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Reposted by Jakob Trendel

Kusterlab @kusterlab.bsky.social · 23/04/2026

🚨📢 New paper online 🚨📢 Four Xlinking flavors in living cells, up to 1000-fold faster. Highlights include Xlinking kinetics of the RNA-binding proteome and a new way to quantify cytosolic RNA interactions only minutes after ribotoxic stress. #RNASky #Chromatin #Proteomics doi.org/10.1093/nar/...

doi.org

Rapid photo-crosslinking in living cells reveals protein–nucleic acid dynamics on a timescale of minutes

Abstract. The activation of chemical reactions in living cells using ultraviolet (UV) light enables the interrogation of biomolecules in their native envir

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Reposted by Jakob Trendel

Kusterlab @kusterlab.bsky.social · 09/09/2025

New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...

doi.org

Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces

Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution. However, current isolat...

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Reposted by Jakob Trendel

Kusterlab @kusterlab.bsky.social · 25/08/2025

New Preprint: High-intensity 365 nm irradiation accelerates photoreactions in living cells by up to 1000×. We show protein–drug 💊, –protein 💪, –DNA 🧬, –RNA 🧬 crosslinking within seconds, and analysis by #massspec for #proteomics, #chembio, #chromatin and #RNAbiology. www.biorxiv.org/content/10.1...

biorxiv.org

Enhanced photo-crosslinking in living cells with high-intensity longwave ultraviolet light

The activation of chemical reactions in living cells using ultraviolet (UV) light enables the interrogation of biomolecules in their native environment with photoreactive probes or crosslinking reagen...

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Jakob Trendel @jtrend.bsky.social · 24/05/2025

Thanks for your help with the first trials. Initially cells had to be irradiated quickly, before the LEDs desoldered 😂

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

Thanks for your contribution, was great to collaborate on this.

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Reposted by Jakob Trendel

Kusterlab @kusterlab.bsky.social · 22/05/2025

🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...

cell.com

The human proteome with direct physical access to DNA

Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes with single-amino-aci...

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

Very happy we pushed this across the finish line. Huge thanks to all the co-authors: Simon, Shuyao @shashuyao.bsky.social, the Greulich lab @franzigmuc.bsky.social, Susi, Karin @baybioms.bsky.social, Sandra, the Kubicek lab, the Uhlenhaut lab, and especially Bernhard @kusterlab.bsky.social. (11/11)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

Overall, we present a resource of nearly 50 photo-crosslinked, i.e. direct physical, DNA interactomes and identify 688 peptide-DNA crosslinks. These crosslinks mark known but also unknown protein-DNA interaction sites, some overlapping with variant sites linked to genetic or somatic disease. (10/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

DNA photo-crosslinking takes 1 minute on ice, while formaldehyde requires 10 minutes at room temperature. We record a time series of photo-crosslinked DNA interactomes during acute BAF inhibition and identify fast-acting restrictors of chromatin accessibility missed by conventional methods. (9/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

We use these quantitative powers to profile three genotoxic drugs and find very distinct reactions in the DNA interactome of cancer cells. This reveals drug-specific vulnerabilities that can be exploited for combination treatments. (8/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

This also works in primary cells, where we see recruitment of inflammation-associated transcription factors to DNA in macrophages challenged with LPS. (7/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

To identify transcription factors or chromatin modifiers responding to changes in a cell, DNA interactomes can be compared between conditions. Treating breast cancer cells with increasing estrogen doses, we find the estrogen receptor and other regulators recruited to DNA dose-dependently. (6/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

In contrast to formaldehyde crosslinking, photo-crosslinking only captures direct interactions (‘zero-distance’). The proteins we find in close proximity to DNA show very high degrees of intrinsic disorder. In fact, intrinsic disorder rises the closer proteins localize to DNA. (5/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

XDNAX extracts are very clean and we discover previously elusive peptide-DNA crosslinks within them. They pinpoint protein-DNA interaction sites to individual amino acids. (4/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

To analyze protein photo-crosslinked to DNA by proteomics, we develop XDNAX: protein-crosslinked DNA extraction. (3/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

Unlike natural DNA, 4ST can be activated by wavelengths far outside the absorption range of most natural biomolecules. This avoids photodamage, allowing us to use high-power LEDs, with ~1000-fold higher intensity than conventional bulbs, for activating 4ST in living cells (www.uven.org). (2/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

UV crosslinking works great for protein-RNA complexes, but DNA is much less photo-reactive and photo-crosslinking not commonly used. Analogous, we find that the photo-activatable nucleotide 4ST (DNA) is about ten times less reactive than the commonly used 4SU (RNA). (1/n)

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Jakob Trendel @jtrend.bsky.social · 23/05/2025

Excited our paper is out in Cell @cp-cell.bsky.social! 🧬⚡ DNA photo-crosslinking proteomics in living cells 🎯 Pinpoints protein-DNA interactions to single amino acids 🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes 🔗 www.cell.com/cell/fulltex... 🧵

cell.com

The human proteome with direct physical access to DNA

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