Sergei Rudnizky

@HFSP postdoc @BostonChildrens @harvardmed w/ @taekjip. Past:@EMBO fellow, @JohnsHopkins. Phd w/ @akaplanz & @LabPMelamed @TechnionLive. I ❤️ #chromatin

[Sergei Rudnizky @nucleosomezky]

🧵1/n Excited to share our new preprint on CTCF dynamics. The small but powerful CTCF binds only ~20 bp, yet controls Mb-scale chromatin loops by directionally capturing a ~7x larger cohesin complex racing along DNA at 1-3 kb/s. How does CTCF do this?

[bioRxiv Biophysics @biorxiv_biophys]

Ultrafast CTCF dynamics control cohesin barrier function https://t.co/U0Nn5nTqyO #biorxiv_biophys

[Sergei Rudnizky @nucleosomezky]

How does RNAP get past a TF bound in its path? Not by merely pushing it off. We think it destabilizes the TF in a distance-dependent manner. The barrier is set by the TF's res. time, which may be tuned by gene-body CpG methylation. Congrats to @Noamnago @akaplanz, and the team!

[Ariel Kaplan @akaplanz]

🧵New preprint! How does an elongating RNA polymerase deal with a DNA-bound transcription factor in its path?

We developed a label-free single-molecule assay that detects RNAP arrival by suppression of fluctuations in a partially unzipped DNA fork.
https://t.co/L8Oscmt02P
1/

[Debbie Toiber @ToiberDebbie]

Alfredo is one of the most talented people I have worked with; he created this amazing resource. It will help us understand how the cell coordinates the DSB response depending on the dynamic interactome of the sensor (HR, NHEJ), give us insight into the topological organization

[Anders Sejr Hansen @Anders_S_Hansen]

(1/16) Our 3-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack is out:

Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)?

A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): https://t.co/wyPaLyvR8A

[Taekjip Ha @taekjip]

We are thrilled to announce an opening for a tenure-track assistant professor in PCMM, Boston Children's Hospital and Harvard Immunology! Apply by August 2, 2026.

[Alberto Marin-Gonzalez @AlbertoMarinG1]

Excited to share our latest pre-print
https://t.co/5ww6esLMM0
where we built a biophysical polymer model of the homology search. This work was led by Tylar Matsuo, an outstanding post-bac student in the Ha lab that I have had the pleasure to mentor. Here is what we found. 1/n

[Quentin Smith @Q_M_Smith]

1/10 In our story out today in @Nature, we showcase the molecular mechanisms that enable Cas9 to bind and cleave negatively supercoiled ((-)SC) off-targets! 🧬🧵

🔗 https://t.co/TagDO5kbRv

#CRISPR #Cas9 #DNATopology #AFM #CryoEM #SingleMolecule #Biophysics

[Epigenome Technologies Inc. @EpigenomeTech]

Epigenetics Update - DNA methylation shapes transcription factor binding beyond canonical CpG contexts https://t.co/b1xK5kb9qQ

Ariel Afek (Weizmann Institute of Science) in PNAS

#Epigenetics #DNAm
---

Perfect for cancer, immunology, and aging; https://t.co/WmSYDGXnzb

[Alberto Marin-Gonzalez @AlbertoMarinG1]

Thrilled to share that my postdoc research is published today in @ScienceMagazine !! We found that DNA repair uses cohesin to build chromatin loops that guide the homology search and boost accurate repair! 1/n
https://t.co/DxArg8suv8

[Sergei Rudnizky @nucleosomezky]

9/n @BostonChildrens @HHMINEWS @harvardmed @JohnsHopkins @UofIllinois @MIT @viennabiocenter @UCPH_Research @tudelft

[Sergei Rudnizky @nucleosomezky]

🧵1/n Excited to share our new preprint on CTCF dynamics. The small but powerful CTCF binds only ~20 bp, yet controls Mb-scale chromatin loops by directionally capturing a ~7x larger cohesin complex racing along DNA at 1-3 kb/s. How does CTCF do this?

[bioRxiv Biophysics @biorxiv_biophys]

Ultrafast CTCF dynamics control cohesin barrier function https://t.co/U0Nn5nTqyO #biorxiv_biophys

[Sergei Rudnizky @nucleosomezky]

8/n @PJMurray14 @HemaniChhabra @aksimentievLab @UrteagaRaq5336 @Sushilpangeni3 @NHatzakis @mosoriov91 @LucasFarnung @seyvos @timp0 @taekjip Jasmin Zarb, Jan-Michael Peters and and other twitter-less collaborators!

[Sergei Rudnizky @nucleosomezky]

7/n We would also like to thank the laboratories of Sua Myong, Bradley Bernstein, Anders Hansen, Frederick Alt, and Carl Wu for their feedback, and all members of our collaborating labs for many helpful discussions!

[Sergei Rudnizky @nucleosomezky]

6/n And a huge thanks to our collaborators: Hemani Chhabra (Aleksei Aksimentiev lab), Laura Caccianini (Seychelle Vos lab), Iain Davidson (Jan-Michael Peters lab), Manuel Osorio-Valeriano (Lucas Farnung lab), and Paul Hook (Winston Timp lab)!

[Sergei Rudnizky @nucleosomezky]

5/n A big thank you to our friends and colleagues in the Ha lab who shared their expertise: Sushil Pangeni, Raquel Merino-Urteaga, Paul Meneses, and Jingzhou Hao

[Sergei Rudnizky @nucleosomezky]

4/n Kudos to graduate students PJ Murray and Emily Sørensen (from the Hatzakis lab), to Theo Koenig, who did a Master’s with us, and to our mentor @taekjip!

[Sergei Rudnizky @nucleosomezky]

3/n In short, powered by its DNA-binding domain (11 zinc fingers!), CTCF ‘searches’ for cohesin without dissociating from its motif. This local search is tuned by chromatin context and by PDS5, a non-extruding cohesin subunit, enabling tunable, multiscale control over the genome

[Sergei Rudnizky @nucleosomezky]

2/n To tackle this, we threw essentially every single-molecule tool we have at the problem - optical tweezers, fleezers, TIRF, AFM, MD simulations, and single-molecule sequencing in cells - to show that CTCF possesses a striking physical property

[Anders Sejr Hansen @Anders_S_Hansen]

(1/8) Excited to see our collab w. @ViraatGoel Ed Banigan @ngaboreden James Jusuf, Leonid Mirny and Gerd Blobel out in @NatureSMB https://t.co/2Ri3nom8jt

This was co-submitted with A Schooley and Job Dekker's preprint https://t.co/0Y6CmePM1Z which should also be online soon.

[Xinyu Feng @xashleefeng]

A brief summary/perspective on my recently published PhD work: Nucleosomes constrain 1D DNA diffusion by eukaryotic transcription factors https://t.co/VnpaEu0gbc @taekjip

[Taekjip Ha @taekjip]

GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion

https://t.co/LbRmYoghXG