Bintu Lab @BintuLab
Single-cell chromatin and gene regulation dynamics for better cell engineering @ Stanford BioE bintulab.com Stanford, CA Joined November 2018-
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@srikosuri @JoshTycko @anshulkundaje @abbythurm As you can see in Fig. 10, it can be quantitative with a good reporter. Here's the comparison with flow (y-axis) vs. pooled screen score (x-axis) for a small (1500) and medium (10,000) library. Each dot is a cell line we made for validation/calibration. 100,000 can be noisier :)
We used HT-recruit repeatedly to discover new protein domains involved in gene regulation and test many mutants. It can be used for domains associated with other functions (if you have a reporter). Now we published a detailed protocol on how to do it: nature.com/articles/s4159…
We hope this protocol is useful for people doing large scale protein function work! nature.com/articles/s4159… Led by @abbythurm from @BintuLab
So we beat on. Gene/cell therapies often use proteins that could be recognized/rejected as non-self by our immune system. We combine algorithms to build proteins that are therapeutically relevant and can masquerade as our own parts doi.org/10.1101/2025.0…
Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia! nature.com/articles/s4158…
Development of compact transcriptional effectors using high-throughput measurements in diverse contexts go.nature.com/3NMu00N
Lastly, I would also like to give a shout out to Nate Hathaway’s lab @UNCPharmacy for writing a beautiful preview article elegantly describing our work. Please check it out here! : shorturl.at/hycOp (4/4)
I'm thrilled to announce that my PhD thesis work from @BintuLab on how the H3.3K36M oncohistone disrupts the establishment of epigenetic memory is now out in the latest issue of @MolecularCell. shorturl.at/X9IZG (1/4)
Online Now: The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation dlvr.it/TF93Ry
Join us in Heidelberg for this great conference! Submit an abstract, we will select 20 talks (you have to register in the system first: embl.ungerboeck.com/PROD/emc00/Pub… )
🧬🙌🏻 Only a week left to submit your abstract for 'Quantitative biology to molecular mechanisms' – over 20 talks will be selected from abstracts, with a priority for early stage researchers, so don't miss your chance! #EMBLOmics ➡️ s.embl.org/omx24-01 📜 Deadline: 27 Aug
🧬How do transcriptional cofactors recognize which genes to regulate?🧬 Check out our new preprint from @fordycelab @BintuLab that tackles this question and provides the first-ever quantitative map of disordered transcriptional protein interactions (1/9) biorxiv.org/content/10.110…
(1/16) Check out our @SimonMJGaudin paper tiny.cc/icuazz from the Canzio lab out in @ScienceMagazine today on how tuning local cohesin trajectories enables differential readout of the clustered Protocadherin (Pcdh) locus across different types of neurons.
Got out of the nucleus! Tested ~30,000 tiles from human RNA-binding proteins, found lots of domains that downregulate RNA&built an inducible synthetic RNA-binding protein for keeping target RNA at constant intermediate levels: biorxiv.org/content/10.110… So many follow-up projects!
Do human RNA-binding proteins have modular regulatory domains that downregulate RNA lifetimes? Our preprint @BintuLab studying this question is now out on bioRxiv, where we indeed identify small domains in RBPs that potently induce RNA degradation! biorxiv.org/content/10.110… (1/9)
Our first RNA-centric preprint is online! Congratulations to @abbythurm and the whole team - we're so excited to continue learning about effector domains in RBPs, and to hear your thoughts about what could come next!
Do human RNA-binding proteins have modular regulatory domains that downregulate RNA lifetimes? Our preprint @BintuLab studying this question is now out on bioRxiv, where we indeed identify small domains in RBPs that potently induce RNA degradation! biorxiv.org/content/10.110… (1/9)
We are hiring a lab manager/research assistant! More details and how to apply here: bintulab.com/2024/06/01/hir…
A little late, but we're excited to share our preprint in collaboration with the Greenleaf lab that uses single-molecule footprinting at an engineered locus in mammalian cells to understand how TF occupancy dictates expression!
Our work using single-molecule chromatin configurations to link TF binding to gene expression is now out on bioRxiv! Amazing effort from @bgrdoughty, @MichaelaThinks, and @juliaschaepe, and an immensely rewarding collaboration with the @BintuLab: biorxiv.org/content/10.110… [1/n]
Finally, I would like to note that the NFZ TAD developed by @JoshTycko, @BintuLab , and Bassik lab (link below) works very well in the synZiFTR toolkit, AND it can be further boosted with our new enhancement. That's all for now -- please stay tuned! 4/n biorxiv.org/content/10.110…
It's a double feature on epigenetic memory today! Check another amazing new preprint on single-cell chromatin compaction and memory establishment from wizard postdoc @fjmrt!
New preprint! We studied how single-cell 3D chromatin structure changes under targeted epigenetic perturbations using multiplexed DNA FISH and synthetic biology tools, and found an intriguing relationship between chromatin compaction and epigenetic memory. biorxiv.org/content/10.110…
@sinha_joydeb Huge thanks to @nickels_jan, @abbythurm, Connor Ludwig, @michaelathinks, @bella_arch, Jun Wan, and of course @BintuLacra for all the support during this project. We’re also grateful for an amazing collaboration with the Dong Fang lab and their chondroblastoma model! (9/9)
@sinha_joydeb Finally, we used all of this data to develop a 3-state chromatin spreading model that integrates H3K9me3 and DNA methylation to predict epigenetic memory for a parameter space that covers a range of KRAB recruitment durations and strengths. (8/9).
We’re excited to announce our new preprint, ‘The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation,’ expertly led by graduate student @sinha_joydeb! (1/9) biorxiv.org/content/10.110…
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