#TEsky Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources doi.org/10.1186/s131...
Client Challenge
doi.org
Rebecca Berrens
@rberrens.bsky.social
Group leader of transposon group in Oxford at IDRM. #new_pi https://sites.google.com/view/berrenslab
Animal retrozymes are nonautonomous sequences of Penelope-like elements.
Animal retrozymes are nonautonomous sequences of Penelope-like elements
Hammerhead ribozymes (HHRs) are small catalytic RNAs found across diverse life forms. In animals, they can occur as dispersed copies or in tandem genomic arrangements. These tandemly organized forms, ...
biorxiv.org
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
nature.com
Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵
We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky
An active Helitron transposon family in wheat - Nature Plants
Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...
nature.com
How do transposons jump when they’re released from host control? I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs. Here’s what we found & excited to share my 1st postdoc paper: “piRNA loss unleashes episodic transposition bursts” www.biorxiv.org/content/10.6...
piRNA loss unleashes episodic transposition bursts
In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...
biorxiv.org
Hi #TEsky, please remember that we have an amazing community in the TransposonsWorldWide slack channel (join.slack.com/t/transposon...), which I encourage you to join. Another great resource is tehub.org. Please share !
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Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
Excited to be in Barcelona for ISCO2026 to learn more about new innovations in the single cell genomics and transcriptomics space and reconnect with old friends and making new connections
🚨 Excited to share a new manuscript from the lab. Here, we have developed a new method, HiCPotts, to identify significant interactions in 3D chromatin data www.biorxiv.org/content/10.6...; package bioconductor.org/packages/HiC.... Big shoutout to an amazing previous PhD in the lab Godwin. 1/n
Exciting #CtrlEpiEdit conference update: Maja Jagodic @ki.se will be joining us in Paris! Check out her fantastic in vivo epigenome editing preprint here: www.biorxiv.org/content/10.6... And register for the symposium here 😉: ctrlepiedit.sciencesconf.org Please repost!
👋 Transposon lovers: registration is now open for the CSHL TE meeting! We have a 🔥 lineup of invited speakers and many slots for short talks selected upon abstract across all areas of TE biology. 🧬➰🧬 #TEsky Abstract deadline: July 10 meetings.cshl.edu/meetings.asp...
Hello world! So proud of our own @germainekaram.bsky.social presenting her PhD project during the #FragileNucleosome seminar! Great line-up with Ujani and Ethan! Please join if you wanna know how rapidly evolving H2A histones regulate maternal chromatin in mammals... #MolaroLab #Histones @igred.fr
a man in a tie is screaming in a kitchen with the words `` oh the excitement '' written below him .
ALT: a man in a tie is screaming in a kitchen with the words `` oh the excitement '' written below him .
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FragileNucleosome@fnucleosome.bsky.social · 3mo ago🔔This Wednesday we are excited to have three amazing ECR talks at #FragileNucleosome by Ujani, @ewholling.bsky.social & @germainekaram.bsky.social ! Don't forget to subscribe to our series! us06web.zoom.us/webinar/regi...
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
biorxiv.org
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
Rebecca Berrens@rberrens.bsky.social · 5mo agoWe 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
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?
PLOS Biology@plosbiology.org · last yr.Yung-Heng Chang & @joshdubnau.bsky.social explore a @plosbiology.org study revealing that the #retrotransposon gag protein of Copia forms virus-like capsids that transfer its own RNA across the fly neuromuscular junction to regulate #synapse formation 🧪 Paper: plos.io/3X71IDa Primer: plos.io/4i6rzmC
Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis www.nature.com/articles/s41...
Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis - Nature Communications
The roles of the piRNA pathway in human oocytes are poorly understood. Here, the authors profile small and long RNAs in single oocytes and show that short piRNAs broadly repress transposable elements,...
nature.com
🎉🧬 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
#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...
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...
doi.org
This fish has cloned itself for 100,000 years. Scientists just figured out how. #evolutionsoup #evolution #gynogenesis #science #fossils #cloning 👇🏿👇🏽 is.gd/PUwN0s
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
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
doi.org
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
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#TEsky A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions pubmed.ncbi.nlm.nih.gov/41797537/
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 …
pubmed.ncbi.nlm.nih.gov
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
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
academic.oup.com
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...
RNA-guided genome protection
The genome carries information across generations, ensuring species survival. To preserve faithful transmission of genetic information, RNA-directed mechanisms safeguard the genome integrity in diver…
meetings.embo.org
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!
Veronica Finazzi@veronicafin.bsky.social · 5mo agoHappy 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
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
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo agoBenchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets https://www.biorxiv.org/content/10.64898/2026.02.26.708244v1
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
🚨📢📄 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 🧵👇
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...
doi.org