Cecile Lorrain

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
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Fig. 3. Significant genomic loci and k-mers associated with temperature shock responses in Zymoseptoria tritici. The horizontal dashed lines indicate the 10% family-wise error rate significance threshold. Genes co-located with significant k-mers are shown as arrows with corresponding descriptions.

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 Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...

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

The biodiversity, genomics, ecology and evolution of mushroom-forming fungi Nature Reviews Biodiversity, Published online: 02 December 2025; doi:10.1038/s44358-025-00107-zMushroom-forming fungi have along evolutionary history and a suite of important ecological roles. This Review highlights advances in understanding of Agaricomycetes evolution and ecology driven by genomic research.

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

The evolution of plasticity and evolvability in a simple gene regulatory network How do organisms adapt to changing environments? Do they respond plastically or evolve through genetic alterations? We present a large-scale simulation stu

#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 - Nature Methods This work describes FX-Cell and its derivatives to achieve single-cell RNA sequencing from challenging and cryopreserved plant tissues, expanding the scope of single-cell genomics across field-grown s...

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

Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...

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

Heterochromatin boundaries maintain centromere position, size and number - Nature Structural & Molecular Biology Carty et al. identify the H3K9 methyltransferases that restrict the size and position of the centromere protein A chromatin domain, maintaining functional centromeres.

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...

FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum - Mobile DNA Transposable elements (TEs) are dynamic components of eukaryotic genomes, playing a crucial role in genome evolution and plasticity, particularly in unstable regions such as chromosome ends. In the gl...

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

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

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® Pathogens’ responses to sudden temperature fluctuations, spanning various temporal scales, are critical determinants of their survival, growth, reproduction, and homeostasis. Here, we combined phenoty...

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 | Molecular Plant-Microbe Interactions® Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using th...

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

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

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.

Genomic traits associated with pathogenicity.

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

So proud of you, @emma--c.bsky.social — congratulations on a brilliant PhD defense! 👩‍🎓🍾 It's been a pleasure to mentor your journey!

And huge thanks to the fantastic committee for the inspiring discussion!

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 🌽!!!

Recent horizontal transfer of transposable elements in Drosophila Transposable elements (TEs) are genetic elements also known as "jumping genes" that increase their copy numbers within a host through various mechanisms of transposition. TEs can also move between spe...

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...

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...

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

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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...

Open Positions ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc

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...