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Miguel Ramirez-Otero

@mckrzo.bsky.social
346 followers 419 following 19 posts

Postdoc in M. Pagano Lab at NYU | PhD with V. Costanzo at IFOM/SEMM/UniMi | DNA replication stress & DNA repair aficionado

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Miguel Ramirez-Otero @mckrzo.bsky.social · 13/08/2026
The forgotten 20 million: why is the world neglecting Afghanistan’s girls and women? www.nature.com/articles/d41...
nature.com
The forgotten 20 million: why is the world neglecting Afghanistan’s girls and women?
It is shameful that half the country’s population continues to be overlooked by the international community.
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Alberto Ciccia @albertociccia.bsky.social · 15/07/2026
Our manuscript on the dependency of ALT-positive tumors on the DNA translocase SMARCAL1 is finally out in @genesdev.bsky.social. Big thanks again to the Min, Lazzerini Denchi and @cejkalab.bsky.social labs! @angelotaglialatela.bsky.social genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
SMARCAL1 is a candidate therapeutic target for ALT-positive tumors
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Marco Trujillo @trujillolab.bsky.social · 16/07/2026
Endogenous molecular glue acts as a signal in human cells - akin to auxin! Metabolite glues as a means of purine sensing and chemotherapeutic response www.nature.com/articles/s41...
nature.com
Metabolite glues as a means of purine sensing and chemotherapeutic response - Nature
Purines can act as endogenous molecular glues in human cells by anchoring a rate-limiting enzyme in purine biosynthesis to its inhibitor, and modifying this mechanism could provide a way to improve th...
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Oded Rechavi @odedrechavi.bsky.social · 04/06/2026
I won't pay $4,000 for a ticket to see my Knicks play in the NBA Finals for the first time in 27 years, but for some reason I routinely pay three times that much for open access to papers that I wrote myself.
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Sholto David @sholtodavid.bsky.social · 28/05/2026
Reluctant to post too much about this but I did want to share my favourite finding from the dozens of manipulated or duplicated ThermoFisher verification blots. This one has a giant square. Enjoy!
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Annual Reviews @annualreviews.bsky.social · 11/05/2026
🎉 Now online! The Annual Review of Biophysics is now online. The most read article is "The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms" by Villalta et. arevie.ws/3R2CANN @sashiw.bsky.social @nucleosomepolice.bsky.social
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Todd Douglas @apoptoddic.bsky.social · 30/04/2026
Our paper is now out in @natcellbio.nature.com! @craigmcrews.bsky.social www.nature.com/articles/s41... We identify a new regulator of the quality control system that protects one of nature's most important molecular machines: the ribosome. QC failure → unmitigated metabolic stress & cell death.
nature.com
The atypical E3 ligase HOIL-1 safeguards the ribosome during cellular stress - Nature Cell Biology
Douglas et al. study the E3 ligase HOIL-1, mutated in patients with a type of myopathy. Mutant HOIL-1 influences the sensitivity to disulfidptosis initiated by ZAKα–ATF4 in glucose starvation and inte...
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Jon Cooper @joncooper-us.bsky.social · 26/04/2026
🎯🎯
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Eric Topol @erictopol.bsky.social · 27/04/2026
This NYT magazine article on longevity science, reversing aging with cellular reprogramming, is over the top. We have no proof that rejuvenation of a human organ is possible, no less the whole body, and there is risk of inducing cancer. gift link www.nytimes.com/2026/04/27/m...
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Komander Lab @komanderlab.bsky.social · 24/04/2026
Check out our latest paper on the ubiquitination of glycogen in cells and tissues! Congratulations to Marco Jochem (@marcojochem.bsky.social) and Simon Cobbold for leading this study and to collaborators @craigagoodman1.bsky.social, @pgregorevic.bsky.social, Kai Hofmann and Thomas Hermanns.
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Zebrafish Rock! @zebrafishrock.bsky.social · 01/04/2026
@mads100tist.bsky.social continues his takeover in this insightful webinar 🤩 Please do attend, if interested (which you are)!
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Lopes_Lab @lopeslab.bsky.social · 01/04/2026
Another great opportunity for genome integrity / replication stress aficionados to attend two excellent seminars with a simple click. Join us in a few days (Tue April 7th)! 👇
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Alessandro Costa @costalaboratory.bsky.social · 01/04/2026
Machines on Genes 2026 8–11 June 2026 | 📍 Heraklion, Crete 🇬🇷 Two deadlines coming up on 8 April 2026 i. abstract submission ii. early bird submission (save €50) Four days of 🧑‍🔬🧬👩‍🔬☀️👨‍🔬🔬❄️🧪🧫 94th Harden Conference by @lapassmore.bsky.social, Dana Branzei, me with @biochemsoc.bsky.social.
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Daniel Durocher @durocher1.bsky.social · 01/04/2026
Great conference, great science and great location!
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Vladimir Volkov 🇺🇦 @vladimirvolkov.bsky.social · 31/03/2026
🤖AI tools for peer-review? I want to share my experience using q.e.d. science (www.qedscience.com), a reviewing tool with high-profile endorsements. I will report results and my impressions from the use /1
qedscience.com
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
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Society for Developmental Biology @socdevbio.bsky.social · 31/03/2026
The next the Ethel Browne Harvey Postdoc Seminar will be held Friday, April 10 at 3 pm Eastern Time with Joaquín Navajas Acedo @mads100tist.bsky.social @biozentrum.unibas.ch and Yiqun Wang @ucsandiego.bsky.social. Register today and join us. bit.ly/42xUhYh #SDBPostdocSeminar
Society for Developmental Biology Ethel Browne Harvey Postdoctoral Seminar Series
Friday, April 10, 2026, 3:00pm - 4:00 pm Eastern Time
Joaquín Navajas Acedo (Biozentrum at the University of Basel)
Spatiotemporal emergence of somatosensory neuron diversity in zebrafish
Yiqun Wang (University of California, San Diego)
Asymmetric mRNA partition mediated embryonic patterning in spiralian development revealed by spatial transcriptomics
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Cell - a Cell Press journal @cp-cell.bsky.social · 21/03/2026
Now online! The E3-ome gene-centric compendium reveals the human E3 ligase landscape
dlvr.it
The E3-ome gene-centric compendium reveals the human E3 ligase landscape
The E3-ome defines the human repertoire of ubiquitin E3 ligases, creating a unified resource that maps their diversity across the ubiquitin and ubiquitin-like systems. By consolidating fragmented knowledge, this framework provides a foundation for studying ubiquitin signaling and accelerating discovery.
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Jakob Farnung @jakobfarnung.bsky.social · 18/03/2026
The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation (TDMD) is now published! 🎉🍾 We, @bartellab.bsky.social and Schulman lab, describe how 2-RNA factors control protein degradation by recruiting an E3 ligase. @mpibiochem.bsky.social www.nature.com/articles/s41...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Reese Richardson @reeserichardson.bsky.social · 06/03/2026
Markus Englund built a tool for identifying repetitive sequences in scientific datasets! Read up here: www.sciencedetective.org/scientific-d...
sciencedetective.org
Scientific datasets are riddled with copy-paste errors
Initial results from scanning through Excel files belonging to 600 published scientific papers.
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GL Moldovan Laboratory @moldovanlab.bsky.social · 05/03/2026
Happy to share our new work on the nuclease EXO1, published in Nature Communications. We show that EXO1 is overexpressed in cancers. This promotes nascent DNA degradation, even in BRCA-proficient cells, resulting in genomic instability and chemotherapy sensitization. www.nature.com/articles/s41...
nature.com
The nuclease EXO1 promotes genomic instability by degrading nascent DNA in BRCA-proficient cells - Nature Communications
DNA repair genes are generally considered tumor suppressors, as they maintain genomic stability. Here, the authors show that the exonuclease EXO1 is overexpressed in a significant proportion of tumors...
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Leo Kiss @leokiss.bsky.social · 05/03/2026
I am incredibly excited to share that I will start my independent lab at the @unidue-zmb.bsky.social at the @unidue.bsky.social as Junior Professor of Cellular Biochemistry. Research in my lab has the goal to decipher the ubiquitin code! There are multiple open positions! (1/3)
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Nature Portfolio @natureportfolio.nature.com · 27/02/2026
A study published in Nature has identified a new mechanism that controls DNA’s ability to replicate – and thereby a cell’s ability to divide. A protein, PAF15, acts as the brake, preventing the replication machinery from becoming overloaded and protecting cells from replication catastrophe. 🧪
go.nature.com
PAF15–PCNA exhaustion governs the strand-specific control of DNA replication - Nature
PCNA–PAF15 has a key role in determining replisome dynamics during genome replication and protecting against genome instability.
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Vincenzo Costanzo @labvincenzo.bsky.social · 05/03/2026
Pleased to share our paper. We found surprising widespread glycogen accumulation in A-T due to mitochondrial impairment that can be improved by targeting the unexpected FNIP2-SERCA2b-axis. #AtaxiaTelangiectasia #ATM #RareDisease #Metabolism #Mitochondria www.nature.com/articles/s41...
nature.com
Targeting the FNIP2-SERCA2b axis improves metabolic and mitochondrial defects in Ataxia Telangiectasia - Cell Death & Disease
Cell Death & Disease - Targeting the FNIP2-SERCA2b axis improves metabolic and mitochondrial defects in Ataxia Telangiectasia
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Leo Kiss @leokiss.bsky.social · 05/03/2026
You are passionate about ubiquitin, proteostasis and cellular biochemistry and want to be part of a collaborative, ambitious, excited and fun team? I am recruiting PhD students via the @imprs-lm.bsky.social graduate school: www.imprs-lm.mpg.de/index.php/le... (2/3)
imprs-lm.mpg.de
Kiss-intro
IMPRS-LM stands for International Max Planck Research School for Living Matter. We are interested in the molecular, chemical and physical properties
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Lopes_Lab @lopeslab.bsky.social · 02/02/2026
Tomorrow (Tue 3rd)! PLEASE NOTE THE ALTERNATIVE ZOOM LINK! 👇
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Cristian Prieto-Garcia @prieto-garcia.bsky.social · 01/02/2026
Our Science paper is out! 😃 www.science.org/doi/10.1126/...
science.org
DNA-protein cross-links promote cGAS-STING–driven premature aging and embryonic lethality
DNA-protein cross-links (DPCs) are highly toxic DNA lesions that block replication and transcription, but their impact on organismal physiology is unclear. We identified a role for the metalloprotease...
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Karolin Luger @nucleosomepolice.bsky.social · 02/02/2026
This just in. So honored and grateful...
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Andrea Musacchio @andrea-musacchio.bsky.social · 02/02/2026
Two new papers from the lab published in The EMBO Journal! link.springer.com/article/10.1... By Kai Walstein, @louisa-hill.bsky.social and others – On role of M18BP1 in CENP-A loading link.springer.com/article/10.1... By Arianna Esposito Verza and others – On mechanism of activation of PLK1
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Miguel Ramirez-Otero @mckrzo.bsky.social · 23/01/2026
Trove of Mexican genomes could help guide prescribing decisions | Science | AAAS www.science.org/content/arti...
science.org
Trove of Mexican genomes could help guide prescribing decisions
Study reveals role of “fine-grained” ancestry in predicting response to painkillers, statins, and other drugs
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Eric Topol @erictopol.bsky.social · 21/01/2026
The new cover and feature @nature.com www.nature.com/immersive/d4...
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Miguel Ramirez-Otero @mckrzo.bsky.social · 16/01/2026
Developing super-tortillas to address malnutrition in Latin America www.nature.com/articles/d41...
nature.com
Developing super-tortillas to address malnutrition in Latin America
Mexican food scientist Raquel Gómez-Pliego works to improve the nutritional value of foods through microbial fermentation.
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Alina Thielen @alinathielen.bsky.social · 13/01/2026
New year, new preprint! 🎊 We are excited to share our recent work on #E3 ligase regulation in #metabolism! www.biorxiv.org/content/10.6... #ubiquitin #targetedproteindegradation #chemicalbiology 1/6
biorxiv.org
A CK2-FBXW11 kinase-E3 ubiquitin ligase cascade is a metabolic sensor regulating Tryptophan 2,3-dioxygenase stability
Small molecules toggling the ubiquitin-proteasome system (UPS) are powerful regulators of protein degradation. Yet, mechanistic knowledge of how endogenous ligands gate UPS decisions remains rudimentary. Here, we define control of UPS access to Tryptophan-2,3-dioxygenase (TDO2), which converts the essential amino acid tryptophan (Trp) to N-formylkynurenine. When Trp concentrations are limiting, TDO2 is degraded to avert tryptophanemia. Using CRISPRi screening and biochemistry, we identify a CK2-FBXW11 kinase-E3 ligase cascade that generates and recognizes tandem TDO2 phosphodegrons when not protected by Trp. Trp binding to an exosite safeguards TDO2 from phosphorylation-dependent ubiquitylation. Effects of Trp analogs on CK2-FBXW11-dependent ubiquitylation indicated that the indole, amino, and carboxylate groups are necessary for substrate shielding. Cryo-EM reveals how these moieties order a region proximal to the phosphodegrons; without Trp, this segment is flexible, enabling phosphorylation-coupled ubiquitylation. Overall, our data uncovered an endogenous small molecule allosterically stabilizing its own metabolizing enzyme through protection from a phosphorylation-ubiquitylation cascade. ### Competing Interest Statement B.A.S. is a member of the scientific advisory boards of Proxygen and Lyterian. The other authors declare no competing interests. Max Planck Society, https://ror.org/01hhn8329 European Union, ERC AdvG, UPSmeetMet, 101098161 to BAS Boehringer Ingelheim Fonds, https://ror.org/00dkye506
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Zebrafish Rock! @zebrafishrock.bsky.social · 14/01/2026
🔍 #AskZebrafish: Does anyone in the US or Canada have any of the following mutant #zebrafish lines and would be willing to share? tert, klotho, cxcl12a, cxcl12b, cxcr4a and cxcr4b Any leads would be appreciated! (Yes, we know ZIRC has some frozen but trying to find live)
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Alejandro Montenegro @aemonten.bsky.social · 13/01/2026
Have you ever thought to yourself, 'I wish I had a bibliography with 50 carefully arranged references, each one showing a different way AI is making everything worse, perhaps with selected quotations from each reference'? Do I have good news for you" sharonkabel.com/genai-fraud
sharonkabel.com
A bibliography of genAI-fueled research fraud from 2025 – Sharon Kabel
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Jakob Farnung @jakobfarnung.bsky.social · 13/01/2026
Check out the newest preprint from the Schulman lab 🎊🎉 Super cool mechanism of how a metabolite regulates the stability of its own metabolizing enzyme! Alina did it all for this project CRISPR screen ✂️, biochemistry 🧪, and cryo-EM ❄️🔬. Congrats!
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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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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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Miguel Ramirez-Otero @mckrzo.bsky.social · 17/12/2025
I was a ‘go, go, go’ academic. A fellowship abroad transformed my approach | Science | AAAS www.science.org/content/arti...
science.org
I was a ‘go, go, go’ academic. A fellowship abroad transformed my approach
“I came back with a recalibrated sense of how I want to live and work,” this professor writes
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María Fernández-Casañas @emefece.bsky.social · 10/12/2025
Our @costerlab.bsky.social review is out! It’s a great read on the impact of DNA secondary structures on eukaryotic replication fork progression - a totally unbiased opinion, of course! www.sciencedirect.com/science/arti... @adityasethi.bsky.social @billiedelpino.bsky.social
sciencedirect.com
How DNA secondary structures drive replication fork instability
DNA secondary structures, such as hairpins, cruciforms, triplexes, G-quadruplexes and iMotifs, are common, dynamic features that replication forks rou…
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Aura Carreira @acarreiralab.bsky.social · 10/12/2025
🚨 Exciting news! Our latest study is out in Nature Communications! We reveal how specific BRCA2 mutations can hijack transcriptional programs—beyond their role in DNA repair. 🔗 rdcu.be/eT1R9 #CancerResearch #BRCA2 #Genomics
nature.com
A recurrent pathogenic BRCA2 truncating variant reveals a role for BRCA2-PCAF complex in modulating NF-κB-driven transcription - Nature Communications
Pathogenic BRCA2 truncating variants in heterozygosis drive distinct cancer-linked mechanisms. Here the authors show that one causes PARPi sensitivity and HR loss via haploinsufficiency, while another...
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The Daily Show @thedailyshow.com · 07/11/2025
New York millionaires: threatening to flee the city since 2009
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Yale Climate Connections @climateconnections.bsky.social · 07/11/2025
Joe Rogan spent a whole podcast episode spouting climate misinformation. @dananuccitelli.bsky.social broke down the tactics Rogan and other climate deniers use so you can call them out when you hear them.
yaleclimateconnections.org
Five ways Joe Rogan misleads listeners about climate change  » Yale Climate Connections
Rogan exposes millions to climate denial. Let’s break down his tactics. 
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Zohran Kwame Mamdani @zohrankmamdani.bsky.social · 05/11/2025
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Arnab Ray Chaudhuri @raychaudhurilab.bsky.social · 30/10/2025
Want to know how homologous recombination defects are caused upon loss of BRCA2? Check out our recent efforts in uncovering this phenomenon just out in Science! www.science.org/doi/10.1126/...
science.org
FIGNL1 inhibits homologous recombination in BRCA2 deficient cells by dissociating RAD51 filaments
Homologous recombination (HR) deficiency upon Breast Cancer Gene 2 (BRCA2) loss arises from defects in the formation of RAD51 nucleoprotein filaments. We demonstrate that loss of the anti-recombinase ...
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Petr Cejka @cejkalab.bsky.social · 27/10/2025
See our paper “Mechanism of trinucleotide repeat expansion by MutSβ-MutLγ and contraction by FAN1”. Using biochemistry, we show how DNA incisions by the MutLγ nuclease can lead to expansions, and how expansion is prevented by FAN1. Well done Issam and Valentina! www.nature.com/articles/s41...
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God @thegodshow.com · 19/10/2025
Spotify is running ICE ads. I went to cancel on mobile and saw that this isn’t allowed on mobile. They make you cancel on desktop. You think that’s gonna stop me, Spotify? I will erase you and forget you ever existed. THOU SHALT CANCEL SPOTIFY!!!
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Geraldine Zimmer-Bensch @zimmer-bensch.bsky.social · 20/10/2025
What if the DNA methylation enzyme DNMT1 isn’t just about DNA? Our new preprint reveals a cytosolic role for DNMT1 as a scaffold controlling neuronal morphology via DOCK7–Rac1/STMN1 signaling & mitochondrial trafficking. A paradigm shift in DNMT1 biology! www.biorxiv.org/content/10.1...
biorxiv.org
A cytosolic function of DNMT1 controls neuronal morphogenesis via microtubule regulation
Proteins traditionally confined to a single cellular compartment are increasingly recognized to exert non-canonical functions in alternative domains. The DNA methyltransferase 1 (DNMT1), classically d...
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Sandra Segura-Bayona @ssegurabayona.bsky.social · 07/10/2025
🧬 Preprint alert! "Distinct ATRX functions cooperate with 9-1-1 and CST complexes to safeguard replication and telomere integrity." Read the manuscript here 👉 www.biorxiv.org/content/10.1...
biorxiv.org
Distinct ATRX functions cooperate with 9-1-1 and CST complexes to safeguard replication and telomere integrity
Mutations in the ATRX chromatin remodeller predispose to a developmental genetic disorder and cancer, but how it safeguards genome and telomere stability remains unresolved. Here, we uncover critical ...
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