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Alberto Marin @albertomarin.bsky.social · 12/06/2026

Link to the bioRxiv below! Thanks again to Tylar Matsuo, for his incredible work, and to Taekjip Ha, for his support and mentorship. 9/n www.biorxiv.org/content/10.6...

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

We found that loops on the broken chromatid promote the initial encounter between the break and the sister chromatid by steering the break toward TAD boundaries. Loops on the sister chromatid drive the subsequent 1D scanning that is the rate-limiting step for homology identification. 8/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

A surprising finding: removing loops in the broken chromatid had a small effect in search dynamics. It is the loops in the sister chromatid that play a dominant role in lowering search times! We looked at individual search instances to understand this. 7/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

Cohesin effects were more pronounced when we simulated searches along a large TAD (~1 Mb), where diffusion alone is inefficient. Hence, cohesin might be especially important in stimulating HR for breaks occuring in large TADs, that likely require more extended searches. 6/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

First, housekeeping cohesins accelerates the search by over 4x compared to 3D diffusion alone; adding break-interacting cohesins (break-anchored loops and cohesive clamp) boost the search by an additional 2x. Thus, searches are approx. an order of magnitude faster when cohesins are present! 5/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

Here, we used polymer simulations to model the homology search on a replicated TAD. Our simulations recapitulate key experimental findings (RAD51 ChIP-Seq profiles, chromosome contacts and HR efficiency) and reveal new insights into how cohesin promotes homology searches. 4/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

Recent works by us and others have shed light into these genomic searches, revealing that they are stimulated by the chromatin looping activity of the cohesin complex. But many questions remained unanswered. What are the dynamics of the process? How does loop extrusion stimulate the search? 3/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

After DNA replication, cells activate a mechanism to fix DNA breaks known as homologous recombination (HR), which restores a broken site using its replicated copy as template. HR is powerful, but it presents a unique challenge: the broken locus needs to search for and find its replicated locus. 2/n

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Alberto Marin @albertomarin.bsky.social · 12/06/2026

Excited to share our latest pre-print: www.biorxiv.org/content/10.6... where we built a biophysical polymer model of the mammalian homology search. This work was led by Tylar Matsuo, an outstanding post-bac student in the Ha lab that I have had the pleasure to mentor. Here is what we found. 1/n

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Alberto Marin @albertomarin.bsky.social · 05/12/2025

Thank you, Federico! And congratulations to you too! The studies complement each other quite nicely, indeed.

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Alberto Marin @albertomarin.bsky.social · 05/12/2025

Thanks, Jan! Congratulations to you too. Really amazing work!

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Last but not least, I am incredibly grateful to my mentor, Taekjip Ha, for giving me the freedom to take risks and for guiding me throughout the project. And co-mentor, Ralph Scully, for all his support and mentorship. 11/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Big thanks to our amazing team – especially co-first authors Adam and @namratan.bsky.social who put so much work into this project. It’s been a huge privilege to work with you. 10/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Thus, chromatin loops don’t just organize the genome to control gene expression – they also protect its integrity by helping a broken DNA find its matching sequence for repair! 7/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

We discovered that instead of searching randomly, cells use an active 1D scanning process: the repair machinery leverages a looping protein called cohesin to ‘slide’ the break along the DNA and find the matching sequence. 6/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Simply relying on random 3D diffusion – letting the broken DNA wander through the nucleus – would be inefficient. Even for a 1 Mb region, the broken DNA would take far too long to find its matching sequence by chance alone. 5/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Now, after DNA replicates, sister chromatids are held together approximately every 1 Mb so the search is confined to ~1 M nucleotides. But finding the right match is still a huge challenge – especially if the sisters aren’t perfectly aligned. 4/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Homologous recombination is key for protecting the genome, but it’s also challenging because the broken DNA must find its matching copy within billions of nucleotides. How can a cell achieve this? This is known as the “homology search” problem. 3/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

When DNA breaks, cells often repair it through a process called homologous recombination, in which a matching (replicated) copy of the broken sequence is used as a repair template. 2/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n www.science.org/doi/10.1126/...

science.org

Cohesin drives chromatin scanning during the RAD51-mediated homology search

Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Link to the publication below! 8/n www.science.org/doi/10.1126/...

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

Thus, chromatin loops don’t just organize the genome to control gene expression – they also protect its integrity by helping a broken DNA find its matching sequence for repair! 7/n

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

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Alberto Marin @albertomarin.bsky.social · 04/12/2025

When DNA breaks, cells often repair it through a process called homologous recombination, in which a matching (replicated) copy of the broken sequence is used as a repair template. 2/n

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

14/n I also want to thank all the other authors: Daniel Nguyen, Violetta Karwacki-Neisius, Andrew G. Li, Roger Zou, Franklin Aviles-Vazquez and Masato Kanemaki. And huge thanks to Yang Liu who made vfCRISPR and to @nucleosomezky.bsky.social and @rezakalhor.bsky.social for discussions!

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

13/n Incredibly thankful to my mentor, Taekjip Ha, who supervised and mentored me on this project, to my co-mentor, Ralph Scully, who designed the mESC exps and mentored me on HR, and to co-first authors Adam Rybczynski and Namrata Nilavar, who helped make this possible!

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

12/n Our model, in a nutshell: cohesin drives homology search via 1D scanning. During HR, a RAD51 filament locally scans the sister chromatid, but this search could be unproductive (e.g., because the donor is far). Cohesin loops would then facilitate long-range scanning to help find a donor!

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

11/n Does loop-extruding cohesin (Nipbl) regulates HR? In the short-range HR-GFP reporter, Nipbl depletion mildly reduces HR (45%). But in the long-range reporters, Nipbl depletion substantially reduces HR (75%). Thus, Nipbl is critical for HR when long searches are required.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

10/n We noticed that the RAD51 domain is constrained by TAD boundaries, suggesting a role for cohesin in mediating the homology search. Indeed, acute degradation of the cohesin unloader WAPL, known to yield elongated loops, resulted in a broader search.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

9/n So, we generated monoclonal mES cell lines with the donor at +441 kb and +563 kb from the break. When we induced the DSB…we found a beautiful RAD51 peak at the exact location of the donor! The RAD51 chromatin domain is thus capturing the homology search.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

8/n We used an HR-GFP reporter system. Upon inducing a DSB, a broken GFP gene can be repaired by HR via use of a 5’-truncated donor, giving a functional GFP. We reasoned that, upon DSB induction, RAD51 should show a peak at the donor, indicative of a successful homology search.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

/n But why does RAD51 spread to such long distances (~0.5 Mb) from the break? End resection was constrained to ~ 5 kb, so the broad RAD51 domain does not come from the RAD51-ssDNA filament. We hypothesized that the RAD51 domain reflects the homology search. We tested this.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

6/n Motivated by this finding, we performed a second time-course experiment, where we looked at the dynamics of RAD51 recruitment, the core HR factor. RAD51 dynamics mimic break-anchored loop formation, suggesting a causal relationship between loops and HR.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

5/n To answer this, we induced DSBs in cell-cycle-synchronized populations. Cells in late S/G2 phases, which are HR-proficient, showed break-anchored loops. But cells synchronized in G1, which are HR-deficient, did not show the loops. Break-anchored loops are HR events!

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

4/n Time-course Hi-C, enabled by our light-activated very fast CRISPR, showed that break-anchored loops are late repair events. Loops form after γH2AX domain, ruling out previous models where break-anchored loops propagate γH2AX at early stages. What is the role of such loops?

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

3/n Using our multi-target CRISPR system – which induces hundreds of DNA double-strand breaks (DSB) on demand – and Hi-C, we found that Cas9 breaks act as anchors for chromatin loops. Cohesin is recruited to the breaks and is required for break-anchored loop formation.

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Alberto Marin @albertomarin.bsky.social · 13/02/2025

2/n The homologous recombination (HR) pathway repairs DNA lesions by copying intact sequence information from a DNA template… but how does a damaged DNA find a correct DNA template in the 3D genome? We provide some answers to this Q, known as the homology search problem.

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