Diego Rodriguez-Terrones

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?

🚨 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...

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...

#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/...

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...

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

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

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/...

Schematics depicting the dorsal and ventral sides of fins and limbs

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...

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...

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

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

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/

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.

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

structure prediction is not science if not experimentally validated. period

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....

only divergence. For instance, in regeneration we have situations where multiple differentiated cell states converge on a dedifferentiated identity before diverging again. Would emplying 3D spaces facilitate modeling these complex cyclic cases? 2/2

Hi, this is great! Had been looking forward to this after following all those UMAP threads. It's a very elegant solution. I was just left wondering what your thoughts were on whether this approach can be extended to also model situations where you have a convergence of cell states rather than 1/2

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 👇

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. ...

💥🥳 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

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!

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/

Many congratulations Juliane!!! 👏

Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵

An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development Mapping transcription start sites across five mammalian species before, during, and after embryonic genome activation unveils widespread transposable element-driven transcription and co-option of evol...

Tour de force! @metorrespadilla.bsky.social & team develop Smart-seq+5′ to map TSS in single embryos with unprecedented res revealing plethora of TE-driven transcripts in 5 mammal species. Some surprisingly old & conserved. Treasure trove of new biology for yrs to come!
www.cell.com/cell/fulltex...