Kaushik Ragunathan

“We saw that these campus use rules were being used specifically to restrict the freedom of expression of faculty members…We don’t think that that is conducive to the type of academic freedom that makes a great university.”

NYU cancels live school graduation speakers - Washington Square News Graduation speakers will no longer give live remarks at school-based ceremonies and must instead record their statements for a video, in compliance with a policy NYU is rolling out this year. The tran...

1 / I’ll have more to say about this soon—in fact, there’s a fair amount in The Overseer Class about the role I probably played in leading to this farce…. www.google.com/url?q=https:...

First 24 hours of embryonic development in 9 different animal species: (From left to right) Zebrafish, Sea urchin, Black widow spider, Tardigrade, Sea squirt, Comb jelly, Parchment tube worm, Roundworm, Slipper snail. Credit to @tessamontague.bsky.social & Zuzka Vavrušová. #ZebrafishZunday #devbio 🧪

A Cinderella story: raising CLIP-tag from the ashes to shine in fluorescence labeling.
www.biorxiv.org/content/10.6...

The key finding: when we model HULC together with the HMD domain of Prf1, the RING domains and Rhp6 snap into a catalytically primed configuration. Without Prf1, the RMSD versus a known primed RING-E2-Ub structure is ~32 Å. With Prf1, it drops to 1.2 Å.

You are finishing your PhD and looking to continue in science?

The Martin lab @biology-unige.bsky.social has an open postdoctoral position in cell biology to study cell-cell fusion. For more information, please consult mocel.unige.ch/research-gro....

Thanks for reposting!

US universities can no longer provide a horizon of political aspiration, let alone an associational network, for colonized elites. The empire has no clothes. This war has not even the fig leaf that Bush and Obama could use to hide the brutality and rapacity of empire.

Trump has decisively collapsed the US empire’s sleight of hand. There is no distinction or space between the brutality of the colony and the empire itself. ICE has brought home colonial barbarity. USAID has disappeared, along with the facade of imperial benevolence.

Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...

Engineering intrinsically disordered regions for guiding genome navigation Intrinsically disordered regions (IDRs) navigate transcription factors (TFs) to their binding sites in genomes, raising the question of how IDR sequen…

Beautiful and intriguing piece of work on the role of hydrophobic residues in IDRs in guiding TFs to their binding sites
www.sciencedirect.com/science/arti...

A new preprint from the @archaeon-alex.bsky.social and Joey Davis (MIT) labs! We solved the structure of the ribosome from the archaeon Haloferax volcanii and discovered a new highly conserved ribosome hibernation factor that we named AHA (AMPKγ–HPF from Archaea) 🧵⬇️ www.biorxiv.org/content/10.6...

And a new paper from the lab. A follow up to a previous study in which we elucidate the mechanism of the nuclear transport. Read the full story: www.nature.com/articles/s41...

Tag line: mirror for US imperialism

🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a “super pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause

Evolution of error correction through a need for speed Kinetic proofreading is a class of error-correcting mechanisms in biology that expend energy to avoid mistakes during replication, transcription, and translation. Proofreading is typically assumed to ...

@science.org Evolution of error correction through a need for speed | Science #evolution 🧬🔬 www.science.org/doi/10.1126/...

Happy to share our Current Opinion review on the key challenges in accurately predicting 3D distances between chromatin segments and computing their dynamics. Thanks to @djost-physbiol.bsky.social @lucagiorgetti.bsky.social for the invitation to write this review! @shuvadipdutta.bsky.social

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation:
www.sciencedirect.com/science/arti...

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

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

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

Congratulations and also thanks for the absolutely lovely summary of the paper!

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

The demystification of piRNA clusters

if you wonder how cells generate piRNAs specifically against transposons & you are looking for a weekend read

check out @86dominik.bsky.social's opus magna (or Dominik's great thread)

a shared project with the one and only Rippei Hayashi, lab alumnus & friend

Come on join us! We are searching for the next technical associate to join our lab ~Summer 2026.

This could be a great position for someone who is graduating this spring and is looking for 2 more years of research experience before starting their PhD:
careers.peopleclick.com/careerscp/cl...

Direct visualization and tracing of chromatin folding in the Drosophila embryo - The EMBO Journal Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models deriv...

We are in EMBO J. See DNA and non-octameric nucleosome-like particles in situ

link.springer.com/article/10.1...

Just another shoutout for Deepshi's paper, hot off the presses at #GENETICS!

Just *look* at that beautiful epistasis data... 😍 May all of our future results be so clear to interpret 🤗

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding - Nature Genetics Acute perturbation of histone acetylation induces changes in chromatin organization that are only partially reversed once the perturbation is removed and are associated with transcriptional memory eff...

TSA treatment may induce cellular and structural memory !! Happy to have been part of this beautiful story, lead by @fpaldi.bsky.social in Giacomo Cavalli's lab. Now published in @natgenet.nature.com 👏.
www.nature.com/articles/s41...

Very excited to see this published - thanks to @djost-physbiol.bsky.social & all co-authors for the fantastic work!

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Interesting. Rather than the questions where we aren’t proximal to power centers wonder if organizing for changing CEO pay within scientific societies is worth pursuing. Thanks for underscoring this insanity. Not that these are mutually exclusive, just actionable.

Not sure why this question has to be interrogated through the lens of scale and has to be said that every effort doesn’t need to scale. I would argue it’s more a question around offering a climate for science that isn’t actively hostile?

I found this quite useful in understanding what it takes : bsky.app/profile/hars...