Cecile Lorrain

Thrilled to share our paper now out in Nature Plants 🎉 We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype. www.nature.com/articles/s41...

🧵 Out today in Nature Communications! How did an ancient reshuffling of the genome shape 3D genome architecture and gene regulation in squid, cuttlefish & octopus? 🦑🐙 We combined Micro-C, RNA-seq & ATAC-seq across species, developmental stages & tissues. doi.org/10.1038/s41467-026-77625-7

It's live! The next @embo.org #EvoChromo meeting will take place next year October in St Feliu de Guíxols (Spain), check it out here: meetings.embo.org/event/27-chr.... It's been great to co-organise with @dodonova-sveta.bsky.social @kellervalsecchi.bsky.social @cedricfeschotte.bsky.social & Nick I.

Killer meiotic driver prevents chromosome loss and enhances fitness in a fungal pathogen https://www.biorxiv.org/content/10.64898/2026.10.04.756499v1

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)

Transcription factors read a second regulatory code in chromatin https://www.biorxiv.org/content/10.64898/2026.09.23.753737v1

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics https://www.biorxiv.org/content/10.64898/2026.09.17.752431v1

Another step in the #Starship story - they move via a circular intermediate. Helps explain how these elements horizontally transfer and means that we can modify them into transformation vectors (starmids). www.biorxiv.org/content/10.6...

Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...

E-PAN training materials can be found on the @ergabiodiv.bsky.social Knowledge Hub knowledge.erga-biodiversity.eu?search=e-pan

The LBGB team at @genoscopeumr.bsky.social, led by @jm-aury.bsky.social, recently released Hobrac, a tool to investigate synteny between genomes! Can be used for assembly validation or comparative genomics. doi.org/10.64898/202... github.com/Genoscope-LB... See below for what Hobrac can do:

Very happy to see our Nature Reviews Genetics article on programmed DNA elimination across eukaryotes out! A fantastic collective effort with an amazing group of colleagues, born from inspiring discussions at the Fondation des Treilles. rdcu.be/tmvKgsPZNhBa @laurarossevo.bsky.social

Evseeva et al. sequenced a historic plant pathogen outbreak that swept across the island of Martinique, highlighting the role of horizontal transfer in shaping the ecological success of the emerging pathogen Ralstonia spp. 🔗 academic.oup.com/gbe/article/... #societyjournal #genome #evolution

How do nuclear compartments form inside cell nuclei? We show RNA glues certain loci together to form a nuclear compartment. This involves special GC-rich regions of highly expressed genes that also associate with nuclear speckles, but interactions between these loci are independent of speckles!

Spray- vs. Host-induced gene silencing: what 89 studies reveal about fighting fungal disease Patrick Barth, Jakob Drumm, Alexandra Erika Schmidt, Florian Hartig and Aline Koch nph.onlinelibrary.wiley.com/doi/10.1111/... #PlantScience @florianhartig.bsky.social

🚨 ‼️ NEW PUBLICATION ‼️ While we start to know a lot about how bacterial genomes are organized in 3D, almost nothing is known about phage genome once it enters a bacterial cell. read the paper here: www.science.org/doi/10.1126/...

Chromatin-Assisted Targeting Enables Precise DNA Methylation Editing in Plants https://www.biorxiv.org/content/10.64898/2026.08.25.747117v1

TEDDY: An integrative workflow for TE-chimeric isoform reconstruction and systematic characterization of TE-dependent transcriptional regulation https://www.biorxiv.org/content/10.64898/2026.08.22.746432v1

Love it! "Equally important though is how a 'basic science' observation in studies of *3D genome reorganization* during senescence can lead to 'applications'!" Congrats Papantonis Lab! 👇🏻👇🏻👇🏻👇🏻👇🏻

Delighted and very proud to see our study (and Anna-Maria's first first-author paper) recently out in PNAS: www.pnas.org/doi/10.1073/... @cambiochem.bsky.social @cruk-ci.bsky.social 1/5

A pathogen α-L-arabinofuranosidase degrades host-derived immunogenic oligosaccharides to suppress plant immunity https://www.biorxiv.org/content/10.64898/2026.08.18.742768v1

New paper with Nick Davies and Kevin Foster in @natcomms.nature.com. We show that often neither selection against transposons’ deleterious effects nor exploitation by parasitic elements is sufficient to keep them in control. Only active host suppression does. www.nature.com/articles/s41...

Out Now! Complex multicellularity is linked with expanded specialized metabolite production in microorganisms #MicroSky

Ruibao's first paper from the lab is out in @nature.com . www.nature.com/articles/s41.... Collab with @multicellgenome.bsky.social & @jennahed.bsky.social. How did cells stick together and form the first animals? The protist Ministeria suggests cellular aggregation had a role. @iuqcb.bsky.social

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

This adds another piece to an emerging evolutionary picture: many fungal effectors may not have evolved de novo to manipulate hosts. Instead, they started as antimicrobial proteins to compete with other microbes — and were repeatedly repurposed as fungi adapted to host-associated lifestyles.

New GreenRobust publication by the group of Eric Kemen on using machine learning to identify beneficial microbiota: www.nature.com/articles/s41...

📣 New preprint! 🧵 Fantastic work led by @antonkraege.bsky.social Fact: Cerato-platanins are everywhere in fungi. Found across the fungal kingdom, implicated in everything from development to virulence to immune activation. But what do they *actually* do? We finally found the answer 👇

Excited to share that our paper on Horizontal Gene Transfer is now out in its final form in @gigascience.bsky.social! 🥳 By analysing 163 high-quality ant genomes, we show that HGT from bacteria is widespread across the ants and likely has adaptive functions! doi.org/10.1093/giga... 🐜📸: Alex Wild

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

our paper starts with an analysis of the dynamics of 3D chromatin in cardiac differentiation, for ventricular and atrial cardiomyocytes. They are different! And by single cell methyl-HiC we can discern subtype differences. www.science.org/doi/10.1126/...

Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides https://www.biorxiv.org/content/10.64898/2026.07.20.739560v1

Super proud and excited about this work, led masterfully by Peiwei Chen! A fun and fruitful collaboration with department colleagues Andy Clark & Alexei Aravin. After 30 yrs of studying transposons, this is one of the very first times I see them jump in real time in their natural host! Hurrah! 🥳

Very interesting and comprehensive study using synthetic activation of enhancers to probe the rules of distal vs. proximal gene regulations:

COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi https://www.biorxiv.org/content/10.64898/2026.07.03.736376v1

🐦 Why are bird genomes so difficult to assemble? Birds have dozens of tiny, gene-rich microchromosomes that are frequently fragmented, misplaced, or missing from genome assemblies despite containing important genetic information. 📖 Read the publication: lnkd.in/gar-GrKZ #BirdGenomics #Biodiversity

Gene regulatory networks to decipher tomato multi-pathogen interactions Multari et al. nph.onlinelibrary.wiley.com/doi/10.1111/...

Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!

A conserved architectural domain shapes centromere evolution in Drosophila https://www.biorxiv.org/content/10.64898/2026.06.30.735607v1

Interested on latest research on the evolution of the first forms of life? Drop by Inder Raj Sing's poster, where he will be showing work from his GBE paper on pre-LUCA TF evolution. 📋 Poster Session A 🗓️ June 29, 6 pm Read the paper here 👉 doi.org/10.1093/gbe/evag141 #SMBE2026 #societyjournal

🌾🧬Plants face multifactorial stress, not single stressors. Combination specific regulatory modules coordinate protective pathways like ROS buffering. Integrative tools offers a path to climate smart crops #plantscience @abioticstress.bsky.social www.sciencedirect.com/science/arti...

Novel Drosophila cis-regulatory elements can be uncovered by footprinting transcription factor binding sites in ATAC-seq data https://www.biorxiv.org/content/10.64898/2026.06.22.733832v1

PhD position open @inrae-bioger.bsky.social ⬇️

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes https://www.biorxiv.org/content/10.64898/2026.06.14.732207v1

"A role for epigenetics in rapid adaptation" by Reid S. Brennan & Melissa H. Pespeni "Epigenetic variation may be key to rapid adaptation and can interact with genetic change during evolutionary rescue. However, key questions remain.." FREE till Aug. 7th at authors.elsevier.com/a/1nH%7EscQb...

Nearly a year after our symposium on Repeat-Induced Point (RIP) mutations, I’m happy to share the fruit of some of our discussions. The fungal RIP hypermutator mechanism has deep eukaryotic roots www.sciencedirect.com/science/arti... We hope to spark interest in this underappreciated mechanism.

LIKE HETEROCHROMATIN PROTEIN 1: a Polycomb-beyond composite regulator of chromatin in development, stress, and defense doi.org/10.1093/plce... #PlantScience @aspbofficial