Bou-Nader lab

Amen 🙏🏻 🤲🏻
A wise person once told me "all antibodies are non-specific until proven otherwise" I was just telling this to my students today 🤯

Excited to share our preprint exploring the structural, biochemical and in vivo properties of DRT7/UG10 reverse transcriptases which produce dsDNA using their primase and polymerase activities and provide broad-spectrum antiphage defense! www.biorxiv.org/content/10.6...

very unusual - a tRNA regulated anion channel

Mechanism of cotranslational modification of histones H2A and H4 by MetAP1 and NatD NAC enables cotranslational N-terminal processing of histones H2A and H4 by recruiting MetAP1 and NatD at the ribosomal tunnel.

Last X-Mas, the ribosome gave you methionine,
but the very next day, MetAP took it away.
This year, to save histones from tears,
NatD gives you an acetyl group. ⭐️

Explore our latest paper with the Deuerling lab @uni-konstanz.de and Shu-ou Chan lab @caltech.edu!

www.science.org/doi/10.1126/...

Chromatin buffers torsional stress during transcription During eukaryotic transcription, Pol II must overcome nucleosome obstacles and, because of DNA’s helical structure, must also rotate relative to DNA, generating torsional stress. However, there is lim...

@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...

It’s out! Using cryo-ET in Dicty cells, we take a fresh in situ look at vaults. Surprisingly, we uncover vaults associated with ER and NE membranes, and find that many vaults enclose ribosomes in defined orientations, opening new avenues to their cellular function! www.biorxiv.org/lookup/conte...

Our latest paper on the molecular mechanisms of XPF-ERCC1 recruitment to SLX4-dependent DNA repair pathways has been published! Congratulations to first author Junjie Feng, and a heartfelt thank you to all our collaborators for their contributions to this study!
www.nature.com/articles/s41...

The dark proteome: translation from noncanonical open reading frames

1⃣5'-UTR 2⃣3'-UTR small ORF/sORF
3⃣out-of-frame 4⃣In-frame overlapping ORF

Translating micropeptide <100aa, proteins distinct from canonical ORFs, or isoforms

#TrendsCellBio 2022
www.sciencedirect.com/science/arti...

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are ...

Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...

❄️ RNA Modifications Newsletter – December 2025 issue no. 6

❄️ December RNA Modifications Newsletter is out! ❄️
rnamodifupdates.substack.com/p/rna-modifi...
❄️🔥RNA modifs = winter’s hottest adaptation toolkit. 🦠
#Ribosome #RNAbiology

From @kylecottrell.bsky.social lab

rnajournal.cshlp.org/content/31/1...

So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and...

Congrats to @chgjohnston.bsky.social , Andreani, Radicella et al.!
Elegant PNAS paper on the ComEC/ComFA/ComFC complex in bacterial transformation. AF3 predictions validated by clever mutagenesis. We tried for years to solve this by cryo-EM/crystallography - never succeeded.

Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?

How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take: www.annualreviews.org/content/jour... (1/3)

ZAK activation at the collided ribosome - Nature The kinase ZAK is activated at collided ribosomes to mediate the ribotoxic stress response.

New work from the Green and Beckmann labs on how ZAK recognizes collided ribosomes.

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

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...

Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

tRNA as an assembly chaperone for a macromolecular transcription-processing complex - Nature Structural & Molecular Biology Here, the authors solve a series of cryo-electron microscopy structures that show how transfer RNAs (tRNAs) can guide the assembly of the multisubunit poxvirus RNA polymerase, uncovering a role of tRN...

Structural insights into the chaperone role of uncharged tRNA(Arg/Gln) in viral RNAP assembly #RNASky 🧪 www.nature.com/articles/s41...

Excited to share our new preprint in collaboration with Ahmet Yildiz's lab. Check out how our team uncovers a novel binding footprint and motor regulation mechanism for MAP9 Congrats to Burak Cetin and @aryantaheri.bsky.social

www.biorxiv.org/content/10.1...

Filament formation and NAD processing by noncanonical human FAM118 sirtuins Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...

Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.

Thank you to our sponsors for the GA RNA Salon @rnasociety.bsky.social and Lexogen- we hosted Dr. Francesca Storici for our annual symposium yesterday @dunhamlab.bsky.social @ghaleilab.bsky.social

A role for human senataxin in contending with pausing and backtracking during transcript elongation Senataxin (SETX) regulates RNA polymerase II (RNAPII) transcription and helps maintain genome stability, at least partly by suppressing R-loops. Howev…

I’m very happy to share Zhong Han’s beautiful work on the biochemical function of Senataxin, encoded by a gene that is mutated in rare and early-disabling neurodegenerative diseases. Turns out it rescues backtracked RNA polymerase II during early transcription! www.sciencedirect.com/science/arti...

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

Regulated decay of microRNAs plays a critical role in controlling body size in mammals! Check out our new paper in @genesdev.bsky.social and see thread previously posted with our pre-print 👇 for more info. Congrats to Collette LaVigne, Jaeil Han, and all authors!
genesdev.cshlp.org/cgi/content/...

An autism spectrum disorder mutation in Topoisomerase 3β causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain Abstract. The loss and mutation of Topoisomerase 3β (TOP3B), the only known eukaryotic topoisomerase with the ability to catalyze RNA strand passage reacti

Very proud of our recently published work in @narjournal.bsky.social led by senior PhD candidate Julia Warrick. #RNA

academic.oup.com/nar/article/...

RNA stability enhancers for durable base-modified mRNA therapeutics - Nature Biotechnology A systematic screen identifies RNA elements that enhance the stability and translation of base-modified mRNA.

Tremendous paper from Narry Kim’s lab identifying a sequence element that recruits cellular factors to exogenous mRNAs to ‘rejuvenate’ their poly(A) tails leading to a huge boost in output. Significant implications for therapeutics. Now, I wonder what the factor X is…

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

Structural basis of herpesvirus helicase-primase inhibition by pritelivir and amenamevir Structural studies of HSV-1 helicase-primase revealed how pritelivir and amenamevir bind and block its helicase activity.

New work from Tahirov x Lim collaboration! @qixianghe.bsky.social from my lab contributed the cryo-EM structures for this work. We are excited to help explain how anti-HSV drugs work and to guide their future development.
www.science.org/doi/10.1126/...
@unmc.bsky.social @uwbiochem.bsky.social