Arjun Udupa

The molecular basis of human transcription-coupled DNA repair - Nature Cell Biology This Review discusses transcription-coupled DNA repair in response to the stalling of RNA polymerase II on different types of DNA lesions and highlights the molecular details for the different steps i...

Dive into the step-by-step choreography of transcription-coupled DNA repair.

In our new review published in Nature Cell Biology, we explore what we know and what’s next in this exciting field of research!

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

Delighted to have our preprint led by @lvchosen1.bsky.social
up: Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells
biorxiv.org/content/10.1...

🧵 below ...

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

tinyurl.com/ydn6e3ac

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model https://www.biorxiv.org/content/10.1101/2025.06.25.661532v1

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u

A short thread follows 1/n

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Characterizing protein sequence determinants of nuclear condensates by high-throughput pooled imaging with CondenSeq Nature Methods - CondenSeq is an imaging-based, high-throughput platform for characterizing condensate formation within the nuclear environment, uncovering the protein sequence features that...

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out!

rdcu.be/eq975

Awesome paper alert! Learn about spectrum of chromatin condensate morphologies due to elastocapillary effects (no, liquids do not need to be spherical!), from amazing duo @dnamystrom.bsky.social & Hongbo Zhao, w/ important contributions from co-authors Jorine Eeftens, Mikko Haataja, Andrej Kosmrlj.

If heterochromatin is really a liquid-like condensate, why is it not spherical?
We investigated whether mechanical interactions between a condensate and a fiber network can explain the variety of morphologies seen in phase-separated nuclear compartments
www.biorxiv.org/content/10.1...

A high-affinity split-HaloTag for live-cell protein labeling https://www.biorxiv.org/content/10.1101/2025.06.15.659771v1

Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity Cis regulatory elements (CREs) interact with their target promoters over long genomic distances and can be identified using chromatin conformation capture (3C) assays. Their regulatory activity can be...

Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others.
www.biorxiv.org/content/10.1...

90% of doing science is being open to new ideas.

🔥 New episode of the Night Science podcast! The brilliant Eve Marder, professor at Brandeis University, talks with us about how "Recipe Science" ruins creativity.
Apple: podcasts.apple.com/us/podcast/n...
Spotify: open.spotify.com/episode/4mSv...

A protein-DNA surface hydrogel mechanically protects the cell nucleus https://www.biorxiv.org/content/10.1101/2025.05.21.655270v1

Many people are busy doing recipe science.. If you ask a grad student what they need to do to get a paper, they'll tell you this & this, & they'll know that 2 years before the project is done. And I'm thinking, what's wrong with this picture?
Eve Marder, on @nightsciencepod.bsky.social

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...

🚨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...

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...

Promoter strength and position govern promoter competition https://www.biorxiv.org/content/10.1101/2025.05.06.652547v1

So excited to see this live! Awesome work from
@giannatbusch.bsky.social on the concept of population-based synergy—using cell-to-cell heterogeneity to uncover new therapeutic vulnerabilities!

I am excited to share the latest paper from my lab where we leverage the selection bias of condensate-promoting oncofusions to uncover molecular rules governing condensate specificity and function. www.cell.com/cell/fulltex....

Oligo-LiveFISH is a high-resolution, reagent-based platform for studying 3D genome dynamics and their links to cellular processes in diverse cell types, including primary cells.

www.cell.com/cell/fulltex...
authors.elsevier.com/c/1kxK7L7PXu...

Low overlap of transcription factor DNA binding and regulatory targets - Nature A near-complete survey of transcription factor activities in Saccharomyces cerevisiae reveals that most transcription factors have both activator and repressor activities and limited overlap between t...

To the top of the "to-read" list. Looks like a heroic amount of work from the Hahn lab (large-scale ChEC-seq compendium!) www.nature.com/articles/s41...

This is a great podcast episode on using ChatGPT and the likes in science! Spoiler alert: A great prompt to make it generate good ideas for you is "Move 37 me!".
@nightsciencepod.bsky.social open.spotify.com/episode/5j73...

Integrator loss leads to dsRNA formation that triggers the integrated stress response Integrator (INT) prevents the escape of immature RNAPII to ensure full-length mRNA production. INT deficiency causes defects in RNAPII maturation that lead to premature termination, accumulation of immunogenic dsRNA, and activation of the integrated stress response (ISR) observed in patient cells.

Now online! Integrator loss leads to dsRNA formation that triggers the integrated stress response

How can we exploit AI's hallucinations to make us more creative by generating new connections and ideas?
We talk about it on this week's Night Science Podcast
@nightsciencepod.bsky.social @emollick.bsky.social
podcasts.apple.com/us/podcast/n...

AI was ridiculed as recently as 5 years ago, but today it’s hard to conceive of a future without it. We must talk about how this tool can make us more creative for coming up with new research ideas and helping us test them. Check out @emollick.bsky.social on the podcast @nightsciencepod.bsky.social

Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11

Contrary to popular belief, what is important in science is as much its spirit as its product: it is as much the openmindedness, the primacy of criticism, the submission to the unforeseen, however upsetting, as the result, however new that may be. – Francois Jacob
www.nature.com/articles/s41...