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The Lewis Lab

@peterlewislab.bsky.social
1.1K followers 791 following 92 posts

Mechanistic dissection of chromatin pathways in development and cancer using biochemistry and genomics. UW-Madison School of Medicine and Public Health TheLewisLab.net

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Reposted by The Lewis Lab
Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 11/09/2026
New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices
dlvr.it
PRC2–RNA interactions through the lens of bioinformatics pipeline choices
Nature Reviews Molecular Cell Biology, Published online: 11 September 2026; doi:10.1038/s41580-026-01028-1Four recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field.
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Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 11/08/2026
Really timely review by @camimoso.bsky.social and @adelmanlab.bsky.social on RNAP in metazoans. I really like the idea of a RNAP having to "mature" in order to become a productive transcriptional machine. Plus it has my #1 favorite snRNP involved... www.nature.com/articles/s41...
nature.com
Regulation of RNA transcript elongation in metazoans and its relevance to disease - Nature Reviews Molecular Cell Biology
This Review discusses how transcript elongation by RNA polymerase II is regulated and how obstacles such as nucleosomes are overcome. Also discussed are the roles of transcription surveillance machine...
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Helen Rowe @RoweLab @labrowe.bsky.social · 14/08/2026
* Hot off the press from the Rowe Lab 📢 * : For in depth insight on LINE-1 jumping genes, from their regulation to their multifaceted roles in cancer immunity, read Holly Jefferson's review here: www.mdpi.com/1999-4915/18...
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Eric Conway @conwayer1.bsky.social · 27/07/2026
Preprint alert! 🚨 We are very excited to share our new manuscript on Bohring-Opitz syndrome, a devastating rare monogenic disorder driven by truncating variants in ASXL1. This project was led by PhD student Emma Doyle, one of the OG Conway lab members 💪. 1/6 www.biorxiv.org/content/10.6...
biorxiv.org
Divergent Pathogenic PR-DUB Complex Variants Converge Functionally Via PRC2 Displacement From Chromatin
The PR-DUB complex is responsible for erasing the repressive histone modification, H2AK119ub1. ASXL1-3 proteins are mutually exclusive catalytic partners of BAP1 in the PR-DUB complex. Somatic heteroz...
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Maxim Greenberg @maxvcg.bsky.social · 21/07/2026
(2/2) www.nature.com/articles/s41...
nature.com
SUMOylation enhances DNMT1 function to repress mega-intergenic RNAs and viral mimicry - Nature Genetics
This study uses a highly selective inhibitor to elucidate DNMT1’s specific functions and their regulation. Notably, RFN4-mediated SUMOylation enhances DNMT1 mobility and DNA methylation, thereby promo...
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Reposted by The Lewis Lab
Jason Tan @yjtan.bsky.social · 30/06/2026
Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...
biorxiv.org
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers
Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...
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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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Hunter Hill @hunterhill.bsky.social · 18/06/2026
Excited to share this preprint!! with @brandonscooper.bsky.social and Bill Sullivan We tested whether endosymbiotic Wolbachia can alter host gene expression through chromatin modifications that persist from spermatogenesis to adulthood.
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Helen Rowe @RoweLab @labrowe.bsky.social · 16/06/2026
‪doi: doi.org/10.1038/s414... 📣 Our study is now out in Nature Communications detailing that the type I interferon pathway is suppressed by HUSH in early human development: Its complete epigenetic lockdown!! Incredible work from James Holt 📣 😎
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Scott Coyle @cellraiser.bsky.social · 16/06/2026
Sub-cellular architectures arise through integrating signaling and structure. @edenchang.bsky.social and @zjmaggiexu.bsky.social show how coupling reaction-diffusion signaling to protein condensation provides a tunable, regulatable landscape for sub-cellular structure www.biorxiv.org/content/10.6...
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Hiten Madhani @hitenmadhani.bsky.social · 13/06/2026
A strong hint from human genetics that changes in DNA methylation may be causal for normal aging. This is the direction that aging (and cancer) research needs to go! www.nature.com/articles/s41...
nature.com
A progeria syndrome links DNA hypermethylation to age-related pathology - Nature Genetics
This study investigates the consequences of hypermethylation in a progeria syndrome caused by gain-of-function DNMT3A mutations, finding effects on adult stem cell function.
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Anna Schulten @sulteavn.bsky.social · 11/06/2026
Our new Review is out now! @carolinedean.bsky.social @miguelmontez.bsky.social We discuss how plants monitor seasonal temperature exposure, highlighting interconnected mechanisms of short-term transcriptional regulation & long-term epigenetic memory rdcu.be/fnLmG 🌱❄️
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Sophie Polo Lab @polosophie.bsky.social · 11/06/2026
Here is our article published in Nature Comm, on new players in chromatin dynamics after UV repair. This work highlights the histone chaperones DNAJC9 and MCM2 as central players in chromatin repair. Our proteomic dataset opens up new perspectives for dissecting epigenome maintenance mechanisms.
nature.com
Proteomic profiling of UV damage repair patches uncovers histone chaperones with central functions in chromatin repair - Nature Communications
Chromatin states need to be maintained during DNA damage repair. Here, the authors expand the histone chaperone network involved in repair-coupled chromatin restoration and highlight a mechanistic coo...
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Emilia Dimitrova @edimitrova.bsky.social · 08/06/2026
Yaay! Well done @bluebuleta.bsky.social and team! Great to see this work finally out! Read the paper to see how SETDB1 and HUSH regulate Xist transcription
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The Lewis Lab @peterlewislab.bsky.social · 08/06/2026
Allosteric activation of PRC2 is coupled to adoption of the compact state. Our new bioRxiv manuscript shows that EZH2 S21-phos, adjacent to the SANT1 domain, restrains this conformational transition and limits activation. With @kasinath-lab.bsky.social & @garcialabms.bsky.social tinyurl.com/4369kmh2
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Reposted by The Lewis Lab
Lluis Morey @lluismorey.bsky.social · 05/06/2026
We’ve recently been awarded a MIRA R35 and an R01 to study non-canonical roles and missense mutations of the Polycomb system in health, cancer, and neurodevelopmental disorders. We are seeking an animal tech with lab manager duties. Please share!
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The Lewis Lab @peterlewislab.bsky.social · 05/06/2026
How do cells tune PRC2 allostery? We find EZH2 Ser21-phos restrains PRC2 adoption of the compact active state. Loss of this restraint promotes H3K27me3, redistributes cPRC1, and impairs differentiation. New bioRxiv with @kasinath-lab.bsky.social & @garcialabms.bsky.social! tinyurl.com/4369kmh2
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Richard Jenner @reggenomics.bsky.social · 27/05/2026
Does PRC2 interact with RNA or is it an artefact? See our preprint showing how stringent denaturing purifications with spike-in controls support direct interaction between PRC2 and RNA in cells. www.biorxiv.org/content/10.6...
UV-crosslinked human cells containing Halo-tagged EZH2 were mixed with crosslinked mouse cells in which the protein was untagged and human EZH2 purified with Halo resin. Enrichment of human RNA (left) or mouse RNA (right) versus input was plotted against RNA abundance in the paired input sample. Windows with significant enrichment (p <10−6; binomial test) are shown in red. Human RNAs show enrichment versus input whereas mouse RNAs do not.
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Reposted by The Lewis Lab
Karolin Luger @nucleosomepolice.bsky.social · 18/05/2026
Out today - structure of the human HIRA histone chaperone complex bound to nucleosomes. Ever wondered how nucleosomes are assembled in the wake of transcription? It takes a 'hulk of a protein complex'. Work by the amazing Wei Tian weetian558.bsky.social. www.biorxiv.org/content/10.6... 🧵
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
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Elias Friman @eliasfriman.bsky.social · 11/05/2026
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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Vijay Ramani @vram142.bsky.social · 06/05/2026
Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...
nature.com
Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
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The Lewis Lab @peterlewislab.bsky.social · 04/05/2026
In a genome not so far away, the most elegant design in the galaxy was already wrapped into ~147 base pairs. #HappyNucleosomeDay, May-The-Fourth Be With You.
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Sally Lowell @cellysally.bsky.social · 10/04/2026
Just look at this graph (Fig 5A,B from Koeber et al). Amazing. Congratulations to the Pollard lab and all authors. www.nature.com/articles/s41...
Data. A mouse model of glioblastoma leads to inevitable death within 50 days. Delivery of HSV+TK plus IL2, driven by a strong and specific synthetic superenhancer, allows almost all mice to survive even after nearly 150 days.  From Fig5 of Koeber et al 2026
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Hironori Funabiki @hirofunabiki.bsky.social · 09/04/2026
Excited to share our structural insights into how microtubules differentially guide phosphorylation of kinetochore-microtubule regulators, Ndc80 and MCAK, for chromosome segregation. Heroic efforts by Yiming Niu with a fun collaboration with Jennifer DeLuca lab! www.science.org/doi/10.1126/...
science.org
Microtubules guide Aurora B substrate geometries for accurate chromosome segregation
Cryo-EM reveals how kinetochore-microtubule attachment is regulated by Aurora B substrate accessibility on microtubules.
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 31/03/2026
Within the field of transcription, the distinctive style of Mark Ptashne and Kevin Struhl stands out. At his best, Kevin Struhl provides a valuable clarification of the relationship between promoters and enhancers in the regulation of transcription. www.annualreviews.org/content/jour...
annualreviews.org
The Semantics and Mechanisms of Enhancers and Promoters: “What Is True for E. coli Is True for the Elephant, Only More So”
Three fundamental classes of gene regulatory elements were identified in Escherichia coli in the 1960s: operators bound by repressor proteins, promoters bound by the basic transcription machinery, and...
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Reposted by The Lewis Lab
Haering Lab @haeringlab.bsky.social · 16/03/2026
Our new preprint in collaboration with @meisterpeterf.bsky.social uncovers the molecular basis for condensin recruitment to X chromosomes in C. elegans and reveals atomic-level details of a previously unknown auto-inhibited state of condensin. www.biorxiv.org/cgi/content/short/2026.03.13.711519v1
Model of the C. elegans condensin I(DC) complex
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Reposted by The Lewis Lab
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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Alice Pyne @alicepyne.bsky.social · 25/03/2026
Supercoiling not only brings DNA to life (and makes it dance) but also changes how key proteins such as #CRISPR interact with it. Thanks @qmsmith.bsky.social for the brilliant collaboration, Sylvia for developing an amazing new #imageanalysis pipeline & @eddierollins.bsky.social for beautiful #AFM.
CryoEM and AFM images of DNA minicircles bound to CRISPR Cas9
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
These separation-of-function mutants show that H3.3 deposition can be genetically uncoupled from ERV silencing. This supports our earlier finding that H3.3 deposition at ERVs is dispensable for repression. Instead, repression depends on the C-terminal SIM and interaction with SUMOylated effectors.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
Which DAXX functions are required for ERV silencing? DAXX mutants defective in ATRX binding or H3.3 deposition still restore ERV repression. By contrast, deletion of the C terminal SIM abolishes silencing. Thus, ERV repression requires the C terminal SIM, but not ATRX binding or H3.3 deposition.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
One SUMOylated protein that binds the DAXX C-terminal SIM is the ATPase MORC3. Removing the SIM abolishes the DAXX-MORC3 interaction and prevents MORC3 recruitment to ERVs. MORC3 knockout cells likewise lose H3.3 accumulation at these loci.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
We previously showed that the DAXX HBD alone is insufficient for H3.3 deposition. Deleting the final eight amino acids, which removes the C-terminal SIM, blocks H3.3 accumulation at ERVs without affecting DAXX localization.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
Previously, we demonstrated that the DAXX four-helix bundle mediates ATRX interaction. But point mutations in this domain, or deletion of it, do not disrupt DAXX binding to ERVs or H3.3 accumulation at these sites.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
The HBD basic patch is required for productive nucleosome assembly in vitro. In cells, basic patch mutants still localize to ERVs but do not restore H3.3 accumulation at those sites.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
We identified a conserved basic patch within the tower domain of the DAXX histone-binding domain. Using recombinant HBD-H3.3-H4 complexes, we found that mutation of this surface weakened interaction with DNA in vitro.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
In our study, we asked how DAXX promotes H3.3 deposition mechanistically. Genome-wide, DAXX is not widely distributed across repeats. It is concentrated at a restricted subset of evolutionarily young ERVK elements, where it restrains ERV expression and influences nearby genes.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
A major challenge in interpreting H3.3 knockout phenotypes is that loss of H3.3 affects more than chromatin incorporation. It also causes a marked drop in DAXX abundance. Thus, ERV derepression in H3.3-null cells could reflect loss of H3.3 nucleosome assembly, loss of DAXX, or both.
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The Lewis Lab @peterlewislab.bsky.social · 23/03/2026
New preprint from our lab! An H3.3 knockout does two things at once: it removes H3.3 from chromatin and destabilizes DAXX. We disentangle those functions and find that DAXX-mediated H3.3 deposition can be uncoupled from ERV silencing. www.biorxiv.org/content/10.6...
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Ming Tommy Tang @tommytang.bsky.social · 20/03/2026
Polycomb repressive-deubiquitinase complex safeguards oocyte epigenome and female fertility by restraining Polycomb activity www.nature.com/articles/s4...
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
The paper closes with a model: Gcn5-containing HAT complexes are targeted to active genes by the transcription machinery, providing a direct link between histone acetylation and gene activation. A fitting paper to revisit 30 years later, on what would have been Dave Allis's 75th birthday, March 22.
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
And then decisive experiment. Recombinant Gcn5p expressed in E. coli had HAT activity in the in-gel assay, whereas uninduced and vector-only controls lacked activity. With that, Gcn5p was assigned a direct biochemical activity, linking histone acetylation more directly to transcriptional activation.
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
The conceptual surprise was in the sequence. Tetrahymena p55 turned out to be highly homologous to yeast Gcn5p, a known transcriptional co-activator: ~40% identity, ~60% similarity, with a conserved bromodomain.
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
Then came the validation. Anti-peptide antibodies detected a single 55 kDa species, tracked with the active RP-HPLC fractions, and immunodepleted ~60% of HAT activity. p55 was not just associated with HAT A. It was the catalytic subunit.
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
Starting from the previously purified active p55 HAT A subunit, Brownell et al. sequenced six internal peptides, designed degenerate primers, and assembled the cDNA by PCR and RACE. The predicted protein sequence then recovered all six peptides from the purified enzyme.
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
Happy 30th birthday to this paper published March 22, 1996, one of the studies that moved chromatin biology from correlation toward mechanism. Brownell et al. linked a transcription-associated Tetrahymena HAT to yeast Gcn5p, providing a biochemical link for chromatin modification to gene activation.
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ME Torres-Padilla @metorrespadilla.bsky.social · 20/03/2026
Just out! 👀 for TFs that regulate TEs.Clara's work with @tamas-schauer.bsky.social @marliesoomen.bsky.social @palmrinmoy.bsky.social and bluesky-less lab members 🌎 identifies TBP as a regulator of specific ERVL class: MaLRs in 🐭embryos -as always -feedback welcome👍 link.springer.com/article/10.1...
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Timothy En Haw Chan @timothykoala.bsky.social · 21/03/2026
How to make a heterochromatin by major satellite repeats transcripts? www.nature.com/articles/s41...
nature.com
Transcriptional competence defines the heterochromatin nucleating potential of isolated MSR units - Nature Communications
Multiple copies of intact MSR nucleate de novo heterochromatin and reveal that the establishment of mouse pericentric heterochromatin is associated with bidirectional repeat RNA, Integrator complex en...
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