On the Decoupling of Evolutionary Changes in mRNA and Protein Levels Abstract. Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is close

My first paper w/ Matt, about how mRNA and protein levels of the same genes should be expected to coevolve. It was carried over from my PhD at Michigan w/ George Zhang, but started too late to be in my thesis.
academic.oup.com/mbe/article/...

Landoni lab & UNIL logos, featuring fluorescent images of mitochondria and nematodes

The Landoni Lab opens this summer at UNIL! @fbm-unil.bsky.social 🔬 Quantitative #imaging + systems biology to decipher how #metabolic architecture & #mtDNA dynamically shape tissue development, #aging and #mitodisease. Beyond excited to fire up the lasers, open positions soon! 🧪 #mitochondria #newPI

This is just hateful. I'm sorry this happened to you... You deserve to be at the table because your opinions and research matters!

I suspect we only get so invested in whether the Central Dogma is broken or not because Crick called it that. If it had been "the principle of protein synthesis" or the "rules of transcription & translation" or something, it would seem less of a big deal. Remember, it's not a "dogma" at all.

I'm looking for #NewPIs (<3 years as lab heads) in the gene regulation/functional genomics space. If you are one or know one, please comment below! 🧪

✋trying to be!

Applying for an ERC grant in the 2027 competitions: what you need to know The ERC plans to launch the grant competitions under its 2027 Work Programme between July 2026 and June 2027, with the calls for proposals introducing several changes to the eligibility rules for appl...

The #ERC just announced new rules!
erc.europa.eu/news-events/...

If you got a B score before, you’re blocked for 2 years (instead of 1). A C score means 3-year exclusion.

This applies to the 2027 call for now, but I’d expect this to stick. Important for anyone planning to apply this round!

Happy to share our new preprint on non-coding genetic variation in the human brain and Parkinson's disease. Great team effort with @alexanrna.bsky.social, @juliedeman.bsky.social, Koen Theunis, and all co-authors, supervised by @steinaerts.bsky.social and @jdemeul.bsky.social.
Thread below:

Come listen to my talk about how enhancers evolve and how promoters emerge from randomly synthesized DNA sequences!

Today!

Harvey Yang and I were fortunate to contribute polymer simulations to this paper from @nicholas-aboreden.bsky.social Zhao... Zhang, Blobel showing that most CRE loops can form de novo after mitosis without loop extrusion
www.nature.com/articles/s41...

🚨New (very special) preprint! 🚨"What is the human germline mutation rate? methodological innovations, challenges, and evolutionary implications" doi.org/10.32942/X2T... The product of many coffees & pains au chocolat with @hhydrochaerus.bsky.social debating the knows and unknowns about mutations 🧬🧪

Actually, what is a gain-of-function mutation? Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien

academic.oup.com/genetics/adv...

Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2

Come listen to my talk about how enhancers evolve and how promoters emerge from randomly synthesized DNA sequences!

We are happy to present the latest preprint from our group led by Ph.D. candidate @lorhab.bsky.social! This piece explores the epistatic tradeoffs within eco-evo fitness landscapes (Give her a follow and wish her luck finishing her thesis!). Any feedback and constructive criticism is appreciated.

Check out our newest preprint! 📝 We find that adaptation on coevolutionary fitness landscapes is highly repeatable, but landscape-specific, and intergenomic epistasis creates coevolutionary fitness load for interacting species due to frequent fitness trade-offs 🏋️

The Semantics and Mechanisms of Enhancers and Promoters: “What Is True for E. coli Is True for the Elephant, Only More So” Three fundamental classes of gene regulatory elements were identified in Escherichia coli in the 1960s: operators bound by repressor proteins, promoters bound by the basic transcription machinery, and...

Within the field of transcription, the distinctive style of Mark Ptashne and Kevin Struhl stands out.

At his best, Kevin Struhl provides a valuable clarification of the relationship between promoters and enhancers in the regulation of transcription.

www.annualreviews.org/content/jour...

Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes - Genome Biology Alternative splicing patterns have diverged rapidly during vertebrate evolution. By integrating genome-wide predictions of stable RNA duplexes, alternative splicing profiles, and proximity ligation-de...

Alu repeats have played important roles in the evolution of (alternative) splicing via exonization and in other ways. In this paper, we show that they mediate interactions across exons to loop them out. Alus inserted this way in evolution render exons alternative. bit.ly/4t8Yahh 1/2

You don’t like the concept of spandrels? I thought it was a nice way to explain pleiotropy and how it confounds what traits we think are actually under selection…

I agree, it should also have utility (and that population is another great example of a subjective evo term). My thoughts go towards de novo genes, promoters, and enhancers. Genes, promoters, and enhancers are not novel, but mutations definitely can create novel ones, with serious evo consequences

But isn’t every term just a subjective human description?
I.e. What is a gene? What is a species? What is homology? What is function? I would argue these are also pretty subjective, but fundamental to evolutionary theory…

yup

Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...

Back in the noughties when I was an academic, my lab did quite a bit of work on (conserved) alternative transcripts. This study in @plosbiology.org presents compelling evidence that most alternative transcripts are deleterious noise journals.plos.org/plosbiology/...

🧵 New preprint: doi.org/10.64898/202...

In 2023, Papkou et al. reported an empirical fitness landscape with a striking property: >500 local optima ("peaks"), spanning both high and low fitness.

Despite this ruggedness, >75% of simulated adaptive walks reached the top ~14% of peaks.

Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...

"Some suggested that transcript diversity is adaptive, while others contended that it is largely deleterious and arises from molecular errors in transcription and RNA processing (...).

The data supports the error hypothesis and suggests that metazoan transcript diversity is largely deleterious"

New Preprint! When one enhancer allele changes another's regulatory output, is that bad? We found it could be a feature — interallelic cis-regulatory dominance buffers outputs AND enables evolutionary innovation. Two for one!

Led by @ottilie.bsky.social from @embl.org

doi: doi.org/10.64898/202...

Excited to share my first preprint from my PhD w/ @justinmcrocker.bsky.social. We show that cell type-specific regulatory dominance promotes robustness and evolutionary innovation through interallelic transcriptional hubs, potentially expanding the mutational paths available to diploids. (1/18)

Truly mind-blowing work, Noa. Great work!

Noa has done some bone-chiling work that incontrovertibly demonstrates that Dominance between developmental enhancer alleles influences possible evolutionary paths within fitness landscapes. There is a lot of epistasis in both masking and enhancing gene expression patterns in specific cell types!

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution - Nature Ecology & Evolution Experimental evolution of fission yeast (Schizosaccharomyces pombe) in the same environment as a previous experiment with budding yeast (Saccharomyces cerevisiae) reveals parallel evolution but distin...

Experimental evolution of fission yeast in the same environment as a previous experiment with budding yeast reveals parallel evolution but distinct molecular mechanisms and targets of adaptation in the two species 🧪 www.nature.com/articles/s41...