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

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

#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...

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

#TEsky

Jumping in the human brain: A review on somatic transposition - PubMed As a Nobel Prize-winning discovery, transposable elements, or "jumping genes", have attracted significant interest due to their roles in providing functional coding and regulatory sequences. A longstanding hypothesis suggests that somatic transposition may preferentially occur in the mammalian brain …

#TEsky Jumping in the human brain: A review on somatic transposition pubmed.ncbi.nlm.nih.gov/41647578/

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism Abstract. Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal spec

Dauphin et al. assembled a telomere-to-telomere reference genome for an ectomycorrhizal fungus with a large, repeat-rich genome, showing its genome expansion was driven by a few lineage-specific TE families in recent history.

🔗 doi.org/10.1093/gbe/evag017

#genome #evolution #TEsky

📣 A fantastic resource for the study of population genomics of transposable elements. Congratulations to all @johannconfais.bsky.social ! Also very happy to see the Brachypodium resource being used for this purpose!
It's 🌈🌈 again! #TEsky #goBrachy

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 🧵👇

#TEsky Arms races between selfish genetic elements and their host defence in termites doi.org/10.1038/s414...

Hao et al. present Imagin as a new gene family derived from a Ginger1 DNA transposon domesticated in the common ancestor of malacostracan crustaceans.

🔗 doi.org/10.1093/gbe/evag010

#genome #evolution #TEsky

Sex-biased Expression of Genes and Transposable Elements in Hybrids from Drosophila mojavensis and Drosophila arizonae Abstract. Sex-biased gene expression is one of the main forces driving differences between sexes. Transposable elements (TEs) have also been shown to displ

Simão et al. analyzed gene expression in two Drosophila species that produce sterile hybrids, with results supporting a role for sex-biased gene and TE expression in reproductive isolation.

🔗 doi.org/10.1093/gbe/evaf247

#genome #evolution #TEsky