Rebecca Berrens

#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?

https://www.biorxiv.org/content/10.1101/2024.01.24.577019

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! 🌟https://www.crick.ac.uk/careers-study/vacancies/2026-02-03-postdoctoral-fellow-moris-lab

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.

#TEsky Heterogeneous Lineages of DNA Transposons Encode a TET/JBP Dioxygenase in Fungi doi.org/10.3390/biol...

🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.

@biorxivpreprint.bsky.social Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells
www.biorxiv.org/content/10.6...

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona!

🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)

Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social

Submit your abstract and present your research!

www.isco-conference.eu

H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations Nitsch et al. show that short-chain acylations of histone H4K16, acetylation (C2), propionylation (C3), and butyrylation (C4) modulate chromatin structure in vitro. These effects can translate in vivo...

Nice paper from @robertife.bsky.social on how metabolism-induced H4K16 acylations correlate with (and may cause) chromatin opening through disruption of tail-acidic patch internucleosomal interactions.

www.cell.com/molecular-ce...

Polar bears in southern Greenland are 'using jumping genes to rapidly rewrite their own DNA' to survive melting sea ice Warming temperatures appear to be driving genetic mutations in some polar bears to help them survive the shifting climatic conditions.

More than one-third of polar bear genome is made up of transposable elements. By contrast, transposons make up about 45% of the human genome

Polar bears in southern Greenland are 'using jumping genes to rapidly rewrite their own DNA' to survive melting sea ice www.livescience.com/animals/pola...

🚨Our story is published! Same bones but + dissection of MERVL’s role integrating signals from #ZGA factors, & + about pathological DUX4 activation of NOXA #TEsky. Thanks to all revs for their helpful comments improving the ms. Even #rev3 - until they ghosted us 😜

www.science.org/doi/epdf/10....

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.

And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Very excited to share our work on locus level transposable elements in development with the @fnucleosome.bsky.social community!