Alex de Mendoza
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alexdemendoza.bsky.social
Alex de Mendoza
@alexdemendoza.bsky.social
Evolutionary epigenomics ( eukaryotes / Transcription Factors / Transposable Elements / DNA methylation ) @ QMUL (London).

Lab website: https://www.demendozalab.com/
Pinned
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/
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...
www.nature.com
Reposted by Alex de Mendoza
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. 🔬✨
September 21, 2026 at 5:40 PM
Reposted by Alex de Mendoza
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!

/+
We watched piRNAs and transposons across development, saw them dance tightly and wrote a paper about it.

It's so cool to see it online and we will make a thread about it all very soon. Stay tuned :-)
A developmental switch in the piRNA pathway ensures stage-specific transposon silencing https://www.biorxiv.org/content/10.64898/2026.08.28.747770v1
September 2, 2026 at 3:10 PM
Reposted by Alex de Mendoza
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/...
September 3, 2026 at 8:09 PM
Reposted by Alex de Mendoza
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.
August 28, 2026 at 12:28 PM
Reposted by Alex de Mendoza
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
📄 That's a wrap 📄 we're excited to share that the latest from @arnaudkr.bsky.social 's lab and Judith Zaugg's lab is at last online at doi.org/10.1038/s415.... Many thanks to my co-first @valentinabaderna.bsky.social and to @embl.org for the wonderful research environment.
August 12, 2026 at 6:45 AM
Reposted by Alex de Mendoza
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...
August 7, 2026 at 9:19 AM
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!
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, ...
docs.google.com
August 6, 2026 at 2:35 PM
Reposted by Alex de Mendoza
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
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...
www.nature.com
August 3, 2026 at 9:08 AM
Reposted by Alex de Mendoza
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...
July 30, 2026 at 6:17 PM
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. 🧵
August 3, 2026 at 9:33 AM
Reposted by Alex de Mendoza
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.
July 20, 2026 at 8:22 AM
Reposted by Alex de Mendoza
🚨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...
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...
www.biorxiv.org
June 15, 2026 at 6:13 AM
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!
¿De dónde venimos? El gran salto evolutivo del que surgieron las células complejas que nos conforman es un enigma. Un estudio de @irbbarcelona.org y @bsc-cns.bsky.social revela que hay más actores implicados de los que pensábamos

El 'ménage à trois' celular 👉 www.elconfidencial.com/tecnologia/c...
June 11, 2026 at 9:38 AM
Reposted by Alex de Mendoza
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...
June 10, 2026 at 3:00 PM
Reposted by Alex de Mendoza
"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.
embo.org EMBO @embo.org · Jun 9
Congratulations to Gautam Dey (EMBL) and Omaya Dudin (University of Geneva) for being awarded the EMBO Gold Medal 2026 in recognition of their outstanding contributions to the #LifeSciences in Europe! 🧪 https://www.embo.org/press-releases/embo-gold-medal-2026-awarded-to-gautam-dey-and-omaya-dudin/
June 9, 2026 at 1:29 PM
Reposted by Alex de Mendoza
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
A unicellular relative links aggregative multicellularity to animal origins - Nature
Nature - A unicellular relative links aggregative multicellularity to animal origins
www.nature.com
June 9, 2026 at 7:59 PM
Reposted by Alex de Mendoza
📣 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
The Feschotte Lab at Cornell
www.thefeschottelabatcornell.com
May 29, 2026 at 4:30 PM
Reposted by Alex de Mendoza
🧪
June 2, 2026 at 5:06 PM
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/
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...
www.nature.com
June 2, 2026 at 9:52 AM
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
www.biorxiv.org
May 26, 2026 at 9:58 AM
Reposted by Alex de Mendoza
🚨 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...
May 19, 2026 at 8:09 PM
Reposted by Alex de Mendoza
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!
May 20, 2026 at 2:42 PM
Reposted by Alex de Mendoza
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...
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
www.biorxiv.org
May 15, 2026 at 2:59 PM
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/...
May 14, 2026 at 2:21 PM