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Aaron Johnson

@chromatownie.bsky.social
67 followers 31 following 7 posts
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Reposted by Aaron Johnson
Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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Soni Lacefield @lacefieldlab.bsky.social · 10/09/2026
I am excited to share our preprint on the meiotic role of Stu2 in error correction of kinetochore-microtubule attachments. We find a heightened requirement for kinetochore-associated Stu2 in meiosis. Work of grad student @batula.bsky.social! www.biorxiv.org/content/10.6...
biorxiv.org
Accurate chromosome segregation is more dependent on kinetochore-bound Stu2 in meiosis than mitosis
Accurate chromosome segregation requires bipolar kinetochore-microtubule attachments. Error correction mechanisms promote cycles of kinetochore-microtubule release and reattachment until bipolar attac...
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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 03/09/2026
Structures of pUG-fold RNA bound to DNMT1 reveal a mechanism for RNA-mediated epigenetic regulation www.biorxiv.org/content/10.64898/20…
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Matthew Taliaferro @jmtali.bsky.social · 12/08/2026
Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
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Claudia Mimoso @camimoso.bsky.social · 04/08/2026
Excited to share our latest review on transcript elongation out now at @natrevmcb.nature.com!! It was an absolute pleasure to work on this review with @isaacfianu.bsky.social and @adelmanlab.bsky.social!
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Kaushik Ragunathan @kaushikr.bsky.social · 03/08/2026
Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...
biorxiv.org
Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback
In Schizosaccharomyces pombe , the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methy...
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Karolin Luger @nucleosomepolice.bsky.social · 25/06/2026
New PARP1 preprintfrom the lab, by Alex Fiorenza and our amazing undergrad Mahika Anand. PARP1 functions in DNA repair, but what about its second gig as a chromatin architectural protein? How does it stay enzymatically quiet? Read all about it here. www.biorxiv.org/content/10.6...
biorxiv.org
PARP1 Exhibits an Enzymatically Inactive Chromatin Binding Mode
Poly (ADP-ribose) Polymerase 1 (PARP1) is an abundant nuclear enzyme that dynamically engages chromatin in diverse cellular scenarios. In the context of DNA repair, PARP1 becomes enzymatically activat...
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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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Srinivas Ramachandran @4everbiochemist.bsky.social · 03/06/2026
New from the lab: cfDNA provides an unexpected window into telomere chromatin state and genome-wide chromatin changes that accompany telomere shortening, from a blood draw. We hope this opens a path toward monitoring telomere biology disorders with a blood test. www.biorxiv.org/content/10.6...
biorxiv.org
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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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Igor Ulitsky @igorulitsky.bsky.social · 01/05/2026
🆕 review with @jpunfried.bsky.social out in Nature SMB. Direct roles of lncRNAs in transcriptional activation. What do we understand about how lncRNAs lure Pol2 and set the stage for RNA production, and what do we still miss? www.nature.com/articles/s41...
nature.com
Direct roles of long non-coding RNAs in transcription activation - Nature Structural & Molecular Biology
This Review discusses how long noncoding RNAs (lncRNAs) control transcription activation by RNA polymerase II, including how they are produced at active enhancers or chromatin-domain boundaries and ac...
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Karolin Luger @nucleosomepolice.bsky.social · 28/04/2026
New work from Sashi Weerawarana on how TFAM compacts mitochondrial DNA 🧬 TFAM oligomerizes on DNA to form compact, homogeneous higher-order complexes (see beautiful mass photometry data below), that still retain dynamic behavior. Congratulations Sashi and Wei. www.biorxiv.org/content/10.6...
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Stefan Niekamp @niekamp.bsky.social · 25/04/2026
Excited to share our latest work in Molecular Cell: www.cell.com/molecular-ce... We show that PRC1 condensates exclude SWI/SNF from chromatin, revealing a physical mechanism for how opposing regulators compete to control gene expression. Huge thanks to all collaborators and mentors!
cell.com
Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation
Niekamp et al. show that biomolecular condensates formed by Polycomb repressive complexes can physically restrict access of the activating remodeler SWI/SNF to chromatin. Establishing this barrier dep...
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poliispeed.bsky.social @poliispeed.bsky.social · 23/03/2026
Happy to share that David and I have a new review out in @annualreviews.bsky.social of Biochemistry! We break down Pol II pausing, its evidence in vitro/in vivo, and its two key fates which are in kinetic competition: pause release vs premature termination. www.annualreviews.org/content/jour...
annualreviews.org
The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate
A signature feature of transcription on most genes in multicellular animals is that RNA polymerase II (RNAPII) piles up approximately 50 bases downstream of the start site at the promoter-proximal pau...
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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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Thomas Schalch @schalchlab.bsky.social · 04/03/2026
🧵 New preprint from our group, in collaboration with the @marcbuhler.bsky.social lab at FMI Basel and the Thalassinos lab at UCL. A long project and a finding we're really pleased with. Thread 👇 www.biorxiv.org/content/10.6...
biorxiv.org
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Sarah Hainer @hainerlab.bsky.social · 27/02/2026
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...
biorxiv.org
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Ben Sabari @bsabari.bsky.social · 06/02/2026
I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...
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Chen Davidovich @davidovichlab.bsky.social · 03/02/2026
H3K79me2/3 is sufficient to antagonise PRC1 www.nature.com/articles/s41...
nature.com
DOT1L provides transcriptional memory through PRC1.1 antagonism - Nature Cell Biology
Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibit...
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Aaron Johnson @chromatownie.bsky.social · 31/01/2026
Updates after feedback, so now’s the time to advertise! Our work with the late, great Charles Kirkpatrick, a force in Clin. Immunology for 60 yrs. We found that B cell immunodeficient patients of his had a hypomorphic variant in EZH2 caused by a defect in allostery. www.biorxiv.org/content/10.6...
Model figure showing EZH2-L50S effect on chromatin and B cell gene expression from https://www.biorxiv.org/content/10.64898/2025.12.08.692979v2.article-metrics.
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eric lai @lucksmith.bsky.social · 23/01/2026
new paper from the Lai lab! Renfu Shang performs careful mechanistic dissection of miRNA cluster assistance and reveals many insights and surprises to this enigmatic regulatory strategy that gives suboptimal miRNAs a boost. if you love Northerns, you'll ♥️ this! 🧬 genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Wyoming Wormboy @wyomingwormboy.bsky.social · 22/12/2025
Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years. One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!
journals.biologists.com
Epidermal cell fusion promotes the transition from an embryonic to a larval transcriptome in C. elegans
Highlighted Article:eff-1–mediated cell fusion drives transcriptomic progression from an embryonic to larval state in the C. elegans epidermis, without which developmental progression is delayed.
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Samara Reck-Peterson @samreckpeterson.bsky.social · 14/12/2025
The Reck-Peterson lab at Weill Cornell Medicine is seeking a technician or staff scientist to work on Aspergillus projects. Broad background in fungal biology and techniques required. Bioinformatics skills preferred. Find out more at: reckpetersonlab.org.
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Effie Apostolou lab @efapostolou29.bsky.social · 14/12/2025
Our study with @stadtfeldlab.bsky.social on the dual mechanism by which EHMT2 is repressing totipotency-associated vs lineage-specific loci is now out @emboreports.org. See thread by @cmuyehara.bsky.social who led the study with K Chatterjee. Full article here link.springer.com/article/10.1...
link.springer.com
Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 via LINE1 regulatory elements - EMBO Reports
Mouse embryonic stem cells (mESCs), in addition to differentiating into the three germ layers, can reverse typical developmental trajectories, as exemplified by their ability to de-differentiate into ...
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Agnese Loda @agneseloda.bsky.social · 15/12/2025
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉 We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
rdcu.be
Escape from X inactivation is directly modulated by Xist noncoding RNA
Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...
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Matthew Taliaferro @jmtali.bsky.social · 15/12/2025
Excited to share that this work is now published in its final form! link.springer.com/article/10.1...
link.springer.com
TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability - The EMBO Journal
The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanism...
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Al-Sady lab @al-sadylab.bsky.social · 12/12/2025
Took us a bit, but proud of this published version. We now examine the genetic interaction of phosphorylation with oligomerization and where bulk and phospho-Swi6 localize. Wonder if chromatin affinity tuning to enable Suv39 H3K9me3 spreading is a conserved mechanism ? doi.org/10.1093/nar/...
doi.org
Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading
Abstract. Heterochromatin formation in Schizosaccharomyces pombe requires the spreading of histone 3 (H3) Lysine 9 (K9) methylation (me) from nucleation ce
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Glennis Logsdon @glennislogsdon.bsky.social · 16/12/2025
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
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Harmit Singh Malik @harmitmalik.bsky.social · 13/12/2025
@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/
biorxiv.org
Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals
The Polycomb Repressive Complex 2 (PRC2) is an ancient, conserved chromatin-interacting complex that controls gene expression, facilitating differentiation and cellular identity during development. It...
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Srinivas Ramachandran @4everbiochemist.bsky.social · 16/12/2025
Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones) But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ : www.biorxiv.org/content/10.6...
biorxiv.org
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Ruben Gonzalez @rubenlgonzalez.bsky.social · 10/12/2025
The Gonzalez Lab at Columbia University is seeking a scientific leader! Join us in a Research Scientist position, driving single-molecule, structural, and biochemical studies of translation, translational control, and other RNA-based processes. Apply: apply.interfolio.com/176949
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Sheila Teves @sheilateves.bsky.social · 07/10/2025
How does a “universal” transcription factor evolve to do species-specific jobs? Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes. Read it here 👉 www.biorxiv.org/content/10.1... #MolecularEvolution #Transcription
biorxiv.org
Molecular determinants underlying functional divergence of TBP homologs
The TATA-box binding protein (TBP) is a highly conserved basal transcription factor and a core component of the pre-initiation complex (PIC) for all three eukaryotic RNA polymerases (RNA Pols). Despit...
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Vijay Ramani @vram142.bsky.social · 20/09/2025
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
biorxiv.org
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
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Laura White @laurakwhite.bsky.social · 22/08/2025
Our paper is out in its final form! Back in April 2023, my coauthor Aleks Radakovic, then a PhD student, approached me after a talk in Chicago to ask what I thought an aminoacylated tRNA would look like if we pulled it through a @nanopore. doi.org/10.1038/s414...
doi.org
Nanopore sequencing of intact aminoacylated tRNAs - Nature Communications
Accurate protein synthesis depends on aminoacylated tRNAs, but their identities have been hard to measure. Here, authors present aa-tRNA-seq, a nanopore-based method that reveals the amino acid, seque...
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Karolin Luger @nucleosomepolice.bsky.social · 26/07/2025
if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial. rdcu.be/exXBX
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Harmit Singh Malik @harmitmalik.bsky.social · 26/02/2025
Today is a devastating reminder that infectious diseases don’t care what your ‘beliefs’ are. Everyone is likely to be affected directly or indirectly. Serious challenges require serious people at the helm. Protect your loved ones. Educate. Advocate. The cost of not doing so will be too much to bear.
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Jeremy Berg @jeremymberg.bsky.social · 15/02/2025
ATTENTION (PLEASE SHARE) If anyone has or knows of any positions that might be appropriate for the NIH staff members who were terminated, please post the information in this thread. There are lots of talented and accomplished people who may be looking for new opportunities.
media.tenor.com
a poster that says if life gives you lemon make lemonade on it
ALT: a poster that says if life gives you lemon make lemonade on it
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