Cecile Lorrain

Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen Abstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines.

Fouché, @oggenfussursula.bsky.social, McDonald & @danielcroll.bsky.social retrace chromosomal degeneration in a fungal pathogen, identifying the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles.

🔗 doi.org/10.1093/gbe/evag037

#genome #evolution

🔥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/...

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors https://www.biorxiv.org/content/10.64898/2026.03.06.710197v1

Genome modelling and design across all domains of life with Evo 2 - Nature Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology.

Nature research paper: Genome modelling and design across all domains of life with Evo 2

go.nature.com/4aMo9Vu

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture Nature Microbiology, Published online: 03 March 2026; doi:10.1038/s41564-026-02260-3Analysis of 37 genomes together with more than 140 phenotypic traits links genomic features to ecological fitness and lifestyle diversity in Trichoderma fungi.

Out Now! Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture #MicroSky

There is a week left to apply for two available positions in my lab @ipbhalle.bsky.social

- PhD: ipb-halle.mhm.jobs/12-phd-posit...

- Postdoc: ipb-halle.mhm.jobs/13-postdocto...
Earliest start date: 01/05/2026.

We are interested in plant immune receptor biochemistry and evolution. Please share!

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

🚨 We’re happy to announce (finally!) the publication of METALoci, in collaboration with @dariloops.bsky.social and heroes: @jrotwitguez.bsky.social & @imotagom.bsky.social.

METALoci integrates #3DGenome and #Epigenetics data into a unified framework we believe is very useful!

Here 👉🏻 rdcu.be/e5sm2

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements Nature Genetics - This Perspective explores the co-evolution of transposable elements and KRAB zinc-finger proteins in relation to their integration into human gene regulatory networks,...

KRAB zinc-finger proteins (KZFPs) are the most abundant family of DNA-binding proteins in humans and primarily induce the epigenetic silencing of transposable elements

www.nature.com/articles/s4...

DNA-damaging combination treatments impose genotype-specific constraints on hypermutator evolvability https://www.biorxiv.org/content/10.64898/2026.02.20.706947v1

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.

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C https://www.biorxiv.org/content/10.64898/2026.02.18.706586v1

Exited to share Current Opinion review on how chromatin hubs involving multiple enhancers and promoters are formed, and their potential roles in gene regulation: www.sciencedirect.com/science/arti...

"Leveraging allelic imbalance in accessible chromatin to prioritize putative causal variants"
by Shea Ping Yip, Chien-Ling Huang, & co

"By leveraging allelic imbalance in ATAC-seq, researchers can bridge the gap between GWAS signals and molecular mechanisms..."

authors.elsevier.com/sd/article/S...

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

www.nature.com/articles/s41...

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

Happy to share our new review on Polycomb-mediated 3D chromatin interactions! Thanks to @mileshuseyin.bsky.social and @andersshansen.bsky.social for great discussions throughout the process :)

New Article: "Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function" rdcu.be/e4yHX

PhytoBabel is an AI model designed to capture the semantic similarity of cis-regulatory sequences across distant species.

Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites Abstract. The evolution of sociality involves shifts in physiology and behavior, most notably the emergence of a reproductive division of labor. Within soc

Ploessl & Jones compared transcription factor binding motifs in 42 bee species, covering multiple independent gains and losses of sociality; findings demonstrate an expansion of TF motifs in lineages which have gained sociality.

🔗 doi.org/10.1093/gbe/evag003

#genome #evolution

Adaptive evolution of transcriptome and transcriptomic plasticity in stable and fluctuating environments https://www.biorxiv.org/content/10.64898/2026.02.16.706080v1

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...

🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

Methods Mol Biol: Nuclei Isolation from Mature Leaves of Arabidopsis thaliana Infected by Bacterial Pathogens for Single-Nucleus Multi-Omics (2026) Single-nucleus omics technologies are increasingly applied in plant biology to investigate transcriptional and chromatin regulation at cellular resolution. A key requirement for these approaches is the isolation of high-quality nuclei, which can be particularly challenging in plant tissues due to cell wall complexity and residual debris. Here, I present a streamlined protocol for isolating nuclei from fresh Arabidopsis thaliana leaves infected with the bacterial pathogen Pseudomonas syringae. This method eliminates the need for density gradient separation and fluorescence-activated nuclei sorting (FANS), reducing hands-on time while maintaining compatibility with single-nucleus RNA and ATAC sequencing using the 10x Genomics platform.

New Publication: Nuclei Isolation from Mature Leaves of Arabidopsis thaliana Infected by Bacterial Pathogens for Single-Nucleus Multi-Omics (2026)
https://www.tsl.ac.uk/publications/163626

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful...

🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉

Postdoctoral position in biology (m/f/d) (2/2026) Leibniz Institute of Plant Biochemistry (Halle) offers a Postdoctoral position in Biology

Please share! We are looking for a postdoctoral scientist (2 years, extension possible) starting from 01/05/2026 at
@ipbhalle.bsky.social! The project focuses on plant immune receptor biochemistry and structural biology.
Deadline 09/03/2026.

Apply at: ipb-halle.mhm.jobs/11-postdocto...

Top: FK506-resistant strains isolated from the Mucor circinelloides complex. Phenotypic analysis of FK506-resistant isolates in Mucor janssenii CBS185.68 (PS1), Mucor bainieri CBS293.63 (PS3), and Mucor atramentarius CBS202.28 (PS6). WT, wild-type; M, mendelian mutant; E, epimutant. Bottom: Schematic overview of epigenetic silencing contributing to antifungal resistance in Mucor species. fkbA expression enables FKBP12 production and FK506 sensitivity (yeast-like morphology). Epigenetic silencing of fkbA via RNAi and/or heterochromatin leads to FK506 resistance and hyphal growth. Generated with BioRender.com.

#Antifungal resistance is a global threat, but epigenetic mechanisms drive rapid, reversible adaptation in fungi. This study shows that #RNAi or #heterochromatin driven #epimutations transiently silence the gene fkbA to confer FK506 #tacrolimus resistance in #Mucor @plosbiology.org 🧪 plos.io/4qdttWc

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm - The EMBO Journal Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms?
Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment
link.springer.com/article/10.1...

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

Genomic and physiological signatures of adaptation in pathogenic fungi - Nature Communications Emerging fungal pathogens have detrimental impacts on crops, animals, and humans, however little is known about their transition to a pathogenic lifestyle. This study demonstrates that the transition ...

What enables a fungus to invade a mammal host? @marco-guerreiro.bsky.social unravels signatures of translation adaptation among pathogenic and non-pathogenic species of Trichosporonales. See more: www.nature.com/articles/s41...

Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity Milovanović et al. uncover a mechanism by which KZFPs restrict the activity of transposon-derived cis-regulatory elements to safeguard cardiomyocyte functionality. This work extends the classical TE-K...

It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports....
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨

Chromatin remodeling at the C-REPEAT BINDING FACTOR cluster controls growth retardation at low ambient temperature Plants adapt to low ambient temperatures using a temperature-sensitive control system that remodels chromatin to control growth.

🌱 How do plants use dynamic chromatin remodeling to fine-tune transcriptional responses to cold?
Polycomb VIL1 uses H3K27me3 to regulate chromatin architecture at the CBF cluster, modulating growth at low ambient temperature.
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🔗 doi.org/10.1093/plce...

#PlantScience #Epigenetics #ChromatinBiology