @druncie.bsky.social, @gcbias.bsky.social, and a collaboration with Andres Moreno and @santiagogmm.bsky.social. Can we quantify the impact of humans on maize dispersal? Plant yourself in a comfy chair and lend me your ear: 1/10

🧵 Just out in Cell after more than 10 years in the making! 🎓 www.cell.com/cell/fulltex... Plants and animals evolve radically different body plans. Do they also operate under fundamentally different molecular evolutionary constraints during organ formation? @cellpress.bsky.social

The plant ontology of cell types #comment #MolecularPlant cell.com/molecular-pl...

Well done, Akie! Identification of a peptide hormone-receptor module bypassing the ABA signaling to close stomata upon drought. A big breakthrough🍃😊 -Local peptide signalling induces stomatal closure under drought stress @natcomms.nature.com www.nature.com/articles/s41...

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Bob was incredible. I spoke with him a week before he passed and all he wanted to talk about was his plans for teaching in the Spring. He was an amazing scientist and pushed for teaching excellence in the department at every meeting. He will be sorely missed. newsroom.ucla.edu/stories/in-m...

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...

NSF policy changes - some updates that PIs should be aware of. www.nsf.gov/policies/doc...

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at [email protected] if you have questions. www.nsf.gov/funding/oppo...

Interesting study suggesting that nucleus, cytoskeleton, and endomembranes preceded acquisition of mitochondria, during eukaryogenesis www.nature.com/articles/s41...

🚀 New preprint! We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱 🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1 #Genomics #GeneRegulation #Maize #Soybean

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

By combining molecular genetics with cell-ablation experiments, we found that vascular cambium stem cells and xylem-identity cells form an interchangeable unit, a stem cell niche. Meticulous work by @xixizhang9001.bsky.social, Ondrej Smetana, Jing Zhang & Xiaoyu Wang 1/x www.pnas.org/doi/10.1073/...

Our latest paper has just been published in Cell! doi.org/10.1016/j.ce... We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

Interested in learning about the latest and greatest research in how plants respond to excess salt, too little or too much water? Come to the GRC in Salt and Water Stress in Switzerland. Lots of opportunities for all career levels. www.grc.org/salt-and-wat.... Please repost!

My department at Dartmouth Medical School is hiring a tenure-track Assistant Professor. We are looking broadly for a biochemist or cell biologist. Please share this add! apply.interfolio.com/171438 @dartmouthbcb.bsky.social @futurepislack.bsky.social

Advances in plant spatial multi-omics data analysis #plantscience