Really cool work !

Love the strong scaling of ZGA timing to genome size and egg volume. It's so simple and elegant.

Highlights the strength of taking a comparative approach

Do you want to know when your favorite species activates its genome?

Just input its genome size (🧬 in bp) and egg volumen (🥚 in um3) here!

ZGA_onset = -2.37 * log10(gDNA/EggVol) + 11.74

This fits the general principle of ZGA being triggered by a 'universal' Genome: Cytoplasm ratio across animals! - and thus a highly conserved mechanism involving titration of a maternal cytoplasmic factor on chromatin.

So, by providing staged embryo mRNA for this beautiful wide comparative study, we now know that zygotic gene activation in Clytia occurs in the early blastula with 512 cells, at around 5hpf (Here termed ZGA cell cycle 9).

“Here, we generated a comprehensive transcriptomic atlas of early embryogenesis from 61 animal species, spanning 13 phyla. By applying a unified computational framework, we systematically inferred the timing of ZGA across species.”

This is a big one from @mirimiam.bsky.social et al. 🔥🧪

@hector-escriva.bsky.social , @arnausebe.bsky.social , @enricodanielloszn.bsky.social , @jpascualanaya.bsky.social , @clytia-vlfr.bsky.social , @isabelalmudi.bsky.social , @chemamd.bsky.social , @arburga.bsky.social and SD'Aniello! 15c/15

@totsese.bsky.social , @perievodevo.bsky.social , @allancarbal.bsky.social , @kguynes.bsky.social , @martaig.bsky.social , @jorgecorbacho.bsky.social , @metteh-thorsager.bsky.social , @arnonelab.bsky.social , @mcgregorlab.bsky.social , @jrmarmor.bsky.social 15b/15

Thanks so much to Jon Pemanyer and Cris Rodriguez and all our collaborators that provided all the essential embryo samples, without whom this project would have been impossible! (Those with handlers listed below!) 15a/15

N/C correlation vs ZGA onset improves even further adding two plant species

In summary, this first systematic and phylogenetically broad characterization of ZGA provides strong evolutionary support for the N/C ratio as a universal timer of ZGA (in animals, and perhaps beyond! 😉) and reveals shared molecular features of genes activated at that stage. 14/15

Regulatory conservation of MAT and ZGA gene sets

Similarly, while ZGA expression was conserved only among specific clades (e.g. within mammals or within nematodes) and at low levels, MAT genes were broadly shared across taxa. Indeed, while we identified only 1 broadly shared ZGA gene, we found > 500 MAT ones! 13/15

Genomic conservation of ZGA and MAT gene sets

Finally, we studied the genomic and regulatory conservation of ZGA and MAT genes. At the genomic (G) level, ZGA genes were much less conserved and evolutionarily novel than other genes, whereas MAT genes were highly conserved. 12/15

Functional enrichments of MAT, ZGA and subsequently activated genes reflect the dynamics and needs of early development

Second, ZGA genes shared functional enrichments across species, particularly on gene expression and RNA processing. In fact, studying also the genes activated 1 or 2 stages after ZGA, we found conserved functional switches that reflect the temporal needs of early development. 11/15

ZGA genes share a common set of genomic features across animals

First, we uncovered a set of shared genomic features of genes activated at ZGA. Across species, these genes tend to be shorter, contain fewer exons, display distinct regulatory architectures, and show strong codon usage bias compared to MAT genes. 10/15

Averaged profile of expression of ZGA and MAT (maternal) gene sets

Then, we switched gears to investigate the genes activated at ZGA. For a fair comparison across species, we defined a "ZGA score" to select the top 500 genes in terms of zygotic activation in each species. We also compared them to highly maternally-deposited (MAT) genes. 9/15

Model of N/C as a universal clock of ZGA

This finding provides broad comparative support for the longstanding hypothesis that the nuclear-to-cytoplasmic (N/C) ratio acts as a timer of genome activation. Moreover, this scaling accurately predicts ZGA timing across diverse animals from genome size and egg volume of a species alone. 8/15

Strong negative correlation between log DNA size / egg volume & ZGA onset in cell cycles

Then, what determines ZGA onset?? We correlated multiple genomic, developmental and ecological features with ZGA timing and, cutting to the chase, we found that the log ratio of genome size vs. egg volume very strongly scaled negatively with ZGA onset in cell cycles! 7/15

No correlation between ZGA onset in hours and cycle and association with gastrulation

What determines this variability? First, ZGA onset in cell cycles is not at all correlated with onset in hours of development, against some hypotheses in the field. Second, ZGA nearly always occurs before gastrulation, as expected, suggesting they impose constraints on each other's onset. 6/15

Distribution of ZGA onsets and attempt to reconstruct ancestral state

We found the timing of ZGA onset to be highly variable across species, covering every possible cell cycle from 1 (rodents) to 14 (flies). While the most common stages were 3-5 cell cycles, we could not really infer an ancestral ZGA stage due to its high variability. 5/15

Landscape of ZGA onset across animals

We analyzed these datasets within a unified framework, using three main data types to identify ZGA onset across species (PCA distances, newly expressed genes and intron/exon read ratio). The result was the first systematic atlas of ZGA onset across animals. 4/15

Sampling of developmental stages across 61 animal species.

Thus, it remains unclear whether and which common principles underlie ZGA across animal evolution.

Here, we took a comparative & evolutionary approach, and generated a comprehensive transcriptomic atlas of early embryogenesis across 61 species spanning 13 animal phyla. 🐁🐟🦟🪱🐌🪼 3/15

Diversity of ZGA onset in animal model organisms

ZGA is a universal and essential transition in animal development, by which embryos take control of their own gene expression. Despite its importance, ZGA has well been characterized in only a handful of model organisms, where both the timing and the identity of the genes involved greatly vary. 2/15

Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬

Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15

www.biorxiv.org/content/10.6...

A terrible, unfair solution to a real, pressing problem.

We’ve reopened the call for a PhD position with Juana Diez at @melisupf.bsky.social within the EVOMG-DN project.

🧬 Viral Codon Usage: A Novel Readout of Virus Evolution and Host Interaction
🗓 Deadline: 10 May 2026
👉 Apply here: www.evomg-dn.eu/call-for-app...

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

🚨 Job Alert - Please share! 🙏

Interested in 3D gene regulation in development & evolution? 🤓🧬

💥 Our lab at @cabd-upo-csic.bsky.social is expanding!

We’re recruiting:
✅ PhD students
✅ Postdocs
💻🧪 Experimental or computational backgrounds welcome

👇 Details below

Molecular #evolution of animal #aging:
A field perspective explores the impact of evolution on aging and offers a multi-angle view on longevity variation across model organisms and environments
link.springer.com/article/10.1...

🚨🧬🚨

We're looking for a specialized Research Assistant to spearhead a project aimed at exploring new RNA therapeutics in diabetes and other metabolic disorders.

Junior or Senior, we're hoping to recruit a highly motivated and self-driven scientist interested in both basic and applied science. 🦄

Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis LINE-1 (L1) retrotransposition generates somatic genomic variation in human cancer, but short-read sequencing has limited our understanding of its structural consequences and dynamics. Using long-read...

Today in
@science.org:
We are pleased to present our last work entitled:
"Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis"
by Zumalave et al.
www.science.org/doi/10.1126/...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.