Do you want to move to Oxford and join our lab? There is a computational biologist position open atm to develop and implement tools to analyse TE expression in single cell long read data and more. Apply! #TEsky #UniversityofOxford #postdoc

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

#TEsky

Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages Abstract. Primary endosymbiosis, resulting in the establishment of a photosynthetic organelle in eukaryotes, has occurred twice: more than 1.5 billion year

Cagliani, @diegoforni.bsky.social et al. find that genes controlling TE activity were common targets of positive selection in primates and during the more recent evolution of human populations.

🔗 doi.org/10.1093/gbe/evag052

#genome #evolution #TEsky

TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model - Molecular Genetics and Genomics Molecular Genetics and Genomics - Transposable elements (TEs) are critical contributors to gene regulatory networks, yet their repetitive and abundant nature complicates efforts to elucidate their...

#TEsky TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model doi.org/10.1007/s004...

Transposon Ecology and the Octopus Genome Transposable elements (TEs) are mobile strands of DNA prevalent in octopus genomes. TE activity in the octopus brain might reflect an organism-beneficial role in cognition; or could be a deleterious ...

#TEsky Another paper in our TE ecology exploration of the Octopus out in BioEssays. Types of niches for TEs and what that could mean for their expression in neural tissue doi.org/10.1002/bies...

🎉🧬 Multiple genomes/pangenome? Time for a parTEA! 🧬 ☕️

Tired of annotating TEs one genome at a time? Same. So we organised a parTEA!

Introducing EarlGrey ParTEA v0.1.3 — consistent TE annotation across all your genomes, in parallel, with one command: github.com/TobyBaril/Ea...

#TEworldwide #TEsky

Gael Cristofari (left) and newly graduated Dr. Larisa Okorokova (right)

Graduation ceremony at @univcotedazur.bsky.social 👩‍🎓Queen of the day: Dr. @larisaokorokova.bsky.social Congratulations !
#TEsky #MobileDNA

LinkedIn This link will take you to a page that’s not on LinkedIn

We are looking for a Postdoc to join our lab at @oxfordbiochemistry.bsky.social. This is a dry-lab focused post on the computational analysis of long read single-cell sequencing data to understand the role of transposable elements (TEs) in early development. my.corehr.com/pls/uoxrecru... #TEsky

Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species Abstract. A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may co

Potapenko et al. studied two species of barley, finding that TE silencing is central to genome size regulation, with selection maintaining smaller genomes among individuals with higher fitness in favorable habitats.

🔗 doi.org/10.1093/molbev/msag051

#evobio #molbio #TEsky #PlantSky

#TEsky

A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions - PubMed Activity-regulated cytoskeleton-associated protein (ARC) is an RNA-binding protein that also serves as a central hub for neuronal protein-protein interactions. It is essential for intercellular signaling and contributes to synaptic plasticity. ARC includes Gag-like sequences of Ty3/Gypsy retrotransp …

#TEsky A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions pubmed.ncbi.nlm.nih.gov/41797537/

The DELAYED ABAXIAL TRICHOMES Helitron has dual functions in vegetative and pollen development in Arabidopsis thaliana - PubMed Transposons drive genetic diversity and evolution by altering the genomic landscape over time. Here, we describe <i>D</i><i>ELAYED</i> <i>AB</i><i>AXIAL TRICHOMES</i> (<i>DAB</i>), a Helitron/RC transposable element in <i>Arabidopsis thaliana</i> that has a role in vegetative phase change and gameto …

#TEsky The DELAYED ABAXIAL TRICHOMES Helitron has dual functions in vegetative and pollen development in Arabidopsis thaliana pubmed.ncbi.nlm.nih.gov/41785314/

A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape - PubMed The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and inte …

#TEsky A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape pubmed.ncbi.nlm.nih.gov/41789145/

Had a great chat with Sophie about this work back in Heidelberg, excited to dive into this preprint!

#TEsky #TEworldwide

🧬🔎 Deep dive into plant #TransposableElements

❓ If you identify all autonomous #TEs, you will automatically also have all non-coding derivates, right? Right?

Well, no! Not even close. Check out here, how much you are missing:

📚 www.biorxiv.org/content/10.6...

#TEsky

#TEsky a short paper from @mbonar.bsky.social , myself and others on our reannotation of TEs in the Octopus vulgaris genome. More work to come using genome ecology to analyze TEs in this species bsky.app/profile/bior...

Check this out, dear #Tesky 👇🏼

Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 Abstract. The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prev

I'm so happy to share our latest paper! Now out in @narjournal.bsky.social 🥳

Did you know that transposable elements embedded in mRNAs can form dsRNA and activate innate immunity? 🧬🦠 Have a look! academic.oup.com/nar/article/...

#TEsky #RNAsky #RNAbiology #immunity #NAR

RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection see also the Perspective by Amanda M. Larracuente and John S. Sproul

#TEsky Missed this last year but I've been playing with it recently: RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection doi.org/10.1111/1755...

#TEworldwide #TEsky

Happy to share our new preprint! 📊

We benchmarked methods for locus-level transposable element quantification in short-read scRNA-seq, using both real datasets and simulations with read-level ground truth.

Huge thanks to @catavallejos.bsky.social and @antonio-scialdone.bsky.social!

#TEsky

#TEsky Classification of SINE Tails in the Porcine Genome and Its Potential Impact on VWA8 Gene doi.org/10.3390/gene...

#TEsky Vertebrate Hox Clusters as Transposon Repellents Against the Genomic Accordion Model doi.org/10.2108/zs25...

#TEsky

Redirecting

#TEsky Comparative genomics reveals LINE-1 recombination with diverse RNAs doi.org/10.1016/j.xg...

A dimeric SINE discovered in shrew mole is structurally similar to primate Alu - BMC Biology Background Short interspersed elements (SINEs) are non-autonomous retroelements that are transcribed by RNA polymerase III from an internal promoter. Most SINE families originate from tRNAs, but a few...

#TEsky A dimeric SINE discovered in shrew mole is structurally similar to primate Alu doi.org/10.1186/s129...

Repeat-associated heterochromatin expansion in Acyclania tenebrosa, a noctuid with one of the largest lepidopteran genomes - BMC Genomics BMC Genomics - Genome size in Lepidoptera is generally constrained, and heterochromatin is typically limited to sex chromosomes. In some cases, the heterochromatin and genome size increased, but...

#TEsky Repeat-associated heterochromatin expansion in Acyclania tenebrosa, a noctuid with one of the largest lepidopteran genomes doi.org/10.1186/s128...

Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus - Scientific Reports Genome size variation is a fundamental feature of plant genomes and plays an important role in phenotypic diversity, ecological adaptation, and plant evolution across angiosperms. In the Coffea genus ...

#TEsky Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus doi.org/10.1038/s415...

#TEsky