Thus spake Zaratiegui
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mikelz.bsky.social
Thus spake Zaratiegui
@mikelz.bsky.social
81 followers 530 following 26 posts
I’m the Hattori Hanzo of tortilla de patata (potato omelette). Transposons, heterochromatin and, more recently, mitochondria.
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Reposted by Thus spake Zaratiegui
natecoevo.nature.com
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution - Nature Ecology & Evolution
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after envir...
www.nature.com
November 20, 2025 at 4:31 PM
Reposted by Thus spake Zaratiegui
jromeijn.bsky.social
The first paper of my PhD is now available as a preprint! 🎉

Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.
www.biorxiv.org
June 20, 2025 at 7:39 PM
Reposted by Thus spake Zaratiegui
jojdavies.bsky.social
Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Reposted by Thus spake Zaratiegui
elife.bsky.social
Lifestyles shape genome size and gene content in fungal pathogens.
buff.ly/tec1Tds
Genomic traits associated with pathogenicity.
November 2, 2025 at 11:01 AM
Reposted by Thus spake Zaratiegui
vaishananth.bsky.social
Thrilled to share that this work has been accepted for publication @currentbiology.bsky.social 🥳
Special shoutout to the editorial team – the process was incredibly smooth and productive. Read more here:
www.sciencedirect.com/science/arti...
November 3, 2025 at 3:56 AM
Reposted by Thus spake Zaratiegui
andrew.heiss.phd
Wrote up a little intervention post/explanation for my class about why using LLMs for trying to learn programming (as first time learners!) is bad and detrimental datavizf25.classes.andrewheiss.com/news/2025-11...
In the first week of class, I had you read an article about how ChatGPT is philosophical “bullshit”, as well as this other post about AI and LLMs in this class. I’ve seen a surprising increase in the amount of ChatGPT-based weekly check-ins and graph interpretations in the exercises. (In the past, I’ve even had students tell me they PDFs of the slides into ChatGPT to generate interesting and confusing things.) Don’t do this! LLMs cannot find three things that you personally found interesting from the readings. LLMs are not you. It’s a huge waste of time for all of us to for me to spend time evaluating and grading output from ChatGPT. I want to read what you think and do, not what a computer invents. NoteMy personal stance on AI and LLMs Many of you have asked about how I think about and use LLMs in my own work (and in the class materials). Please check this short little page where I explain what I do with text, images, code, research, and learning. In short, I do not use LLMs to create any of the materials for this class, and I do not use them to grade or evaluate any of your work. I’ve even had several students submit completely made up stuff for mini projects and final projects. In your final project, your job is to take a dataset, make three different plots with it, and combine the plots into one graphic that tells some sort of story. I’ve (really truly) received projects like this: (a ChatGPT-generated plot of completely made up data from gapminder) At a very quick glance, that looks like a plausible image. But holy crap it falls apart fast, both comically and tragically. Comically because, like, look at the y-axis in the scatterplot; or the x-axis ticks in the population grown chart that are sometimes spaced every 20 years, sometimes every 10 years, and has 1980 there twice; or the weird blobs in the map. Tragically—and most importantly—literally nothing in this image is real and none of the annotations make sense and none of the colors make sense and everything here is completely meaningless and devoid of any information. It’s pure philosophical bullshit—an image “produced without concern for its truth.” That’s what I mean when I say that it’s a forgetful and unreliable resource. Lots of that code is helpful as an illustration of what’s going on. Lots of the explanation is good and fine. But it subtly changed its mind halfway through and didn’t realize it (because it can’t realize it! it’s just a chain of statistically likely text!) Hopefully you can see where this is dangerous for learning. It can often “teach” you wrong, and you can only recognize that if you know stuff already. It’s extra dangerous if you then take that example output, paste it into your exercise, and submit it. I’m not even concerned about the plagiarism aspect of that—code is code and there are only a few ways to write {dplyr} code that will do this, and it’s easy to adapt from real human-based examples online, so I’m less worried about stealing other people’s work here. I’m concerned that it’s not real data. It made up values of 1, 2, 3, and 4 for some countries to illustrate grouping and summarizing. That’s good and normal. None of that is real. Don’t treat it as real.
November 2, 2025 at 10:17 PM
Reposted by Thus spake Zaratiegui
tobybarilbio.bsky.social
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

www.biorxiv.org/content/10.1...
October 29, 2025 at 9:02 AM
Reposted by Thus spake Zaratiegui
dodonova-sveta.bsky.social
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 28, 2025 at 3:07 PM
Reposted by Thus spake Zaratiegui
carmeloferrai.bsky.social
A conserved H3K14ub-driven H3K9me3 for chromatin compartmentalization

www.nature.com/articles/s41...
A conserved H3K14ub-driven H3K9me3 for chromatin compartmentalization - Nature
G2E3-catalysed H3K14 mono-ubiquitination is crucial for SUV39H compartmentalization and H3K9 trimethylation in pericentromeric heterochromatin, which is essential for proper euchromatin organization a...
www.nature.com
October 18, 2025 at 7:09 AM
Reposted by Thus spake Zaratiegui
plosbiology.org
Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx
Widespread shifts in genome architecture and trophism across fungi. Phylogenetic positions of the shifts identified for genome size. Negative values denote an identified decrease in the genomic trait value while positive values denote an increase in the genomic trait value.
October 16, 2025 at 7:58 AM
Reposted by Thus spake Zaratiegui
mendell-lab.bsky.social
Colliding ribosomes are potent signals of cellular stress. But do cells use ‘programmed’ ribosome collisions to regulate gene expression? I’m excited to present a new story from my lab led by Frederick Rehfeld(@fred-rehfeld.bsky.social) which revealed that the answer is YES! Read on to find out how👇
Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins
Selenocysteine, incorporated into polypeptides at recoded termination codons, plays an essential role in redox biology. Using GPX1 and GPX4, selenoenzymes that mitigate oxidative stress, as reporters,...
www.biorxiv.org
October 14, 2025 at 10:28 PM
mikelz.bsky.social
Proteasome Prevents Pombe Petite Positivity
Client Challenge
rdcu.be
October 14, 2025 at 1:58 PM
Reposted by Thus spake Zaratiegui
dfachinetti.bsky.social
Thanks to @erhardtlab.bsky.social for the news and views on our paper on DNA methylation¢romere www.nature.com/articles/s41....
Dipping into the function of DNA methylation at centromeres - Nature Genetics
Human centromeres contain a small chromatin region with low levels of DNA cytosine methylation that resides with CENP-A. Salinas-Luypaert et al. find a role of DNA methylation in maintaining the size and function of centromeres by controlling the binding affinity of key centromere components.
www.nature.com
October 6, 2025 at 6:58 AM
Reposted by Thus spake Zaratiegui
scaffidilab.bsky.social
Histone acetylation - not always about transcriptional activation: H4K16ac safeguards the genome replication program by repressing premature replication of heterochromatin. Well done Marta Milan! tinyurl.com/yuy9m8t3
September 30, 2025 at 12:14 PM
Reposted by Thus spake Zaratiegui
fmattiroli.bsky.social
The latest work from ours and @vram142.bsky.social lab is out! True teamwork to visualize nascent chromatin with strand resolution, using a fully reconstituted system. Very proud of superstar-PhD student Bruna, and @palindromephd.bsky.social. Learning so much from Vijay’s amazing technologies! RT
September 21, 2025 at 7:12 AM
Reposted by Thus spake Zaratiegui
juliusbrennecke.bsky.social
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...
September 17, 2025 at 10:39 AM
Reposted by Thus spake Zaratiegui
yuripritykin.bsky.social
Happy to share our new paper!

We present high-resolution Micro-C maps across Drosophila embryogenesis, integrated with 149 ChIP-seq datasets. This systematic analysis enabled clustering of loops & boundaries into 4 distinct classes with distinct regulatory roles.

www.cell.com/cell-genomic...
3D chromatin structures precede genome activation in Drosophila embryogenesis
Dolsten et al. map the 3D chromatin architecture across early Drosophila development using high-resolution Micro-C, and, by integrative analysis with 149 public ChIP-seq datasets, identify four classe...
www.cell.com
September 16, 2025 at 7:57 PM
Reposted by Thus spake Zaratiegui
elphegenoralab.bsky.social
New preprint with @gfudenberg.bsky.social

We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.

This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇

www.biorxiv.org/content/10.1...
NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion
Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...
www.biorxiv.org
August 16, 2025 at 3:03 AM
Reposted by Thus spake Zaratiegui
plantepigenetics.ch
Here’s an interesting new paper on ROS1, an enzyme that removes DNA methylation and that is POSITIVELY controlled by DNA methylation.
It’s repression during heat stress 🥵🌱 is crucial to suppress transposon mobility! 🧬
www.nature.com/articles/s41...
Plants repress ROS1 expression to attenuate heat-induced transposon burst - Nature Plants
Plants suppress the DNA demethylase ROS1 under heat stress to limit transposon activation, preventing genome instability. This conserved mechanism balances stress adaptation with genome protection.
www.nature.com
August 11, 2025 at 1:57 PM
mikelz.bsky.social
Ph'nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn. Iä! Iä! Cthulhu fhtagn!
August 13, 2025 at 6:06 PM
Reposted by Thus spake Zaratiegui
altnih4science.bsky.social
Rapid response media isn’t just for political campaigns anymore.

NASEM and Harvard and AAAS need rapid response digital and comms teams to track down misinformation and shut it down, aggressively. This is now a core function for any science institution. And which of them have this?!
August 10, 2025 at 2:27 AM
Reposted by Thus spake Zaratiegui
lianafaye.bsky.social
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
www.biorxiv.org
August 7, 2025 at 8:29 AM
Reposted by Thus spake Zaratiegui
trompoukilab.bsky.social
Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation: Cell www.cell.com/cell/fulltex...
Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation
This study reveals that composite transposons with bivalent histone marks can serve as RNA-dependent enhancers, controlling key developmental and aging-related gene programs.
www.cell.com
August 7, 2025 at 10:42 AM
Reposted by Thus spake Zaratiegui
bffo.bsky.social
From @plos.org #Computational #Biology | LabOps: A flexible self-hosted workflow of open source tools for efficient collaboration within research laboratories | #OpenSource #Bioinformatics #Education #OpenScience | 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
LabOps: A flexible self-hosted workflow of open source tools for efficient collaboration within research laboratories
Author summary Is there anything beyond Slack, Microsoft Teams, Google Drive, and OneDrive? Effective collaboration is crucial for success in academic environments, yet a standardized suite of open-so...
journals.plos.org
July 19, 2025 at 7:28 PM
Reposted by Thus spake Zaratiegui
samillingworth.com
🐭🧬 Bi-paternal mice reach adulthood

A new study shows that editing 20 imprinted genes in embryos from two male parents can overcome lethal barriers to development – producing viable, adult mice.

🔗 www.sciencedirect.com/science/arti...

#SciComm #Genetics 🧪
Adult bi-paternal offspring generated through direct modification of imprinted genes in mammals
Imprinting abnormalities pose a significant challenge in applications involving embryonic stem cells, induced pluripotent stem cells, and animal cloni…
www.sciencedirect.com
June 22, 2025 at 4:26 AM