🧬 SPECIAL ISSUE REVIEW 🧬 In this review, Lee & Seo highlight the hierarchical organization of plant genomes, emphasizing recent advances in understanding local chromatin structures shaped by cohesins and gene borders as fundamental structural units. 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...

CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1

Can we tune a plant’s epigenetic toolkit to disrupt plant homeostasis in ways that enable phenotypic innovation? 🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social! www.sciencedirect.com/science/arti...

Have you ever wondered how new DNA methylation patterns are established? Paradigm shift ahead! We discovered a new mode of DNA methylation targeting in plants that relies on transcription factors and sequence motifs rather than chromatin modifications to regulate the methylome. rdcu.be/eQ6L5 1/8

Editor’s Pick! Silvia Minana-Posada et al. combined multiple approaches to investigate how the wheat pathogen Zymoseptoria tritici responds to and recovers from temperature shocks. Read the open access Editor’s Pick to learn more: https://doi.org/10.1094/PHYTO-02-25-0057-R

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis! www.nature.com/articles/s41...

Extensive horizontal transfer of transposable elements shapes fungal mobilomes @currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social www.cell.com/current-biol...

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system https://www.biorxiv.org/content/10.64898/2025.12.02.690432v1

New online! The biodiversity, genomics, ecology and evolution of mushroom-forming fungi

#paper How do organisms adapt to changing environments? Through plasticity, evolution, or a combination of both? Find out in our new paper by Alger Jorritsma, where we show which strategies evolve under different environmental conditions. @journal-evo.bsky.social academic.oup.com/evolut/advan...

FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples www.nature.com/articles/s41...

Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...

Very proud to have our latest work now online in @natsmb.nature.com. A wonderful team effort across the centromere community, across @jansenlab.bsky.social @naltemose.bsky.social @dfachinetti.bsky.social and Giunta labs. Happy reading! 1/4 www.nature.com/articles/s41...

#TEsky FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum doi.org/10.1186/s131...

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file. No RNA-seq. No protein homology. No repeats, hints, or curated evidence. Raw genome → accurate gene models. Deep learning + HMM, published in @natmethods.nature.com www.nature.com/articles/s41...

Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....

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.

Improved gene annotation of the fungal #wheat pathogen #Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence doi.org/10.1094/MPMI...

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1

Nature research paper: Specificity, length and luck drive gene rankings in association studies go.nature.com/47Fsqax

New OA Article: "Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana" rdcu.be/ePaOY GWAS identifies CDCA7 as a regulator of DNA methylation in Arabidopsis thaliana . CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.

Lifestyles shape genome size and gene content in fungal pathogens. buff.ly/tec1Tds

Packed room for Emma Corre's PhD defense on transposable elements in rust fungi genomes. Congratulations Dr @emma--c.bsky.social 👏👏👏 And what a lovely tribute to Barbara McClintock who discovered transposable elements in 🌽!!!

My awesome grad student Shashank and I wrote this paper trying to look at broader patterns of HT in TEs. HT is happening everywhere! DNA transposons jump further than other classes! www.biorxiv.org/content/10.1...

Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!

Epigenetics Update - RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis go.nature.com/47jvfiF Guifang Jia (Peking University) in Nat Plants #Epigenetics #Plants #Chromatin --- Empower your research with high-res epigenetic insight at epigenometech.com

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes! www.biorxiv.org/content/10.1...

Want to understand how entire fungal chromosomes can be horizontally transferred? Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available. fungal-evolutionary-genetics.de/open-positio...

Thrilled to share our most recent paper describing the antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular mycobacteria in macrophages and zebrafish. Outstanding work headed by Yara Tasrini, John Jairo Aguilera Correa, Miguel Gisbert and others. rdcu.be/eAcN4

Hominoid-specific retrotransposons fuel regulatory novelty in early brain development , by @retrogenomics.bsky.social. ➡️ www.cell.com/cell-genomic...

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

🚨 First pre-print from my team !! TL;DR: presence of polymorphism (sequence differences between the homologous chromosomes) can *increase* the local rate of recombination in Arabidopsis thaliana, turning cold regions of the genome hot (purple v. grey) !

Weng et al. examined 431 genomes of butterflies and related lineages, revealing that horizontal transfer of digestion and detoxification genes facilitated the evolution of herbivory, enabling butterflies to co-evolve with angiosperm hosts. 🔗 doi.org/10.1093/gbe/evaf156 #genome #evolution #HGTsky

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance www.nature.com/articles/s41...

📝New preprint! #MicroSky 🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy. 🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation. www.biorxiv.org/content/10.1...

Apple is entering the protein folding arena. SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;) www.nature.com/articles/s41...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life. www.nature.com/articles/s41...

Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply! Please repost!

Come and join our team! A 2-year postdoc position is available in our "Genome Evolution" department at Univ Paris Saclay. We want to play with phylogenetic models accounting for horizontal transfers of transposable elements. Application& details on the official portal: emploi.cnrs.fr/Offres/CDD/U...

Check out our new preprint! We compare sequence versus synteny approaches for resolving a challenging #phylogenetic problem. In this case, synteny is far more informative! Also includes the first chromosome-level #genome for the enigmatic #fish family Gyrinocheilidae. doi.org/10.1101/2025...

New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3 Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.

Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below! doi.org/10.1126/scie...

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity. But how does piRNA-guided target interaction translate into silencing? PhD student Júlia Portell Montserrat has an intriguing answer www.cell.com/molecular-ce...

Active learning enables discovery of transcriptional activators across fungal evolutionary space https://www.biorxiv.org/content/10.1101/2025.09.12.675635v1

Our new review is out in Trends in Cancer. We had fund writing this :) We discuss the roles of retrotransposons in immune modulation in normal and malignant hematopoiesis. www.cell.com/trends/cance...

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods https://www.biorxiv.org/content/10.1101/2025.08.29.672809v1

Vesalius 2.0 is in ‪‪@natcomms.nature.com‬ ! We show how using spatial context improves cell-to-cell mapping across heterogenous spatial samples. Thanks to the reviewers, editors, and collaborators for making this possible. GitHub: github.com/WonLab-CS/Ve... Paper: www.nature.com/articles/s41...