Cecile Lorrain
@ccilelorrain.bsky.social
SNSF Ambizione Fellow | Junior PI in Plant Pathology @ ETH Zürich | Specializing in fungal genome architecture & TE-driven evolution
lorrainlab.owlstown.net
lorrainlab.owlstown.net
Reposted by Cecile Lorrain
Reposted by Cecile Lorrain
Reposted by Cecile Lorrain
🧬 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 🧪
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 🧪
December 24, 2025 at 10:32 AM
🧬 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 🧪
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 🧪
Reposted by Cecile Lorrain
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...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
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...
www.nature.com/articles/s41...
Reposted by Cecile Lorrain
CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1
December 12, 2025 at 11:16 PM
CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1
Reposted by 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...
🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social!
www.sciencedirect.com/science/arti...
December 12, 2025 at 11:49 AM
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...
🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social!
www.sciencedirect.com/science/arti...
Reposted by Cecile Lorrain
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
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
December 11, 2025 at 9:56 PM
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
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
Reposted by Cecile Lorrain
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
December 10, 2025 at 7:12 PM
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
Reposted by Cecile Lorrain
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...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
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...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
Reposted by Cecile Lorrain
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...
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
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...
www.nature.com/articles/s41...
Reposted by Cecile Lorrain
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...
@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social
www.cell.com/current-biol...
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...
www.cell.com
December 6, 2025 at 9:22 AM
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...
@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social
www.cell.com/current-biol...
Reposted by Cecile Lorrain
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
December 3, 2025 at 2:31 AM
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
Reposted by Cecile Lorrain
New online! The biodiversity, genomics, ecology and evolution of mushroom-forming fungi
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.
bit.ly
December 2, 2025 at 5:06 PM
New online! The biodiversity, genomics, ecology and evolution of mushroom-forming fungi
Reposted by Cecile Lorrain
#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...
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...
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
academic.oup.com
December 2, 2025 at 12:18 PM
#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...
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...
Reposted by Cecile Lorrain
FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
November 29, 2025 at 9:52 AM
FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples
www.nature.com/articles/s41...
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...
link.springer.com/article/10.1...
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 ...
link.springer.com
November 28, 2025 at 12:43 PM
Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Cecile Lorrain
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...
@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...
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.
www.nature.com
November 27, 2025 at 9:58 PM
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...
@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...
Reposted by Cecile Lorrain
#TEsky FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum doi.org/10.1186/s131...
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...
doi.org
November 25, 2025 at 1:06 PM
#TEsky FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum doi.org/10.1186/s131...
Reposted by Cecile Lorrain
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...
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...
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...
www.nature.com
November 26, 2025 at 6:00 AM
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...
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....
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...
apsjournals.apsnet.org
November 21, 2025 at 1:00 PM
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....
Reposted by Cecile Lorrain
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.
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.
November 5, 2025 at 5:20 PM
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.
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.
Reposted by Cecile Lorrain
Improved gene annotation of the fungal #wheat pathogen #Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence doi.org/10.1094/MPMI...
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...
doi.org
November 19, 2025 at 12:41 PM
Improved gene annotation of the fungal #wheat pathogen #Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence doi.org/10.1094/MPMI...
Reposted by Cecile Lorrain
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1
November 19, 2025 at 3:35 PM
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1
Reposted by Cecile Lorrain
Nature research paper: Specificity, length and luck drive gene rankings in association studies
go.nature.com/47Fsqax
go.nature.com/47Fsqax
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
go.nature.com
November 10, 2025 at 11:36 AM
Nature research paper: Specificity, length and luck drive gene rankings in association studies
go.nature.com/47Fsqax
go.nature.com/47Fsqax
Reposted by Cecile Lorrain
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.
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.
November 10, 2025 at 1:23 PM
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.
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.