Sandipan Brahma

Our paper on RNAPII-BAF-TF synergy is now out in @NatureGenet! Since publishing the preprint (🧵➡️ tinyurl.com/36jtfraj), we added expt to show that enhanced nucleosome eviction upon stabilization of BAF by RNAPII, assayed by CUT&RUN.ChIP, is ATP-dep. ➡️rdcu.be/dsJPk

GCBA Seminar Series announces Dimple Notani, PhD, EMBO Global Investigator, National Centre for Biological Sciences - TIFR presenting "RNA as a Key Regulator of Enhancer Hierarchies and Promoter Priming." @DimpleNotani @UNMC_GCBA @UNMC_BISB

GCBA Seminar Series announces Jean-Paul Armache, PhD, PennState University, Department of Biochemistry presenting " Translating Motion and Heterogeneity into Insights Using Cryo-EM" @UNMC_GCBA @UNMC_BISB @valendraica

Nice paper. It's kind of cool/funny to watch over the last few decades the idea that low-affinity motifs play an important role in gene regulation going from basically the lunatic fringe to mainstream.

Proud to be part of the Upper Midwest Emerging Scholars Exchange Program! Read about how we're building collaborative networks across institutions to advance #CancerResearch @GrinuMathew @BrahmaComplex @UWCarbone @MCWCancerCenter @UMNCancer unmc.edu/newsroom/2025/…

Thanks, @NEDHHS and brahmalab.org members! We are excited to take our tools and fundamental mechanistic insights on chromatin regulation to the next level and apply them directly to address critical knowledge gaps in cancer biology. @UNMC_GCBA @CHRI_ResearchNE

The 2025 Henry M. Lemon Short Course in Cancer Biology was outstanding! Thanks to incredible speakers @BlaineBartholo2 (@MDAndersonNews) @HargreavesLab (@salkinstitute) @TheRobertsLab1 (@StJudeResearch) Anthony Imbalzano (@UMassChan) & faculty hosts Angie Rizzino @BrahmaComplex!

My lab has been working for the past 15 years to develop a method to isolate specific genomic loci to identify its chromatin composition & protein interactome. Finally,… our superb physician/scientist Dr. Bercin Cenik @bkcenik did it and here it is cell.com/molecular-cell… Not only was she able to develop this method, which she calls TurboCAS, she was able to identify known & novel regulators of heat shock & Myc expression. Cannot wait to see what Bercin and TurboCAS will discover about the molecular basis of transcriptional regulation with great impact on clinic in the next few years! @NU_BMG_SQE @NUFeinbergMed @MolecularCell

My guidelines for exploratory data analysis

GCBA Seminar Series announces Aparna Bhaduri, PhD, Assistant Professor, University of California, Los Angeles (UCLA), Dept of Biological Chemistry presenting "Characterizing Cell Fate Specification in the Developing Human Brain and Glioblastoma" @BhaduriLab @UNMC_GCBA @UNMC_BISB

Thrilled to share our new work @biorxivpreprint: biorxiv.org/content/10.110… Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live cells. We reveal genome chromatin is essentially replicated from regions with greater nucleosome motions. 1/2

Kudos to my outstanding team for developing genomic and epigenomic maps of mouse satellite regions (centromeres and pericentromeres), which account for ~11% of the mouse genome. Very excited to share the preprint. biorxiv.org/content/10.110…

With David and the Baker Lab in the spotlight today, I wanted to share some insights into the @UWproteindesign and how it operates, a glimpse behind the curtain. I had planned to write this post-graduation, but now seems as good a time as any. (Got twitter blue free trial so this could all fit in less tweets!) First, the lab is enormous. ~60 grad students, ~60 postdocs, a handful of visitors, undergrads, and a surrounding institution of another 150 or so. Collaboration is strongly encouraged (even mandated) by David, who sets up pro-collaboration incentives. Notably, he's fine with grad students graduating without a sole first-author paper—it's acceptable to "only" have worked as a co-first author. This is a key ingredient in the secret sauce: the tight collaboration between wet lab and dry lab. It ensures that all our work is ultimately grounded in strong wet-lab validation—our "oracle" is the real world, not another computational model. While we have regular meetings for different subgroups and the entire group, much information travels through the lab via informal one-on-one interactions. In some ways, it reminds me of a classic "tribe of humans in the state of nature"—100-200 people with no clear hierarchy, passing information via "gossip". It’s maybe not the most complete way of ensuring everyone is on the same page, but saves time as we aren’t drowning in endless meetings. Does David stay in touch with all these grad students and post-docs? Remarkably, yes. Unlike some very large labs known for being run entirely by post-docs, he knows exactly what everyone is working on and the stage of their projects. Each member has monthly one-on-ones with him, and monthly subgroup meetings that David attends. If he suggests you try something at your previous one-on-one, you'd better have it done by the next. Does he actually contribute research ideas, or is he more of a detached big-picture project manager? Definitely the former. He understands the intricacies of a shocking range of topics. I'll be discussing some arcane deep learning concept with him, and then he'll turn around and talk to someone about the details of a catalytic mechanism. He's actually the most hands-on PI I've ever had—if anything, he verges on over-managing rather than being too detached. How does he keep track of everything? Partly, he's just a brilliant person with exceptional recall. But he has also built infrastructure above and below him in the lab to handle many of the details, bureaucracy, big picture, and management tasks. This allows him to spend most of his day doing what he's most passionate about and skilled at: walking around talking to people about science. He also lives very much in the moment and in his own words, “never thinks very far ahead". To keep up with tools, methods, and wet lab techniques, he does the occasional project and design campaign himself on the side when time allows. It's still a tremendous cognitive load to keep all this in his head, but as much as possible, he has offloaded non-scientific cognitive burdens. It helps that he’s in the lab in person most days of the year, rarely traveling for conferences or talks, instead doing them over Zoom or not attending. (1/2).

Happy to contribute to this new preprint by @ElenaPugachev12, @boris_ctcf & Co. What determines differential CTCF binding, beyond DNA methylation and TF/nucleosome competition? Answer: a specific nucleosome downstream of CTCF motif. Directionality matters! biorxiv.org/content/10.110…

Excited to share the latest story from the @arnaud_kr lab @embl ! Together with @ChristineMoene we used Single Molecule Footprinting to reveal that RNA Pol II occupancy occurs at surprisingly low-frequency at mammalian promoters! Thread below (⬇️) 1/11

This looks pretty cool!

🎊🎉 #FragileNucleosome is back! You can now register for our 25th of September seminar session! We are excited to have @RemiXCoux and @VondriskaLab talk about their research and kick-off #FragileNucleosome seminar series! 🗓️us06web.zoom.us/webinar/regist…

@poly_microbial Congratulations, that's awesome!

I’m excited to share my 1st postdoc paper! The thread below summarizes the main findings of our study. biorxiv.org/content/10.110…

The first paper from our lab is now out in peer-reviewed form @LSAjournal. Huge congratulations to the first author Mary Bergwell, @STEMinistSkater, now in grad school at UPenn, and second author @JY_Park102! I am very proud of their hard work. They even let me do a few expts!

Transcriptional control from stochastic action at the single-molecule scale

Awesome new paper just popped up in my feed. Congrats @kirkland_lab! life-science-alliance.org/content/7/11/e…