Capolavoro 🎨 alert 🚨! What is the role of gene body methylation in invertebrates? Despite extensive speculation linking it to plasticity and environmental responses, its mechanistic effects and heritability remain unclear. Our take out in @natecoevo.nature.com: www.nature.com/articles/s41... 1/

Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian - Nature Ecology & Evolution

Experiments in the cnidarian Nematostella vectensis show a role of gene body methylation in transposable element suppression and that epigenetic inheritance is constrained by chromatin context and tra...

nature.com

How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇

🧬 New research from the Burga lab! We took a closer look at a rogue selfish protein and caught evolution in the act of turning something old into something radically new 💡 (a.k.a. neofunctionalization) @imbavienna.bsky.social www.biorxiv.org/content/10.6... Curious? Here’s a breakdown:

Retrovirus insertions in host transcripts trigger de novo piRNA immunity: Kirsten-André Senti, @juliusbrennecke.bsky.social et al investigate the 20th-century invasion of D. melanogaster by iERV Tirant to reveal piRNA-pathway evolution in response to new threats link.springer.com/article/10.1...

Retrovirus insertions in host transcripts trigger de novo piRNA immunity - The EMBO Journal

How host organisms adapt their defense systems to newly invading transposable elements remains poorly understood. Here, we show how Drosophila melanogaster acquired PIWI-interacting RNA (piRNA)-mediat...

link.springer.com

Recursive Repeat Extender (RRE): A recursive approach to automatically extend repeat element models https://www.biorxiv.org/content/10.64898/2026.04.14.718546v1

Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬 Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15 www.biorxiv.org/content/10.6...

Ancient persistence and newfound diversity of CR1-group retrotransposons across chordates https://www.biorxiv.org/content/10.64898/2026.01.13.699120v1

Chavez in 2009, while being labelled as paranoid, outlines exactly what is happening today.

Very happy to share my postdoc work (on preprint), where we try to understand a long-standing transcription-silencing paradox, and uncovered a hidden RNA decay arm of nuclear piRNA pathway, see detailed threads quoted from @juliusbrennecke.bsky.social

Julius Brennecke@juliusbrennecke.bsky.social · 8mo ago

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.

Happy to share that my PhD project is finally published!🪱✨ Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?

Nature Ecology & Evolution@natecoevo.nature.com · 8mo ago

Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis 🧪 www.nature.com/articles/s41...

🚨 New paper alert! Scientists in the Burga lab show for the first time how toxin-antidote elements—selfish genetic elements that perpetuate by poisoning those embryos that don’t inherit them—evolved from normal cellular proteins. More: https://imba.science/3M3fRyq

piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders Donal O’Carroll and coworkers www.embopress.org/doi/full/10....

💸 Stem cell culture that’s ~95% cheaper and weekend-free: a win-win for PIs and trainees! Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1... Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!

1/ How do animals develop immunity against a newly encountered transposable element from scratch? Our study reveals that the mobility of TEs is their Achilles heel, allowing hosts to develop a powerful small RNA-mediated silencing response. www.biorxiv.org/content/10.1...

Antisense transposon insertions into host genes trigger piRNA mediated immunity

Transposable elements pose a persistent threat to genome integrity, yet how host defense systems adapt to newly invading elements remains poorly understood. Here, we reveal how Drosophila melanogaster...

biorxiv.org

bioRxiv Genetics@biorxiv-genetic.bsky.social · last yr.

Antisense transposon insertions into host genes trigger piRNA mediated immunity https://www.biorxiv.org/content/10.1101/2025.07.28.667215v1

#Preprint alert! 📣 We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements www.biorxiv.org/cgi/content/...

MLL2 facilitates long-range gene regulation through LINE1 elements

Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 d...

biorxiv.org

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics

Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

nature.com

We have created a new DNase I- & ATAC-seq peak caller that uses an adaptive background model that controls for copy number variation & aneuploidy. It performs a per-nucleotide test (+FDR correction) and is very fast. Please try it out and give us feedback! github.com/vierstralab/...

GitHub - vierstralab/hotspot3: A chromatin accessibility peak caller with an adaptive background model

A chromatin accessibility peak caller with an adaptive background model - vierstralab/hotspot3

github.com

We take for granted that our hands have two sides and can articulate in an endless number of ways. But what about a fish’s fin? Can a fish know something “like the back of its fin,” or have its future told with a fin palm reading? Check out this bluetorial to find out 👇🧪🧬🐟 doi.org/10.1101/2025...

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression

Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

science.org

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

nature.com

Exciting and rare opportunity to join the @maxperutzlabs.bsky.social and the @viennabiocenter.bsky.social as a Full Professor! www.nature.com/naturecareer...

Full Professorship in Molecular Mechanisms of Disease - Vienna BioCenter, Austria job with Max Perutz Labs, University of Vienna | 12841053

Join theMax Perutz Labs as Full Professor to unravel disease mechanisms—from metabolism and stress to RNA regulation, epigenetics, and immunity.

nature.com

structure prediction is not science if not experimentally validated. period

Diego del Alamo@delalamo.xyz · last yr.

Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this threadreaderapp.com/thread/19384...

REFEREE 1: “I conclude with a simple, direct statement - this is the best paper I have read all year!” #TransparentPeerReview Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses @juliusbrennecke.bsky.social et al www.embopress.org/doi/full/10....

How does the genome find its place in the 3D space of the nucleus after fertilization? Out now @cellcellpress.bsky.social: cell.com/cell/fulltext/… 👇 A thread 👇

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS

Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

pnas.org

Join our team as a postdoc and explore the exciting world of transposable elements and developmental biology with us! @imbavienna.bsky.social @vbcscitraining.bsky.social

I'm super grateful for this FWF funding to explore the 'fossilized' transposon landscape of the axolotl genome! Thrilled to uncover how these ancient sequences helped sculpt many of our organs and structures!

Institute of Molecular Biotechnology@imbavienna.bsky.social · last yr.

Diego Rodriguez-Terrones, postdoc in Elly Tanaka’s Lab, was awarded a Principal Investigator Projects Grant by the Austrian Science Fund (FWF) for his “genomic archaeology” research in the axolotl. Read more: https://imba.science/4kUNwaF

Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?

Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less' Lots of interesting new TE (& genes) biology Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/