Alex de Mendoza
@alexdemendoza.bsky.social
Evolutionary epigenomics ( eukaryotes / Transcription Factors / Transposable Elements / DNA methylation ) @ QMUL (London).
Lab website: https://www.demendozalab.com/
Lab website: https://www.demendozalab.com/
Pinned
Thrilled to share that the lab has been awarded a @wellcometrust.bsky.social Discovery Award to keep exploring the evolution of 6-methyladenine #6mA in Eukaryotes. We'll open postdoc (3️⃣) and tech (1️⃣) positions to start in 2026, please share with candidates or reach out if you’d like to join us.
Reposted by Alex de Mendoza
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Alex de Mendoza
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
November 19, 2025 at 9:39 PM
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
Reposted by Alex de Mendoza
Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.
November 18, 2025 at 4:15 PM
Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.
And also out, the short Research Briefings summarising our #6mA findings, with an honest explanation of the origins of this project (tldr: this was never planned, but a serendipitous branching point of another project): www.nature.com/articles/s41...
November 20, 2025 at 10:34 AM
And also out, the short Research Briefings summarising our #6mA findings, with an honest explanation of the origins of this project (tldr: this was never planned, but a serendipitous branching point of another project): www.nature.com/articles/s41...
Reposted by Alex de Mendoza
TE x ZFP = Evolution!
Writing this with Olga @orpsf.bsky.social & Didier @trono-lab.bsky.social was a major highlight of my 🇨🇭sabbatical. Such a treat! 🍫Hope you enjoy it as much as we enjoy piecing it together.
Writing this with Olga @orpsf.bsky.social & Didier @trono-lab.bsky.social was a major highlight of my 🇨🇭sabbatical. Such a treat! 🍫Hope you enjoy it as much as we enjoy piecing it together.
November 18, 2025 at 3:16 PM
TE x ZFP = Evolution!
Writing this with Olga @orpsf.bsky.social & Didier @trono-lab.bsky.social was a major highlight of my 🇨🇭sabbatical. Such a treat! 🍫Hope you enjoy it as much as we enjoy piecing it together.
Writing this with Olga @orpsf.bsky.social & Didier @trono-lab.bsky.social was a major highlight of my 🇨🇭sabbatical. Such a treat! 🍫Hope you enjoy it as much as we enjoy piecing it together.
Reposted by Alex de Mendoza
Fun week for DNA methylation research! Here is a thread of three cool papers that came out, all with an evolution angle. And a bonus 4th that examines DNAme/PcG interplay (certainly an interest for our lab!) #Epigenetics
November 19, 2025 at 9:48 AM
Fun week for DNA methylation research! Here is a thread of three cool papers that came out, all with an evolution angle. And a bonus 4th that examines DNAme/PcG interplay (certainly an interest for our lab!) #Epigenetics
Reposted by Alex de Mendoza
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
November 13, 2025 at 11:54 AM
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Reposted by Alex de Mendoza
1/ I’m very excited to share my postdoc work with @kseskv.bsky.social, in collaboration with @oligriffith.bsky.social. We explore embryonic DNA methylation reprogramming in the fat-tailed dunnart, an Australian marsupial 🦘🌏 www.biorxiv.org/content/10.1...
www.biorxiv.org
November 12, 2025 at 2:57 AM
1/ I’m very excited to share my postdoc work with @kseskv.bsky.social, in collaboration with @oligriffith.bsky.social. We explore embryonic DNA methylation reprogramming in the fat-tailed dunnart, an Australian marsupial 🦘🌏 www.biorxiv.org/content/10.1...
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by Alex de Mendoza
🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
October 30, 2025 at 5:50 PM
🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
Reposted by Alex de Mendoza
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
CREation of an expanded plant memory gene circuit toolkit
Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new mol...
www.biorxiv.org
October 31, 2025 at 9:24 AM
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
Reposted by Alex de Mendoza
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates
Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...
rdcu.be
October 29, 2025 at 1:40 PM
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Come join the #LondonEvoDevo network half day meeting, hosted at @ucl.ac.uk on Friday November 7th, 2025. Submit your abstract by Oct 27th (or your interest in joining) here: forms.gle/TRbdrCkQTcY2.... Friendly vibes and free registration. More info here: londonevodevo.co.uk.
LondonEvoDevo
meeting's website
londonevodevo.co.uk
October 20, 2025 at 1:42 PM
Come join the #LondonEvoDevo network half day meeting, hosted at @ucl.ac.uk on Friday November 7th, 2025. Submit your abstract by Oct 27th (or your interest in joining) here: forms.gle/TRbdrCkQTcY2.... Friendly vibes and free registration. More info here: londonevodevo.co.uk.
Reposted by Alex de Mendoza
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 16, 2025 at 10:01 PM
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social
rdcu.be/eLbaZ
rdcu.be/eLbaZ
October 15, 2025 at 7:58 PM
We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social
rdcu.be/eLbaZ
rdcu.be/eLbaZ
As a Transposable Element aficionado and a birder, this paper is just the best. Oenanthes are such beautiful birds.
1/9 New in @science.org www.science.org/doi/10.1126/science.ado8005
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.
A mosaic of modular variation at a single gene underpins convergent plumage coloration
The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and ...
www.science.org
October 17, 2025 at 2:08 PM
As a Transposable Element aficionado and a birder, this paper is just the best. Oenanthes are such beautiful birds.
Reposted by Alex de Mendoza
Our latest paper on a histone methyltransferase-independent function of PRC2 controlling small RNA dynamics during programmed DNA elimination in Paramecium is now published in #NAR.
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium
Abstract. To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms
academic.oup.com
October 17, 2025 at 11:58 AM
Our latest paper on a histone methyltransferase-independent function of PRC2 controlling small RNA dynamics during programmed DNA elimination in Paramecium is now published in #NAR.
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
Reposted by Alex de Mendoza
Reposted by Alex de Mendoza
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
October 5, 2025 at 10:35 AM
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Reposted by Alex de Mendoza
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster
Abstract. Phenotypic variation in species arises from genetic differences and environmental influences on gene expression. Differences in epigenetic modifi
academic.oup.com
October 9, 2025 at 8:30 AM
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
Reposted by Alex de Mendoza
It was fantastic welcoming back Chema Martin @chemamd.bsky.social from @qmulsbbs.bsky.social at the Centre today 👏 He shared with us his latest work on spiralian larvae evolution, with fascinating insights on the timing of gene expression during development. Thank you for visiting us!
October 10, 2025 at 2:28 PM
It was fantastic welcoming back Chema Martin @chemamd.bsky.social from @qmulsbbs.bsky.social at the Centre today 👏 He shared with us his latest work on spiralian larvae evolution, with fascinating insights on the timing of gene expression during development. Thank you for visiting us!
Reposted by Alex de Mendoza
Connecting different “neighborhoods” of a genome has many benefits. For one, it can allow a gene to be regulated by multiple sources, increasing the possibility for more complexity.
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 10, 2025 at 8:04 PM
Connecting different “neighborhoods” of a genome has many benefits. For one, it can allow a gene to be regulated by multiple sources, increasing the possibility for more complexity.
Reposted by Alex de Mendoza
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 Oct. Not only did he make a discovery that laid the foundations for stem cell research, he also created one of the best environments for research at the Wellcome/CRUK Gurdon Institute wellcome.org/news/sir-joh...
Sir John Gurdon, 1933-2025 | Wellcome
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 October. He made a discovery that opened up the field of cloning research, and created one of the best environments for res...
wellcome.org
October 9, 2025 at 1:39 PM
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 Oct. Not only did he make a discovery that laid the foundations for stem cell research, he also created one of the best environments for research at the Wellcome/CRUK Gurdon Institute wellcome.org/news/sir-joh...
Reposted by Alex de Mendoza
Our latest: combining single-cell RNA-seq from 16 species and HCR validation, we show that monoaminergic neurons share a conserved transcriptional identity across Bilateria. In contrast, we find no evidence for this program in non-bilaterian metazoans. www.biorxiv.org/content/10.1...
Monoaminergic neurons share transcriptional identity across Bilaterian animals
The evolutionary conservation of cell types over deep time has long been theorised but remains difficult to demonstrate. Monoaminergic neurons, which produce molecules such as serotonin and dopamine, ...
www.biorxiv.org
October 10, 2025 at 9:43 PM
Our latest: combining single-cell RNA-seq from 16 species and HCR validation, we show that monoaminergic neurons share a conserved transcriptional identity across Bilateria. In contrast, we find no evidence for this program in non-bilaterian metazoans. www.biorxiv.org/content/10.1...