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Bou-Nader lab

@bounaderlab.bsky.social
164 followers 181 following 30 posts

Our team studies #Rloop & #RNA 🧬 with #biochemistry #cryoEM 🔬❄️ #crystallography💎 to understand how they control life! Views from Charles biochem.emory.edu/bou-nader-lab

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David McQuarrie @davidmcquarrie.bsky.social · 01/08/2026
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins doi.org/10.1093/nar/...
doi.org
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins
Abstract. Efficient purification of specific RNAs from lysates remains a major challenge. Existing methods, such as MS2 tagging or oligonucleotide hybridiz
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Basil Greber @bjgreber.bsky.social · 24/07/2026
Happy that our most recent paper on nucleotide excision repair mechanisms has now been published in Science Advances. This project was led by @natalia-mg.bsky.social and @callumhaste.bsky.social and focused on visualising early steps of the NER process by #cryoEM. www.science.org/doi/10.1126/...
science.org
Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair
Cryogenic electron microscopy captures nucleotide excision repair complexes assembling on damaged DNA templates.
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Joe Yesselman @josephyesselman.bsky.social · 17/07/2026
New paper! While it has been known that DMS encodes more information than secondary structure, it has never really been characterized. So we did the first large study to look: 7,500 RNAs, all with known 3D structures. We found a lot of cool structural relationships. doi.org/10.1093/nar/...
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Jonathan Kagan @jkagan1.bsky.social · 17/07/2026
A new PAMP, a new innate immunity principle and a new preclinical application. I am so pleased to share our study on STING activation mechanisms in health and disease. Led by the fantastic Stephanie Ragland, follow the link below for a summary of all we learned. www.cell.com/immunity/ful...
cell.com
Purine and pyrimidine-based bacterial cyclic dinucleotides egress the phagosome and activate the innate immune sensor STING
Innate immune recognition of bacteria is thought to center on cell-surface or endosomal pattern recognition receptors such as TLRs. Ragland et al. identify an intraphagosomal cyclic dinucleotide (CDN)...
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Doudna Lab @doudna-lab.bsky.social · 16/07/2026
Our AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!
science.org
Structure and evolution-guided design of minimal RNA-guided nucleases
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic ...
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Ci Ji (CJ) Lim @cijilim.bsky.social · 17/07/2026
Kaitlyn continues to break barriers with her innovations for using LEA proteins to solve another major cryo-EM sample prep issue! This work should be of great interest to friends who are struggling with particle orientation bias. Another funtastic Lim X Grant collaboration! @uwbiochem.bsky.social
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Karim Majzoub @karimaj.bsky.social · 17/07/2026
RNA structure programs endogenous ADAR for precise and efficient editing
cell.com
RNA structure programs endogenous ADAR for precise and efficient editing
LEAPER 3.0, a structurally optimized dual-bulge ADAR-recruiting RNA design platform, achieves precise and efficient endogenous A-to-I RNA editing across diverse ADAR contexts.
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Arturo Carabias @arturocdr.bsky.social · 16/07/2026
🧬 Thrilled to share our latest @biorxiv-microbiol.bsky.social preprint! Here we find that Retron-IX build crazy supramolecular rings scaffolded by DNA molecules that sense phage infection! www.biorxiv.org/content/10.6... Read more below🧵! (1/X)
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Mara Mueller @muellermara.bsky.social · 19/02/2026
Mammalian cells form hibernating disomes akin to those in bacterial cells - but connected via ribosomal RNA www.science.org/doi/10.1126/... co-first with: @andschwarz.bsky.social with: @lea-dietrich.bsky.social, @sgiando.bsky.social, @erin-schuman.bsky.social and many more 🧵 0/6 #MolBio 🧪
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Jan Philipp Kreysing @jpkreysing.bsky.social · 11/04/2025
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
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Plaschka lab @plaschkalab.bsky.social · 18/06/2026
Now published! We investigated how polyadenylated RNAs are targeted for decay in the human nucleus. www.nature.com/articles/s41... (1/5)
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Haaris Ahsan Safdari @haarissafdari.bsky.social · 19/06/2026
🚨 Our Nature paper on Manikomycin is a Research Highlight in Nature Reviews Drug Discovery. A new antibiotic. A new ribosomal target (E-site). Activity against MDR pathogens. doi.org/10.1038/d415...
doi.org
New antibiotic targets novel ribosomal site
Discover the world’s best science and medicine | Nature.com
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Waggoner Lab @labwaggoner.bsky.social · 19/06/2026
Independent of sequence, disordered regions promote the stable chromatin occupancy required for pioneer-factor activity www.science.org/doi/10.1126/...
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Molecular Cell @cp-molcell.bsky.social · 19/06/2026
The DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavage
dlvr.it
The DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavage
Yang et al. reveal a dynamic DdmDE-mediated plasmid clearance pathway. Transient DNA bubbles permit promiscuous DdmE binding, while target specificity arises from slower dissociation at matched sites. DdmE then recruits a DdmD dimer to drive target-centered, bidirectional dsDNA unwinding. Free DdmD subsequently coats extruded ssDNA to enable site-specific endonucleolytic cleavage.
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Andrii Bugai @abugai.bsky.social · 17/06/2026
Check out our latest research, just published in Nature @nature.com @molbiolau.bsky.social @au.dk Molecular basis of polyadenylated RNA fate determination in the nucleus www.nature.com/articles/s41...
nature.com
Molecular basis of polyadenylated RNA fate determination in the nucleus - Nature
Biochemical, structural and cell biological analyses reveal that UAP56 (DDX39B) assembles with a TREX-2–like module that redirects non-functional polyadenylated RNAs from export to degradati...
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Yunsun Nam @yunsunnam.bsky.social · 05/06/2026
Excited to share our latest work! The oncogenic m5C writer NSUN2 achieves substrate specificity by recognizing RNA structure and conformational dynamics. RNA folding shapes methylation! Congratulations to the team! Thank you, colleagues and supporters! ttps://nature.com/articles/s41586-026-10582-9
nature.com
Substrate selectivity of the human RNA m5C methyltransferase NSUN2 - Nature
NSUN2 is an enzyme that adds a small chemical mark to RNA molecules and uniquely selects its targets based on specific sequence patterns and structural features.
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Bret Freudenthal @freudlab.bsky.social · 05/06/2026
How does a DNA repair enzyme find a needle in a haystack? 🧬 Our latest paper in NAR, led by the one and only C-trap queen Kaitlin Dehart, uses single-molecule imaging to watch APE1 scan DNA and lock onto AP-sites. @lumicks.bsky.social academic.oup.com/nar/article/...
academic.oup.com
A dynamic search mechanism enables APE1 to identify AP-sites in DNA
Abstract. Apurinic/apyrimidinic (AP) sites are among the most frequent DNA lesions, arising thousands of times per cell each day. These lesions threaten ge
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Alessandro Costa @costalaboratory.bsky.social · 28/05/2026
New preprint from our lab! We've been working out how the CMG replicative helicase gets built. 🧵 1/3
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Seychelle Vos @voslab.org · 29/05/2026
⚡New preprint from the lab⚡: A key early checkpoint in gene expression is promoter proximal pausing of RNA polymerase II. For over 20 years, we as field have not been able to recreate pausing under realistic cellular conditions. @robertovn.bsky.social shows that ELOF1 is the missing piece.
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Kedrov Lab @ HHU @kedrov-lab.bsky.social · 30/05/2026
That celebration has waited for a long time... One year ago we uploaded the preprint and started the endeavor through the peer-reviewing. Lots of emotions on the way 🎭, lots of work, and quite some learning on "friend or foe"... Probably, deserves another post 🤫 But now - the paper is accepted!
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Roger Castells @rcastellsg.bsky.social · 31/05/2026
Excited to share our latest research on leveraging machine learning with helical fusions for the design of novel protein cages! Preprint: “Design and structure of protein cages based on helical fusion and machine learning” Link: www.biorxiv.org/content/10.6...
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Rémi Fronzes @fronzeslab.bsky.social · 26/05/2026
New preprint. In S. sanguinis, a C5a peptidase-like protease (ScpH) polymerizes along eDNA, turning it into a catalytic biofilm scaffold. Great work from @robinanger.bsky.social in our lab, with Pelicic lab @lcbofficiel.bsky.social www.biorxiv.org/content/10.6...
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 07/05/2026
#RIP Pierre Chambon (1931-2026) 1963 PARP 1970 RNA Pol II 1975 Nucleosome 1977 Split genes 1980 Promoter 1983 enhancer 1986 Nuclear receptor
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Christine Mayr @christinemayr.bsky.social · 08/05/2026
If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.
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Carter Lab @carter-lab.bsky.social · 05/05/2026
Our story on RNA recognition by Egl-BicD is now published! Also delighted to share the accompanying News & Views article by Florence Besse and Andres Ramos, which beautifully highlights the work. Paper: www.nature.com/articles/s41... News & Views: www.nature.com/articles/s41...
nature.com
Structural basis for recognition of diverse localizing mRNAs by Egl–BicD - Nature Structural & Molecular Biology
Singh et al. combine cryo-electron microscopy and functional studies to reveal how a single protein complex selects diverse mRNAs for subcellular localization using a combination of shape, positional ...
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The Matić Lab @maticlab.bsky.social · 08/04/2026
The paper describing our sensitive poly-ADPr antibodies and a few other things is now out in Nature Communications. Congrats to all the authors!! www.nature.com/articles/s41...
nature.com
Versatile and sensitive detection of mono- and poly(ADP-ribosyl)ation reveals XRCC1-dependent remodelling of PARP1 signalling - Nature Communications
ADP-ribosylation regulates DNA repair, but its distinct forms have been difficult to distinguish. Here, the authors develop sensitive, modular antibodies to precisely detect mono- and poly-ADP-ribosyl...
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Nikolai Slavov @slavov-n.bsky.social · 31/03/2026
AI is powerful, but hype gives it pseudoscience vibes. When claims are unfalsifiable, detached from reality, or driven by tools looking for problems, we risk undermining real progress. Overselling AI does not accelerate science: It erode trust. stevensalzberg.substack.com/p/ai-is-star...
stevensalzberg.substack.com
AI badly needs a dose of skepticism
Some scientists are too eager to believe their own claims
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Aaron Whiteley @aaronwhiteley.bsky.social · 27/03/2026
Out now–our work on bacterial cGAS-like enzymes making 2′,3′-cGAMP! Read Uday's thread for updates since the preprint including determining our lab's first protein structure and developing a new system to study bacterial STING homologs in phage defense👇
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Ahmad Jomaa @jomaalab.bsky.social · 27/03/2026
A very exciting day-our work on the mechanism of AMD1 stalling is also out today, a great collaboration with the Baranov and Yordanova labs at UCC! Huge congratulations to Emir, first author on both papers! www.science.org/doi/10.1126/...
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Karim Majzoub @karimaj.bsky.social · 28/03/2026
Kudos to @nadinelaguette.bsky.social team and all co-authors on this nice paper where our lab had a modest contribution! @viroscope.bsky.social 🔥
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Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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Ahmad Jomaa @jomaalab.bsky.social · 27/03/2026
Check out the final version of this work, out today! @natcomms.nature.com www.nature.com/articles/s41...
nature.com
A molecular switch in NAC prevents mitochondrial protein mistargeting by SRP - Nature Communications
How ribosome-bound NAC distinguishes mitochondrial precursors from ER clients has remained unclear. Here, authors reveal a molecular switch in NAC that limits SRP access to nascent mitochondrial precu...
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Dr Zeinab Rekad 🔬🧬🧪 @zeinabrekad.bsky.social · 24/02/2026
Amen 🙏🏻 🤲🏻 A wise person once told me "all antibodies are non-specific until proven otherwise" I was just telling this to my students today 🤯
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Malgorzata Figiel @mfigiel.bsky.social · 25/02/2026
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...
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Oli Clarke @olibclarke.bsky.social · 18/12/2025
very unusual - a tRNA regulated anion channel
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The BanLab @thebanlab.bsky.social · 20/12/2025
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/...
tinyurl.com
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.
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Di Jiang @dijiang319.bsky.social · 19/12/2025
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
science.org
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...
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Katharina Geißler @kgeissler.bsky.social · 16/12/2025
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...
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Basil Greber @bjgreber.bsky.social · 16/12/2025
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...
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Hao Yin @haoyin.bsky.social · 13/12/2025
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...
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Doudna Lab @doudna-lab.bsky.social · 09/12/2025
✨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🧬 🔗👇
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Frances Yap @ribo1214.bsky.social · 04/12/2025
Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...
science.org
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 ...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 03/12/2025
❄️ December RNA Modifications Newsletter is out! ❄️ rnamodifupdates.substack.com/p/rna-modifi... ❄️🔥RNA modifs = winter’s hottest adaptation toolkit. 🦠 #Ribosome #RNAbiology
rnamodifupdates.substack.com
❄️ RNA Modifications Newsletter – December 2025
issue no. 6
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Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 25/11/2025
From @kylecottrell.bsky.social lab rnajournal.cshlp.org/content/31/1...
rnajournal.cshlp.org
ZYS-1 is not an ADAR1 inhibitor
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
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Jason Nomburg @jnoms.bsky.social · 25/11/2025
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!
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Rémi Fronzes @fronzeslab.bsky.social · 25/11/2025
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.
pnas.org
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...
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Polina Tikanova @polinatikanova.bsky.social · 24/11/2025
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?
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Plaschka lab @plaschkalab.bsky.social · 21/11/2025
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)
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Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 20/11/2025
New work from the Green and Beckmann labs on how ZAK recognizes collided ribosomes. www.nature.com/articles/s41...
nature.com
ZAK activation at the collided ribosome - Nature
The kinase ZAK is activated at collided ribosomes to mediate the ribotoxic stress response.
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Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2025
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/...
science.org
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.
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