OK Kids, our ERK story is finally heading out into the world. After 9 years of having funding, losing funding, losing staff, getting funding, gaining staff...it's ready!

We discovered a novel stage of what is an otherwise extensively studied process: how cells respond to extracellular signals. 1/n

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

Fun primer with @ForeverYHChang highlighting a lovely Travis Thomson lab paper!

Did animals co-opt viral gag for intercellular (trans synaptic) communication? Or did viruses co-opt retrotransposon gags that animals had previously co-opted for intercellular use?

Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis www.nature.com/articles/s41...

🎉🧬 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

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...

This fish has cloned itself for 100,000 years. Scientists just figured out how.

This fish has cloned itself for 100,000 years. Scientists just figured out how.
#evolutionsoup #evolution #gynogenesis #science #fossils #cloning
👇🏿👇🏽
is.gd/PUwN0s

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

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

#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/

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

Join us at the EMBO Workshop “RNA-guided genome protection” 🇨🇭 June 16–20. Transposon silencing • stem cell biology • RNA-guided immunity. Keynotes: Déborah Bourc’his + Ian MacRae. Register now + submit your abstract! meetings.embo.org/event/26-gen...

Transposable elements are increasingly studied in single-cell data, but how reliable are current locus-level quantification methods in short-read scRNA-seq data?

If you work with single-cell RNA-seq or TEs, we hope this is a useful resource — feedback very welcome!

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

How does the piRNA system first recognize a new transposon or virus as foreign?

www.biorxiv.org/content/10.1101/2024.01....

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 🧵👇

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

Very last chance to join us (Deadline tomorrow Feb 10!) at this Developmental Biology meeting!
Have a nice story? Come and discuss it with editors from @embojournal.org @plosbiology.org and @dev-journal.bsky.social !
A one hour info session from @erc.europa.eu will also be presented!

A confocal image of a 3D human Trunk-like Structure (hTLS) made from pluripotent stem cells, showing a neural tube (cyan) and segmented somites (magenta).

We're recruiting a #devbio Postdoctoral Fellow to explore the hTLS system! If you know any fab PhD students finishing, or candidates wanting to get their hands on #SCBEM embryo models, do get them to apply! 🌟www.crick.ac.uk/careers-study/vacancies/...

We've got two exciting chromatin talks coming up on Wednesday next week:

@epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social!

register and join us: us06web.zoom.us/webinar/regi...

Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it)

It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...

The speed at which Oxford Nanopore is cancelling support for their devices is just mind boggling 😳
P2 solo will be decommissioned soon!!! This is not sustainable!
@nanoporetech.com

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood—including how sequence context modulates affinity, how TFs search DNA, the kinetics of TF occupancy, and how motif grammars coordinate binding. To resolve these questions for a human TF, erythroid Krüppel-like factor (eKLF/KLF1), we quantitatively compare, in high throughput, in vitro TF binding rates and affinities with in vivo single-molecule TF and nucleosome occupancies and in vivo-derived deep learning models. We find that 40-fold flanking sequence effects on affinity are consistent with distal flanks tuning TF search parameters and captured by a linear energy model. Motif recognition probability, rather than time in the bound state, drives affinity changes, and in vitro and in nuclei measurements exhibit consistent, minutes-long TF residence times. Finally, in vitro biophysical parameters predict in vivo sequence preferences and single-molecule chromatin states for unseen motif grammars.

Schaepe et al, 2026. Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.cell.com/cell/fulltex...

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from im...

📣Excited to announce a new pre-print from the lab 📣

Led by my student @storiesofisobel.bsky.social in collab with Hemali Phatnani @nygenome.org
We discovered a novel class of TDP-43 dependent cryptic gene-TE spliced transcripts: crypTEs

#TEsky #RNAsky #ALS
doi.org/10.64898/2026.01.09.698641

Really excited to share our recent work here today and connect all of you :)

What a cool story. Particularly like the fact of expansion and different TF bdg sites! Really speaks for each locus being differential key regulated.

GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

☕Earl Grey v7.0.0 brewed fresh☕

Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.

Happy new year to the TE folks! 🧬

github.com/TobyBaril/Ea...

#TEsky still have to read the paper but sounds very interesting.