Ariel Kaplan

Congrats Courtney and the team! Very interesting work.

Oldies but Goldies. from 2007. Light-powering Escherichia coli with proteorhodopsin www.pnas.org/doi/10.1073/...

@arielchazan.bsky.social @galitzlil.bsky.social

Graphs showing 25 years of budgets for the National Institute of Health, NASA, and the NSF. In all cases, the proposed budget for next year is far, far below any year of the previous quarter century.

There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd.
It's not just budgets but research, institutions, expertise, and training the next generation.

The White House Vision for Dismantling Science in One Simple Plot Proposed NIH, NSF, and NASA budgets would be catastrophic for innovation and discovery. But they aren’t reality yet. The time to speak up is now.

open.substack.com/pub/joshuasw...

‘Scienticide’ in Argentina sparks huge protest by researchers Hundreds of activists wearing gas masks took to the streets to call out their government for slashing science funding.

www.nature.com/articles/d41...

Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis - Nature Communications The authors establish the ChIP-CryoEM method, which combines chromatin immunopurification coupled with cryo-electron microscopy, to visualize native human RNAPII elongation complexes in action, with a...

Nice work by the Kurumizaka Lab in @natcomms.nature.com

Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

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

Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity Transcription factors (TFs) regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo. Intrinsically disordered regions (IDRs) have emerged as ...

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New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?

www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics

Super cool work on the function of intrinsically disordered regions in regulating transcription factor DNA binding.

Direct observation of conformational dynamics of intrinsically disordered proteins at the single-molecule level Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are integral to many biological processes, including neurotransmitter regulation, microtubule regulat...

The energy landscape of a single disordered protein (tau) and the impact of PTMs is resolved. An important step to understanding the function and dysfunction of disordered proteins from their conformational ensemble. Not yet peer reviewed. www.biorxiv.org/content/10.1...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...

Thanks!

Thanks!
We don't know specifically about the sliding length - but that's definitely something we would like to look at.
And thank you for reminding me about your paper, very relevant and interesting.

Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity Transcription factors (TFs) regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo. Intrinsically disordered regions (IDRs) have emerged as ...

n/
www.biorxiv.org/content/10.1...
technion.bsky.social

#Transcription #TranscriptionFactors #IDPs #SingleMolecule #Biophysics
#IDRs #IntrinsicallyDisordered #OpticalTweezers #FacilitatedDiffusion
#DNAunzipping

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Kudos to Nir Strugo (nirstrugo.bsky.social)‬ who led the work, with help from Carmit Burstein, Noam Nago, and Hadeel Khamis, and also Saddam Hossein from the Hoffman Lab.
Thanks to Hagen Hofmann, Naama Barkai, Moshe Goldsmith, Gabi Rosenblum and vmindel.bsky.social��� for comments and/or help!

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Bottom line:
Using single-molecule assays, we show that IDRs modulate Msn2 binding to its target motif by tuning genome exploration.
This occurs via non-specific (or rather quasi-specific) association and sequence-sensitive facilitated diffusion, shaped by disordered regions.

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Together, our results support a model in which IDRs:
1. Facilitate initial non-specific association, stabilized by the DBD. Association, stabilization, or both, are sensitive to the sequence.
2. Enhance sequence-dependent diffusion toward the motif.

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What about the diffusion? sequence-sensitive ?
We perturbed IDR function during the sliding phase only (post-binding).
This had no effect for the arb. seq. but reduced STO probability and delayed detection for Hap4
⇒ IDRs enhance diffusion in a sequence-sensitive manner.

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Can we pinpoint which specific phase of the search is sequence-sensitive?
Hap4 showed increased non-specific binding, while dissociation rates (very low for both environments) were similar.
Conclusion: initial association, but not dissociation, is sequence-sensitive.

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Can this mechanism explain Msn2’s promoter selectivity?
We tested by replacing our "arbitrary" flanking region with a segment from the Hap4 promoter (a native Msn2 target).
Strikingly, STO binding increased to ~100%, and TFs were detected faster.

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Surprisingly, TFs were detected at the motif in ~30% of molecules, despite no free TFs in solution and irreversible dissociation conditions. This required intact IDRs, supporting a search mechanism based on non-specific binding and 1D diffusion on DNA.

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To test this, we developed a new assay, which we called Sliding-to-Target Occupation (STO):
We unzip DNA, incubate with TFs for 1 min, and then move to a TF-free channel where we perform repeated unzipping cycles to detect binding at the motif.

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Since IDRs increased both non-specific binding and association to the motif, we asked:
Can these non-specifically bound proteins ultimately reach the motif by sliding on DNA?

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We also found that Msn2 interacts with single-stranded DNA through its IDRs. This was evident in rezipping hysteresis, EMSA, and the kinetics of DNA hairpin closing.
These interactions may be relevant for binding melted promoter regions during activation.

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Based on these assays, and complementary EMSA and mass photometry experiments, we could conclude that IDRs promote cooperative formation of non-specific multimeric Msn2–DNA complexes, which are further stabilized by the DBD.

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During unzipping, we also detected non-specific binding events, evident as peaks far from the canonical motif.
These were frequent with full-length Msn2, rare with the DBD alone, and absent with the IDRs only or in protein-free controls.

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So IDRs affect the affinity, but is this due to a change in association or dissociation rate?
With our previously developed fluctuation assay (Khamis 2021), we saw that IDR deletion didn't affect k_{off} but reduced k_{on} 6-fold
⇒IDRs enhance association, not stability.

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Charge-mediated interactions mediate IDRs contribution: Adding free L-arginine reduced binding, but the effect was reversed at pH 9.8, where arginine is neutral. Notably, the DBD-only variant was less affected, giving us a tool to selectively perturb IDRs.

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Removing the IDRs sharply reduced both the probability and strength of binding at the recognition motif.
This suggests that IDRs enhance binding affinity.

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Msn2 has a canonical zinc finger DNA-binding domain (DBD) flanked by long IDRs.
What role do these IDRs play in DNA binding?
We used a single-molecule DNA unzipping assay capable of detecting DNA-bound proteins, and three variants: WT, DBD-only, and IDR-only.