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Alex de Mendoza

@alexdemendoza.bsky.social
1.3K followers 635 following 163 posts

Evolutionary epigenomics ( eukaryotes / Transcription Factors / Transposable Elements / DNA methylation ) @ QMUL (London). Lab website: www.demendozalab.com

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Reposted by Alex de Mendoza
Svetlana Dodonova @dodonova-sveta.bsky.social · 06/10/2026
🧬 Mark your calendars! Our EMBO Workshop "Chromatin evolution from molecules to genomes" is coming to St Feliu de Guíxols (Spain), 4–7 Oct 2027 🌊 Amazing programme! #EMBOchromatinEvo meetings.embo.org/event/27-chromatin-evo Register early!
meetings.embo.org
Chromatin evolution from molecules to genomes
Technological advances over the past decade have enabled genome-wide mapping of chromatin organization across diverse organisms at unprecedented resolution. These studies have uncovered both conserve…
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Alex de Mendoza @alexdemendoza.bsky.social · 06/10/2026
It's live! The next @embo.org #EvoChromo meeting will take place next year October in St Feliu de Guíxols (Spain), check it out here: meetings.embo.org/event/27-chr.... It's been great to co-organise with @dodonova-sveta.bsky.social @kellervalsecchi.bsky.social @cedricfeschotte.bsky.social & Nick I.
meetings.embo.org
Chromatin evolution from molecules to genomes
Technological advances over the past decade have enabled genome-wide mapping of chromatin organization across diverse organisms at unprecedented resolution. These studies have uncovered both conserve…
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Reposted by Alex de Mendoza
Philipp Radler @radler92.bsky.social · 01/10/2026
The first paper of my PostDoc in Christa Schlepers group (@archaea-vienna.bsky.social) on the dynamics of Asgard archaea is now out in Nature! www.nature.com/articles/s41... This was a great team effort and I am looking forward to uncover the complex behavior of these cells further!
nature.com
Dynamic protrusions mediate crawling motility in Asgard archaea - Nature
Anoxic live-cell imaging shows actin-dependent crawling motility and dynamic protrusions in Asgard archaea, providing insights into cellular innovations that may have contributed to eukaryotic evoluti...
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Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 28/09/2026
We have a new branch in the family tree of animals: Atreyea- a previously unrecognized lineage among the closest unicell relatives of animals. Led by @konsmitsi.bsky.social & @freejakoba.bsky.social together with a fantastic team of collaborators. 🔗 papers.ssrn.com/sol3/papers.... #protistsOnSky
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Alex de Mendoza @alexdemendoza.bsky.social · 25/09/2026
For those of you who, like me, missed the Vatican #EvoDevo: www.pas.va/en/events/20..., don't worry, there will be a more earthly local version next week (Friday) in Cambridge Dept of Zoology, program here: londonevodevo.co.uk. Can't promise cardinal vestments in the background though.
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 21/09/2026
Must admit, ever since I was a kid, I’ve dreamt of seeing microscopy images of #protists in @lemonde.fr Today, protists are everywhere, and several images were taken by the team. And seeing #ichthyosporeans there too?! 🥹 One step closer to showcasing the beauty of the invisible microbial world. 🔬✨
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Peter Andersen @germline.bsky.social · 02/09/2026
Finally - the 🧵! So, the piRNA pathway defends the animal germline from transposons. But most of what we know comes from narrow developmental windows like late oogenesis, where it's easiest to study. We asked if the pathway is the same across development. It is not! /+
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Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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Margarida Cardoso Moreira @margaridamcm.bsky.social · 28/08/2026
Dear #LondonEvoDevo colleagues, don't forget to register for our next meeting (deadline on Sep 15th). It would be wonderful to see a lot of our #Cambridge colleagues.
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Arnaud Krebs @arnaudkr.bsky.social · 12/08/2026
How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org
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Isabel Almudi @isabelalmudi.bsky.social · 07/08/2026
What happens when evolution adds an extra pair of eyes? Male mayflies evolve an extra pair of dorsal compound eyes, the Turbanate eyes, thought to help males detect females during mating swarms. we have investigate how this remarkable evolutionary novelty develops. www.biorxiv.org/content/10.6...
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Alex de Mendoza @alexdemendoza.bsky.social · 06/08/2026
The #LondonEvoDevo goes to Cambridge! Kindly hosted by @emiliapsantos.bsky.social, mark on your calendars *October 2nd* at the Main Theatre in the Department of Zoology (Cambridge). Registration (£0.00): docs.google.com/forms/d/e/1F.... All welcome to present: #PI #PhD #PostDocs, submit abstracts!
docs.google.com
LondonEvoDevo meeting - October 2026
This event will take place on Friday October 2nd, 2026, at the Department of Zoology (Main Lecture Theatre), University of Cambridge, Downing Street CB2 3EJ, 12:30 - 18:30. There will be no posters, ...
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Geoff Faulkner @faulknerlab.bsky.social · 30/07/2026
Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...
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Alex de Mendoza @alexdemendoza.bsky.social · 03/08/2026
Sailing in @biorxivpreprint.bsky.social ready for summer, our study on the iconic Portuguese man o' war 🪼 is out: www.biorxiv.org/content/10.6.... We use (epi)genomics to understand a critter that fascinates me since childhood. Massive team effort with @obog.bsky.social, Cummins and Neely groups. 🧵
the indo-pacific bluebottle (Physalia utriculus)
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 20/07/2026
The third chapter in our coral single-cell trilogy is here. After mapping cell type diversity in Stylophora (Levy 2021) and exploring facultative symbiosis in Oculina (Levy 2025), we now uncover cell type-specific responses to heat stress. Find out more in @xgrau.bsky.social's thread below.
biorxiv.org
Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery
Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are dis...
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Maxim Greenberg @maxvcg.bsky.social · 15/06/2026
🚨Preprint Drop🚨 We are very pleased to release our study on DNA methylation dynamics at enhancers during ESC differentiation! This work was led by Marlet Morales-Franco and Priscillia Lhoumaud 🧵(1/13) www.biorxiv.org/content/10.6...
biorxiv.org
Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency
Cis-regulatory elements, such as enhancers, play an essential role in coordinating gene expression programs during cellular transitions. As such, substantial efforts have been made to characterize enh...
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Alex de Mendoza @alexdemendoza.bsky.social · 11/06/2026
Funny to get quoted on a pun about the origin of eukaryotes being a bit of a promiscuous relationship in the 🇪🇸 press, but glad to help communicate @tonigabaldon.bsky.social & his team's fatnastic work, which highlights the importance of giant viruses 👾 in eukaryotic origins @nature.com. Congrats!
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 09/06/2026
"Humbled to receive this recognition. This belongs as much to my team, my family, & to my home, Palestine: the people, the place, the joyful stubbornness to enjoy life." Cheers buddy @gautamdey.bsky.social Thx to my mentors @sophiemartinlab.bsky.social, @paveltomancak.bsky.social, & Pierre Gönczy.
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Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 09/06/2026
10/10 Perhaps aggregation is not an evolutionary dead end after all! Perhaps it was one of the evolutionary experiments from which animal multicellularity emerged. Link: www.nature.com/articles/s41... @icreacommunity.bsky.social #AnimalOrigins #Evolution #Multicellularity
nature.com
A unicellular relative links aggregative multicellularity to animal origins - Nature
Nature - A unicellular relative links aggregative multicellularity to animal origins
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Cedric Feschotte @cedricfeschotte.bsky.social · 29/05/2026
📣 POSTDOC position available in the Feschotte Lab at Cornell to work on #TRANSPOSONS! More details below. Pls send informal application or inquiry ASAP by DM or email to cf458_at_cornell.edu. Pls spread the word 🙏 #TEsky www.thefeschottelabatcornell.com
thefeschottelabatcornell.com
The Feschotte Lab at Cornell
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Ed Hagen @edhagen.net · 02/06/2026
🧪
Meme
Wait, it's all transposons?
Always has been
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Alex de Mendoza @alexdemendoza.bsky.social · 02/06/2026
Capolavoro 🎨 alert 🚨! What is the role of gene body methylation in invertebrates? Despite extensive speculation linking it to plasticity and environmental responses, its mechanistic effects and heritability remain unclear. Our take out in @natecoevo.nature.com: www.nature.com/articles/s41... 1/
nature.com
Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian - Nature Ecology & Evolution
Experiments in the cnidarian Nematostella vectensis show a role of gene body methylation in transposable element suppression and that epigenetic inheritance is constrained by chromatin context and tra...
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Evgenii Protasov @evgenii-protasov.bsky.social · 31/05/2026
Infection cycles of viruses of the phylum Nucleocytoviricota #microbiology #virology #virus #MicroSky @natrevmicro.nature.com doi.org/10.1038/s415...
doi.org
Infection cycles of viruses of the phylum Nucleocytoviricota - Nature Reviews Microbiology
In this Review, Abergel et al. overview infection cycles across the Nucleocytoviricota phylum, highlighting shared mechanisms and lineage-specific features spanning viral entry, viral factory formatio...
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Alex de Mendoza @alexdemendoza.bsky.social · 26/05/2026
New preprint! In an fun collaboration with @imaeso.bsky.social and @mirimiam.bsky.social led by Manu F-M, we set to explore the potential adaptation of transposable elements 👾 to host adenine DNA methylation by recruiting prokaryotic DAM methyltransferases: www.biorxiv.org/content/10.6.... 1/6
biorxiv.org
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Chema Martin @chemamd.bsky.social · 19/05/2026
🚨 We discovered a new mode of Hox gene regulation in annelids! 🪱 A distal enhancer acts as a "global control region", lifting Hox genes from Polycomb repression. This is reminiscent of Hox gene control in vertebrates, but the two modes likely evolved convergently. www.biorxiv.org/content/10.6...
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Maxim Greenberg @maxvcg.bsky.social · 20/05/2026
Exciting #CtrlEpiEdit conference update: Maja Jagodic @ki.se will be joining us in Paris! Check out her fantastic in vivo epigenome editing preprint here: www.biorxiv.org/content/10.6... And register for the symposium here 😉: ctrlepiedit.sciencesconf.org Please repost!
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Will Ratcliff @wcratcliff.bsky.social · 15/05/2026
1/35 New preprint! We show that obligate multicellularity removes fundamental population genetic barriers to multicellular adaptation. Even a brief unicellular phase can dramatically constrain the evolution of beneficial multicellular traits. www.biorxiv.org/content/10.6...
biorxiv.org
Obligate multicellularity circumvents population genetic barriers to collective-level adaptation
Complex multicellularity has evolved in just five lineages (animals, plants, brown algae, red algae, and fungi) and in each case, these organisms develop clonally and are obligately multicellular. While prior work has shown that clonal development plays a critical role in the evolution of complex multicellularity, none has disentangled this from the impact of obligate vs facultative multicellular life cycles. Here we use experimental evolution with engineered snowflake yeast ( Saccharomyces cerevisiae ) to directly test how life cycle structure affects multicellular adaptation. We created isogenic strains capable of switching between unicellular and clonal multicellular phases, then evolved populations for 192 days under obligately multicellular, facultatively multicellular, and obligately unicellular regimes. Obligately multicellular populations rapidly evolved larger size, primarily driven by a whole genome duplication, in all five replicates. Facultative populations showed dramatically constrained evolution, with tetraploidy evolving in only 2/10 facultative populations despite experiments demonstrating that it is strongly beneficial across the full life cycle. Mathematical modeling reveals the mechanistic basis for this constraint: facultative life cycles create establishment barriers through two population genetic effects. Group formation dramatically reduces the number of units of selection, making beneficial multicellular mutations vulnerable to drift. This asymmetry in population size between life cycle phases also allows cell-level selection to overpower group-level selection, eliminating mutations that provide group-level benefits but carry cell-level costs. These findings demonstrate that obligate multicellularity circumvents fundamental population genetic barriers to collective-level adaptation, helping explain why complex multicellularity has evolved exclusively in obligately multicellular lineages, and suggesting similar constraints may operate in other evolutionary transitions in individuality. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, DEB-1845363 Howard Hughes Medical Institute Gilliam Fellowship National Science Foundation Graduate Research Fellowship
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Alex de Mendoza @alexdemendoza.bsky.social · 14/05/2026
Join us for the @qmulepigenetics.bsky.social annual conference on June 18th in Mile End, should be a nice full day covering various angles on epigenetics, from evolution to disease. See more details here: www.qmul.ac.uk/epigenetics/...
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Schubeler Lab @schubelerlab.bsky.social · 07/05/2026
Excited to share our new study on CpG islands (CGIs) regulation by transcription factors (TFs)! CGIs drive most transcription initiation with unclear regulation. We find that chromatin-opening TFs are key players—following a surprisingly simple rule. 🧵 www.biorxiv.org/content/10.6... 1/9
biorxiv.org
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Grand Lab @grandlab.bsky.social · 07/05/2026
Excited to share our first story led by @martinacapriati.bsky.social! How do cells control the expression of viability genes? We find that single transcription factors can drive both chromatin opening and gene activation from densely co-bound CpG island promoters, including at essential genes
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Yehu Moran @yehumoran.bsky.social · 01/05/2026
A very nice piece about our latest paper published in Open Biology by @royalsocietypublishing.org It's about how venom-producing stinging cells use chromatic modifications to determine their biochemical identity: royalsociety.org/blog/2026/04...
royalsociety.org
The secret life of stinging cells: chromatin regulation in sea anemones | Royal Society
This Open Biology study uncovers how specialised stinging cells used for prey capture and defence, are regulated at a deeper level than ever before.
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Isabel Almudi @isabelalmudi.bsky.social · 29/04/2026
Exhausted but extremely happy for the two past days of very exciting Science! The EvoDevOmics Spanish Network gathered together in BCN to discuss about evodevo & omics, lots of great talks, discussions and future collaborations. 🤩 #evodevo
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 24/04/2026
Thanks to Hollie Marshall, James Ord, @alexdemendoza.bsky.social & everyone who joined us this week for the DNA Methylation workshop. It was a fantastic week of discussion, hands-on work, and shared ideas across ecology and evolution. Great to see such strong engagement throughout the course!
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 20/04/2026
We are very happy to kick off the #DNAmethylation course with @alexdemendoza.bsky.social Hollie Marshall James Ord and a great group of attendees from all over the globe! www.physalia-courses.org/courses-work...
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Alex de Mendoza @alexdemendoza.bsky.social · 17/04/2026
Very proud of my 2nd PhD student, Pedro Romero Charria, who defended his viva yesterday. Big thanks to @michael-imbeault.bsky.social and Roman Arguello for the discussion. Pedro's main work on #6mA in protists was published late last year (www.nature.com/articles/s41...), but there's more to come!
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Rakyan Lab @rakyanlab.bsky.social · 10/04/2026
Super happy to share the published version of our study: “Germline sequence variation within the ribosomal DNA is associated with human complex traits” in Cell Genomics www.cell.com/cell-genomic...!
cell.com
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The EMBO Journal @embojournal.org · 10/04/2026
How come giant mimivirus virions retain icosahedral symmetry like smaller viruses? Chantal Abergel, Hugo Bisio @molbiolgv.bsky.social et al use bioinformatics, genetics & interactomics to elucidate spatial & functional organization of mimivirus virion morphogenesis link.springer.com/article/10.1...
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Alex de Mendoza @alexdemendoza.bsky.social · 10/04/2026
Last day to submit an abstract! This is a meeting aimed at all career stages, but especially geared on early career scientists (PhD/postdoc), don't feel you need to have a perfectly polished story to present!
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Alex de Mendoza @alexdemendoza.bsky.social · 02/04/2026
Nice opportunity to join QMUL as a PhD student (or postdoc). Lee works on cool insect symbiosis projects, and I am co-supervisor on this one. Don't miss it if you're into microbiome / host-microbe interactions.
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Alex de Mendoza @alexdemendoza.bsky.social · 23/03/2026
May 5th: if you are around London, please join the London #EvoDevo symposium at QMUL / Charterhouse campus, as usual we will have selected talks and post-event 🍻. A warm up for #EED2026 in Glasgow. Registration £0, more info here: londonevodevo.co.uk
londonevodevo.co.uk
LondonEvoDevo
meeting's website
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QMUL Centre for Epigenetics @qmulepigenetics.bsky.social · 04/03/2026
We're excited to announced that our 2nd Annual QMUL Centre for Epigenetics Conference is happening on June 18th, 2026 at Mile End! To find out more and book your ticket, please follow this link: www.qmul.ac.uk/epigenetics/... The deadline to book your tickets is Monday, June 8th 2026.
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Philip Donoghue @phil-donoghue.bsky.social · 08/01/2026
Our latest: Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history, led by @meleonora-rossi.bsky.social with help from friends @bristolpalaeo.bsky.social including @anariesgo.bsky.social @evopalaeo.bsky.social Davide Pisani and many others
science.org
Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history
Sponges have a cryptic Ediacaran history because ancestral sponges were soft-bodied and had low fossilization potential.
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imaeso.bsky.social @imaeso.bsky.social · 07/01/2026
Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l
rdcu.be
Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes
Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...
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Laura Eme @lauraeme.bsky.social · 13/12/2025
Microbial eukaryotes keep challenging assumptions about eukaryotic cell and genome biology. Our upcoming workshop explores the frontier of protist genomics and how it shapes cell biology, ecology and evolution. Please save the date! Talks, posters and ECR events Websites and details coming soon
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Ákos T Kovács @evolvedbiofilm.bsky.social · 06/12/2025
Extensive horizontal transfer of transposable elements shapes fungal mobilomes @currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social www.cell.com/current-biol...
cell.com
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...
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Rob Klose @robklose.bsky.social · 11/12/2025
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost! www.biorxiv.org/content/10.6...
biorxiv.org
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
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Alex de Mendoza @alexdemendoza.bsky.social · 11/12/2025
It is amazing that @dudinlab.bsky.social beautiful #ExM composition has been selected to highlight our #6mA work for the cover of @natgenet.nature.com. #Protists (and ichthyosporeans in particular) in the cover of NG must be quite unique!
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Alex de Mendoza @alexdemendoza.bsky.social · 09/12/2025
Really happy to have been granted a #ERCCoG, grateful to the team who made this possible, and to the community who considered this work promising! If you (or someone you know) are/is interested in #chromatin evolution and #giantViruses, please do get in touch, there will be positions available.
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