Darío Lupiáñez

Darío Lupiáñez

@dariloops.bsky.social

A bit of 3D gene regulation, single-cell omics and transgenic models. Born and raised in the bay of Algeciras. Enjoying Science and Flamenco at CABD, Seville. Lab website: https://lupianezlab.github.io/Website/ Email: dario.lupianez@csic.es

1.1K followers297 following154 posts

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Darío Lupiáñez
@dariloops.bsky.social

10/15 But when did loop-extrusion TADs emerge? Hi-C experiments in sea lamprey, a cyclostome, demonstrates that this mode of genome organization was already present at least in the last common ancestor of all vertebrates

Darío Lupiáñez
@dariloops.bsky.social

11/15 Based on this, we hypothesize that the emergence of CTCF-mediated loop extrusion may have facilitated the regulatory expansion of vertebrate genomes following whole-genome duplications events Increased potential for distal interactions with great capacity to insulate regulatory domains

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Darío Lupiáñez
@dariloops.bsky.social

8/15 But what happens in the reverse direction? By introducing mouse CTCF in a fly background, we show that this ortholog per se is not sufficient to form “vertebrate-like” TADs The vertebrate protein causes loss-of-function effects, similar to CTCF KO, despite binding on invertebrate chromatin

Darío Lupiáñez
@dariloops.bsky.social

9/15 We reveal evolutionary shifts in CTCF DNA-binding: - At the base of chordates, motif expanded at 5′ end - Coinciding with shift to more distal binding than near promoters - Vertebrate motif lacks 3′ terminal C, a 5mC site, facilitating binding far from promoters in methylation-rich context

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Darío Lupiáñez
@dariloops.bsky.social

6/15 But the invertebrate sea squirt (Ciona) CTCF ortholog still showed remarkable functionality! It bound pervasively across the vertebrate genome and rescued many of the dysregulated genes associated with depletion of endogenous mouse CTCF

Darío Lupiáñez
@dariloops.bsky.social

7/15 Most strikingly, the sea squirt CTCF rescued the lethality associated with mouse CTCF depletion mESCs carrying this ortholog could grow without noticeable TADs (although slower) This demonstrates that CTCF transcriptional and architectural functions are evolutionary uncoupled

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Darío Lupiáñez
@dariloops.bsky.social

4/15 Here we investigated how 3D chromatin organization and CTCF has evolved by replacing the endogenous gene by an orthologous of a different species, in a mouse ESC degron background. Invertebrate orthologs -> fly, sea urchin, sea squirt Vertebrate orthologs -> zebrafish, mouse

Darío Lupiáñez
@dariloops.bsky.social

5/15 Hi-C experiments revealed major differences between invertebrate and vertebrate CTCF Invertebrate CTCF orthologs failed to form TADs in mouse ESCs Thus, the capacity to modulate loop extrusion is largely encoded in the vertebrate protein

Darío Lupiáñez
@dariloops.bsky.social

2/15 TADs are pervasively found across animal species, but the mechanisms underlying their formation can be very different For example, in mammals, loop extrusion plays a major role. In flies, TAD-like structures are largely driven by chromatin compartmentalization

Darío Lupiáñez
@dariloops.bsky.social

3/15 Interestingly, CTCF, a key architectural factor for TAD formation, is widely conserved across Bilateria Has its function remained the same throughout evolution? Or has CTCF acquired new roles in different lineages?

Darío Lupiáñez
@dariloops.bsky.social

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 🧪 Experimental backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

Darío Lupiáñez reposted

Paolo Crosetto
@paolocrosetto.bsky.social

Small interview by @tumorijournal.bsky.social where I discuss the main current problems of scientific publishing, where you can learn about the strain (direct.mit.edu/qss/article/...) & drain (arxiv.org/abs/2511.04820) of scientific publishing, and hear my horrible Italian accent in English. Enjoy!

arxiv.orgThe Drain of Scientific PublishingThe domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and ...
Tumori Journal - TJ@tumorijournal.bsky.social

Thank you so much, Prof. Crosetto @paolocrosetto.bsky.social, for accepting our invitation and for your thorough, engaging contribution. We truly appreciated it. youtu.be/cOhw4Jk6vF0?...

youtu.beThe strain on scientific publishing: a scenario with various players, but only one benefitsYouTube video by Tumori Journal

Darío Lupiáñez reposted

Mark A. Hanson
@hansonmark.bsky.social

I'm surprised a community of publishing writers can blame AI for the problems of peer review when those same writers cite our study, "the strain on scientific publishing", which characterizes how this problem existed before AI. bit.ly/StrainQSS It's the incentives structure, not the AI. 1/n

scholarlykitchen.sspnet.orgAsk the Chefs: Peer Review Capacity — Uncomfortable Truths and Overlooked Conversations - The Scholarly KitchenFor Peer Review Week 2026, we asked the Chefs two questions: What is one uncomfortable truth about peer review that the scholarly publishing community doesn’t talk about enough? And, beyond recruiting...

Darío Lupiáñez reposted

heardlab.bsky.social
@heardlab.bsky.social

NEW PREPRINT FROM THE LAB IS OUT — DON’T MISS IT! www.biorxiv.org/content/10.6... We asked whether the 3D architecture of the inactive X -  and in particular CTCF and cohesin -  is what keeps escapee genes active. Spoiler: it isn’t.

biorxiv.orgX-inactivation escapee domains are CTCF-cohesin independent chromatin compartmentsX-chromosome inactivation involves chromosome-wide gene silencing accompanied by extensive chromatin changes, as well the loss of topologically associating domains. Yet discrete regions of the inactiv...

Darío Lupiáñez reposted

Rada-Iglesias Lab
@radaiglesiaslab.bsky.social

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

nature.comMechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature GeneticsDevelopment depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

Darío Lupiáñez reposted

Akis (Argyris) Papantonis
@akispapantonis.bsky.social

Newest from the lab - and the only of our manuscripts since the introduction of bioRxiv that we did not preprint (it will become obvious why). "Targeting addiction to HMGB2-driven transcriptional programs in pancreatic cancer" A thread...

Darío Lupiáñez reposted

Cabimer
@cabimer.bsky.social

🔬 Metástasis: ¿su punto débil? @alteamanzanolab.bsky.social  @eleconomista.es 

eleconomista.esLa científica española que busca el punto débil de la metástasis del cáncer: "El gran reto es entender qué hace que estas células tengan superpoderes"Tener 'superpoderes' no siempre es positivo y tampoco se asocia siempre a héroes que salvan el mundo. Se define como una habilidad o facultad extraordinaria, es decir, fuera de lo común, y es lo que ocurre con las células tumorales capaces de iniciar la metástasis. Patricia Altea (Sevilla, 1988), directora del grupo de Regulación Metabólica y Señalización en Cáncer del Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) quiere descubrir porqué estas unidades concretas tienen dicha cualidad y junto con su equipo en el CABIMER investiga cómo funciona este proceso para cambiar el pronóstico de las pacientes con cáncer de mama. Ella fue la ganadora del premio a la mejor investigadora joven de los Premios Hipatia de elEconomista.es en su última edición.

Darío Lupiáñez reposted

Tineke Lenstra
@tinekelenstra.bsky.social

Sign up now for the EMBO meeting 'quantitative biology to molecular mechanisms'. Fantastic speaker lineup and plenty of speakers slots selected from abstracts. Submit your abstract before Sept 11!

EMBL Events@events.embl.org

You only have until 11 Sep to submit your abstract for #EMBOomics! ➡️ s.embl.org/omx26-01-bl Join us to discuss the latest developments in the field with leaders in genomics, dynamic proteomics, quantitative imaging, and synthetic biology.

Darío Lupiáñez reposted

Teresa Rayon
@trayon.bsky.social

Our work on the role of the proteasome in developmental tempo is out!!!! 🐭⌛️👤⏳ Six years after identifying an association between protein stability and developmental tempo, we now demonstrate a causal link between protein turnover and developmental tempo through proteasomal degradation

Developmental Cell@cp-devcell.bsky.social

Online now: Proteasome-dependent protein degradation shapes developmental tempo in mouse and human neural progenitors #biology #science

dlvr.itProteasome-dependent protein degradation shapes developmental tempo in mouse and human neural progenitorsWhy do mammalian species develop at different speeds? Nakanoh, Stamataki, et al. show that mouse neural progenitors have faster protein synthesis and proteasome-mediated degradation than human. Manipulating proteasome activity alters the pace of neural development, implicating protein turnover in the evolution of developmental tempo.

Darío Lupiáñez reposted

Arnaud Krebs
@arnaudkr.bsky.social

How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org

Guido Barzaghi@guidobarzaghi.bsky.social

📄 That's a wrap 📄 we're excited to share that the latest from @arnaudkr.bsky.social 's lab and Judith Zaugg's lab is at last online at doi.org/10.1038/s415.... Many thanks to my co-first @valentinabaderna.bsky.social and to @embl.org for the wonderful research environment.

doi.orgCumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency - Nature GeneticsThis study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...

Darío Lupiáñez reposted

EvodevogenomeUB- Cañestro’s lab
@evodevogenomeub.bsky.social

🫵🏼 If you want to do a PhD studying this wonderful creature of the pic, WE ARE NOW HIRING 💰!! Go to our profile for more info ℹ️. Postdocs are also welcome to get in touch!! 👇🏼👇🏼👇🏼👇🏼

Genetics UB@geneticsub.bsky.social

🎨 We merge science and art in our #PicOfTheMonth at @geneticsub.bsky.social 🔬 The image shows a lateral view of the trunk of an adult Oikopleura dioica, the closest living invertebrate relative to humans and other vertebrates. 📸 by @alfonso233.bsky.social @evodevogenomeub.bsky.social

Darío Lupiáñez reposted

Luca Giorgetti lab @FMI
@lucagiorgetti.bsky.social

Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...

nature.comThe genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature GeneticsWe show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

Darío Lupiáñez reposted

Arnau Sebé-Pedrós
@arnausebe.bsky.social

The third chapter in our coral single-cell trilogy is here. After mapping cell type diversity in Stylophora (Levy 2021) and exploring facultative symbiosis in Oculina (Levy 2025), we now uncover cell type-specific responses to heat stress. Find out more in @xgrau.bsky.social's thread below.

biorxiv.orgCell-resolved transcriptional responses during heat-induced coral bleaching and recoveryCoral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are dis...
Xavier Grau-Bové 🌾@xgrau.bsky.social

I'm happy to share our latest on #coral single-cell biology: a transcriptomic timecourse of heat stress in Stylophora pistillata, from bleaching to recovery 🪸🌊 This project was spearheaded by Shani Levy and carried through in @arnausebe.bsky.social's lab at @crg.eu. www.biorxiv.org/content/10.6...

Darío Lupiáñez reposted

Akis (Argyris) Papantonis
@akispapantonis.bsky.social

Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...

nature.comSenescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature AgingPalikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...
Darío Lupiáñez
@dariloops.bsky.social

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

Darío Lupiáñez reposted

Pablo Navarro
@pablonavarrolab.bsky.social

Epigenetics means different things for different people. In this workshop we will discuss two major views anchored on transcriptional memory: chromatin vs networks. Come and share with us our excitement for the topic and the magnificent place, the Andalusian Baeza. urldefense.com/v3/__https:/...

urldefense.comWorkshop Transcriptional memory in health and diseaseThe idea that cells remember past states to prepare their future endeavors has split into two parallel languages that rarely converse. On one side, chromatin epigenetics defines inheritance through th...

Darío Lupiáñez reposted

Toni Gabaldón
@tonigabaldon.bsky.social

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...