Cecile Lorrain

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis - Nature Communications Single-cell multi-omics in Drosophila testis reveals enhancer-driven gene regulatory networks and shows how Wnt signaling and key transcription factors orchestrate stem cell maintenance and lineage pr...

I am so happy to announce that our Drosophila testis multiome paper is now published in Nature Communications !!! I am very happy and proud of all who contributed, in particular Patrick and Pallavi who did an amazing job! www.nature.com/articles/s41...

We are looking for a student to continue our work on chromatin evolution:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...

The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.

More info: recruitment.crg.eu/content/jobs...

1/2 Somatic TE transposition in plants is getting traction again (70 years after McClintock's discovery of "controlling elements")! A very large collection of somatic TE insertions in A. thaliana described by Ambreen et al.(www.biorxiv.org/content/10.1...).

Conservation of chromatin states and their association with transcription factors in land plants The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conse...

New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development - Nature Ecology & Evolution Single-cell comparison of developing bat and mouse limbs reveals conservation of cell populations and gene expression patterns, and suggests repurposing of genes involved in proximal limb development ...

How bats developed their wings? 🦇

Turns out they reutilize existing gene programs 🔧

Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs

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

🚨Our latest work on selfish centromeres is published @currentbiology.bsky.social 🐭🧬We found that the spindle checkpoint contributes to non-Mendelian segregation! Huge congrats to our lab manager, Zaak Walton, who led the project🎉

Free link:
authors.elsevier.com/a/1lQzN3QW8S...

Gene regulatory networks and essential transcription factors for de novo-originated genes Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Model of Starship mediated transfer of the ToxA gene, that is present on a separate mobile element named ToxhAT. Blue: ToxhAT; Green: Starship Horizon; Yellow: Starship Sanctuary.

Curious about how novel #plant #pathogens emerge? Check out our microreview on whether #fungal disease outbreaks are instigated by Starship #transposons. We present three examples that we think are evidence of outbreaks caused by Starship HGT. bsppjournals.onlinelibrary.wiley.com/doi/10.1111/...

Animal origins: looping back in time How did the chromatin folding mechanisms controlling gene regulation emerge during animal evolution? Kim et al. surveyed chromatin folding at high-resolution in unicellular relatives of animals as wel...

An insightful @cp-trendsgenetics.bsky.social perspective on our recent article about the early evolution of genome regulation in animals.

www.cell.com/trends/genet...

Thank you Omar and @ferdix.bsky.social!

Viral genomes might encode more proteins than we initially thought!

Intrigued? Come see my poster on the identification of potentially new ORFs in the potato virus X genome.

Tuesday 9:55-11:30, P-266
@geminiteamlab.bsky.social
#2025ISMPMI

Machine learning reveals genes impacting oxidative stress resistance across yeasts - Nature Communications Yeasts are exposed to oxidative stress during routine metabolism, bioproduction, and interactions with other organisms. Here, the authors use a machine learning classifier to identify genes that are p...

In another fruitful collaboration with the @rokaslab.bsky.social, Hittinger Lab members @katarina-aranguiz.bsky.social and @linder-surprise.bsky.social , et al. established a ML framework to identify gene families in the yeast subphylum Saccharomycotina whose copy numbers predicted ROS resistance.

Spatio-temporal tracking of three novel transposable element invasions in Drosophila melanogaster over the last 30 years Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a sigfinificant influence on evolution throug

super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Structural variants in the 3D genome as drivers of disease - Nature Reviews Genetics Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects ...

🚀 Thrilled to share our new review on how structural variants reshape 3D genome architecture and cause disease! 🧬🔀
Out now in Nature Reviews Genetics: www.nature.com/articles/s41...
#3D-Genome #StructuralVariants #uksh

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies Abstract. Although the mechanisms driving genome size evolution are not yet fully understood, one potentially important factor is the dynamics of the accum

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies

academic.oup.com/mbe/article/...

The evolution of high-order genome architecture revealed from 1,000 species https://www.biorxiv.org/content/10.1101/2025.07.05.663309v1

@science.org Zincore-coregulator dedicated to zinc🖐️ TFs essential in development www.science.org/doi/10.1126/...
@rborza.bsky.social @sgregoricchio.bsky.social @amazouzi.bsky.social @zwartlab.bsky.social @lindersimon.bsky.social @tassosperrakis.bsky.social @thijnbrummel.bsky.social + al.

Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10....
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Evolutionarily recent transcription factors partake in human cell cycle regulation Pulver and Forey et al. generated a novel atlas reporting (1) gene expression over the cell cycle and (2) how systematic gene depletion affects cell cycle progression. They thereby identified evolutio...

🚨 Check out the latest from @trono-lab.bsky.social showing how evolutionarily young transcription factors contribute to human cell cycle regulation!
Brilliant work led by Romain Forey and Cyril Pulver, now published in Cell Genomics. Check it out !
www.cell.com/cell-genomic...

The first paper of my PhD is now available as a preprint! 🎉

Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.

Impact of the Zinc Antiviral Protein on the Genomic Composition of RNA Viruses Infecting Vertebrates Abstract. The composition of viral genomes, influenced by host-specific biases, offers insights into their evolutionary history. Vertebrate cells counter v

Simón, @gonzamoratorio.bsky.social et al. trace the evolution of ZAP, an antiviral protein targeting CpG-rich RNA that originated >400 Mya in the tetrapod–lungfish ancestor. Their findings point to complex coevolution of host antiviral defenses.

🔗 doi.org/10.1093/molbev/msaf135

#evobio #molbio

Confocal image showing a nucleus of a maize endosperm cell expressing proNAC130:NL-mCherry counterstained with DAPI.

Our latest on cell death and our second on maize: Using single-nucleus RNAseq of maize endosperm, Nicolas Doll (now @rdplab.bsky.social‬) shows that KIL transcription factors promote endosperm cell death to facilitate embryo growth - with a genomic imprinting twist! academic.oup.com/plcell/advan...

Pangenome and pantranscriptome as the new reference for gene family characterisation – a case study of basic helix-loop-helix (bHLH) genes in barley Short Summary: Traditional gene family analyses were limited and biased toward gene content in a single reference genome, which failed to account for the gene presence/absence variations (gPAVs) in th...

Pangenome and pantranscriptome as the new reference for gene family characterisation – a case study of basic helix-loop-helix (bHLH) genes in barley. #Pangenome #Pantranscriptome #PlantCommunications 🧬🖥️
www.cell.com/plant-commun...

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD - Nature A comprehensive analysis of the cell-specific molecular regulatory mechanisms underlying post-traumatic stress disorder in the human prefrontal cortex.

Nature research paper: Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

https://go.nature.com/44963IH

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance - Genome Biology Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced inputs. Using DArTseq, we genotype 461 wheat landraces and cultivars and evaluat...

VERY HAPPY to share our last publication...In a world full of SNPs...k-mers made the most biological sense out of the complex wheat genome! 🌱🧬
genomebiology.biomedcentral.com/articles/10....
Grateful to Benjaming Jaegle for the trust, & co-authors for their collaboration!

Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis - Nature Insights into the dogrose genome and centromeres explain their ability to achieve stable sexual reproduction.

Nature research paper: Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis

https://go.nature.com/407PRGm