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Posts by Pedro Rocha

Home | Levine Lab

📣 Exciting news: my lab is moving to the Krembil Institute at the University of Toronto’s University Health Network in Fall 2026.

We’ll be recruiting for all roles, so reach out if you’re interesting in joining us to study spinal circuits for sensorimotor control

www.levine-lab.org

17 hours ago 94 25 9 3

Congratulations Takashi!

10 hours ago 0 0 1 0
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I’m tenured! Thank you so much to everyone here, mentors, lab mates, colleagues, and the meiosis/centromere community for your support. This achievement was made possible by all the hard work by my amazing lab members over the past 6 years!🥳

13 hours ago 48 2 7 0
Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields

New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵

1 week ago 49 21 2 1

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...

2 days ago 113 56 4 9

We got the cover of @natneuro.nature.com April issue for Mukund's article!

1 week ago 23 1 1 0

Our study with @melnicklab on the discovery of a transient and tightly-regulated, plastic state of mature B cells during physiological immune response and potential links to aggressive lymphomas now out at NCB.👇Detailed threat by the amazing lead author @lscourzic.bsky.social!.
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3 months ago 3 3 1 1

🚨🚨 New preprint 🚨🚨
We found that the ovary directly controls protein appetite in Drosophila.
Yes — the ovary doesn’t just make eggs… it tells the fly what to eat!
www.biorxiv.org/content/10.6...
If you want all the details, click above ☝️
If you just want the fun, GIF-guided overview, keep reading 👇

3 weeks ago 53 23 4 7
A dual role for CTCF in development CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

1 month ago 112 55 7 4
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🚨 Job Alert - Please share! 🙏

Interested in 3D gene regulation in development & evolution? 🤓🧬

💥 Our lab at @cabd-upo-csic.bsky.social is expanding!

We’re recruiting:
✅ PhD students
✅ Postdocs
💻🧪 Experimental or computational backgrounds welcome

👇 Details below

1 month ago 41 38 1 5
Flyer for symposium: https://ctrlepiedit.sciencesconf.org/

Flyer for symposium: https://ctrlepiedit.sciencesconf.org/

Very excited to announce the FIRST symposium on epigenome editing! These tools are becoming widely used in mol bio, ag & therapy. It's time to bring leaders together to discuss this rapidly growing and exciting field. And why not in Paris! Please register & share! (1/2) ctrlepiedit.sciencesconf.org

1 month ago 84 58 3 6

We are very proud to present our newest paper on the role of Wnt signalling in abscission dynamics in stem cells! A brief thread to entice you to read Snježana’s exciting foray into signalling.

1 month ago 47 14 3 0

Can we make brains “smarter”? By boosting mitochondrial metabolism in neurons of memory circuits, we improved memory in flies and mice. Thrilled to see this work out - congrats to @amrapalianjali.bsky.social for spectacular work, and to all lab members for invaluable contributions!

2 months ago 58 20 1 6
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Come on join us! We are searching for the next technical associate to join our lab ~Summer 2026.

This could be a great position for someone who is graduating this spring and is looking for 2 more years of research experience before starting their PhD:
careers.peopleclick.com/careerscp/cl...

2 months ago 17 11 0 1
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Liver-X-receptor agonism enhances T cell priming and activation to promote anti-tumor immunity Ostendorf et al. show that activation of liver-X-receptors preconditions T cells to render them more receptive to adopting effector states upon activation.

Delighted to share our new paper on LXR agonism pre-conditioning T cells to more readily adopt effector states, out in @jem.org today. This was a long project started in @sohailtavazoie.bsky.social's lab and completed across the atlantic here in Berlin at Charité.

2 months ago 10 4 4 0

New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.

2 months ago 44 22 4 1
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LoopBin – a VaDE-based neural network for chromatin loop classification Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling. ### Competing Interest Statement The authors have declared no competing interest.

Preprint alert! 🥸

Yajie Zhu (PhD graduate) and Mariano Barbieri (postdoc, @spp2202.bsky.social Accelerator award) produced a package that will classify loops in your #3Dgenomics data based on (whichever) epigenomic data you have available. Keep reading...

1/n

www.biorxiv.org/content/10.6...

3 months ago 24 11 1 0

Preprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them!

www.biorxiv.org/content/10.6...

3 months ago 26 16 0 0
Client Challenge

Our work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41...
Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)

3 months ago 37 18 2 2
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Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...

Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l

3 months ago 71 32 7 1
Read in Nature: nature.com/articles/s41586-025-09899-8

Read in Nature: nature.com/articles/s41586-025-09899-8

Stress controls epigenetic inheritance!

A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8

3 months ago 36 22 3 4
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Glad to share our latest work that came out recently. We dive into the mechanisms of how Transcription Factors (TFs) like the nuclear receptor, ERα navigate the genome to find their targets.

3 months ago 20 9 3 0

🚨Seeking developmental or cell biologists🔬!🚨
Our department @ucl-cdb.bsky.social is looking to support scientists seeking to establish their lab with a fellowship. Deadline: 30 Jan. Apply here: www.ucl.ac.uk/work-at-ucl/...

4 months ago 9 9 0 1

Superstar

4 months ago 1 0 1 0
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🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨

#PhD #3DGenome

5 months ago 36 37 0 3
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We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇

5 months ago 16 14 0 0
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Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

5 months ago 209 79 6 11
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Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...

Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!

…and I’m currently on the job market looking for a new scientific home!

www.nature.com/articles/s41...

5 months ago 51 17 1 1
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In vitro approaches to study centriole and cilium function in early mouse embryogenesis Although centrioles and primary cilia play an essential role in early mammalian development, their specific function during the interval between their initial formation and the subsequent arrest of em...

Really excited to see this out in the open: www.life-science-alliance.org/content/9/1/...! @isabellavoelkl.bsky.social explored and compared different in vitro developmental model systems to study ciliogenesis.

5 months ago 16 9 2 0

Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!

5 months ago 36 51 1 0