Count Slopula

Gene conversion empowers natural selection in a clonal fish species - Nature Analysis of the asexually reproducing Amazon molly Poecilia formosa and its sexually reproducing progenitors Poecilia mexicana and Poecilia latipinna reveals that it maintains a divergent mutational l...

Excited to share a new study co-written with Ed Ricemeyer (LMU Munich), supervised by Manfred Schartl (U. of Würzburg) & Wes Warren (U. of Missouri).

We investigated how the Amazon molly has survived for 100,000 years (more generations) despite clonal reproduction.

www.nature.com/articles/s41...

Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity Milovanović et al. uncover a mechanism by which KZFPs restrict the activity of transposon-derived cis-regulatory elements to safeguard cardiomyocyte functionality. This work extends the classical TE-K...

It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports....
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨

Figure 1. Imagin, a multi-exon integrase-like gene in malacostracan crustaceans. (A) Structure of the PjImagin gene. The transcript is shown in light blue and the CDS in white. The YPYY motif is colored yellow, the H2C2 zinc finger is colored sky blue, the defunct DDE catalytic core is colored in pink, and the disordered region is shaded in gray. Gray vertical lines denote the positions of key residues denoted in panels C and D, with the last two lines being shaded to indicate the corresponding positions for the lost D and E residues (Panel E). (B) The genomic context of PjImagin and orthologs. PjImagin is flanked by exons 14 and 15 of methylmalonyl-CoA mutase, mitochondrial-like (MMUT) gene, which runs on the opposite strand. Note that the Imagin gene of the swimming crab (Portunus trituberculatus) lies on an unrelated position. MMUT CDS is colored green, and MMUT exons corresponding to exons 14 and 15 of P. japonicus MMUT are connected with light green ribbons. CDS of other genes are shaded gray. (C) Domain architectures of malacostracan Imagin proteins. The coloring scheme follows that of panel (A). (D) Conservation of the YPYY motif and the H2C2 (HHCC) zinc-finger domain in integrase proteins. Species names are listed on the left, with protein accession numbers provided on the right. Entries Ginger1-1_HM, Ginger1-2_HM, and Ginger1-3_HM were adopted from (Bao et al. 2010). (E) Loss of the DDE catalytic residues in crustacean Imagin proteins. Species names are listed on the left, with protein accession numbers provided on the right. Note that some residues may be missing from this alignment because regions containing long gaps were automatically suppressed by DALI. Each residue is shaded by background color according to the secondary structure assignments by DSSP: light green: loop; dark green: helix; blue: strand. Conserved aspartic acid (D) and glutamic acid (E) residues comprising the DDE motif are highlighted in black.

Figure 3. Imagin is a domesticated Ginger1 DNA transposon. (A) Maximum-likelihood phylogenetic tree of 121 DDE integrases and derivatives (136 sites; model: VT+R6). (B) Subtree of (A) showing the phylogenetic relationships of Ginger1-like elements. The bar beside the tree indicates amino acid substitutions per site. The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each).

Figure 2. Phylogenetic analysis of decapod Imagin proteins. A total of 463 sites were used for the maximum-likelihood phylogenetic analysis using IQTREE v3.0.1 (substitution model: Q.MAMMAL+F+I+G4). The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each). The bar indicates amino acid substitutions per site. Euphausiacea and Stomatopoda were used as the outgroup. Imagin proteins from brachyuran crabs formed a long branch relative to the other taxa, suggesting accelerated evolution following the translocation event in this lineage.

𝘐𝘮𝘢𝘨𝘪𝘯: an integrase-like gene conserved across malacostracan crustaceans derived from a Ginger1 DNA transposon
We discovered a domesticated transposon in crustaceans, which has abandoned its mobility for a host function (likely reproductive).
doi.org/10.1093/gbe/...

A transposase-derived gene required for human brain development PGBD5 is required for brain development in humans and mice through genetic and nongenetic mechanisms.

A transposase-derived gene required for human brain development | Science Advances www.science.org/doi/10.1126/...

New work on CR1 retrotransposons by my lab friends Alex and Chandler! Happy to have helped out along the way

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis -regulatory contribution of TEs to immune cell d...

New Year, New Paper!🎊

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...

Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵

Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...

Antiviral reverse transcriptases reveal the evolutionary origin of telomerase Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?

Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...

JSCBB Biotech Building in Boulder, CO

Are you bravely deciding to do a postdoc in the US? And also interested in some combination of genomics, immunology, and transposons? If so, consider applying to my lab at the BioFrontiers Institute in Boulder, Colorado!

jobs.colorado.edu/jobs/JobDeta...

🧪🧬 #TESky #interferosky

Just dropped our Mobile DNA review on HERVH, an ancient retrovirus now repurposed to build and defend the early human embryo. Call it genomic up-cycling!
I felt HERVH went unnoticed this year, so we published this as a refresher; two fresh data papers - coming soon.
🔗 doi.org/10.1186/s131...
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SCROTUS

I want to share our latest work on a forward simulation framework on transposable element evolution. The TE Evolution Simulation Suite, or TESS, contains three components that can simulate many scenarios of genome evolution under the impact of TEs.

A geranium with mottled pink petals.

Seeing transposons in action is just the pick me up I needed today!

📢The peer-reviewed version of our work on TEs driving innovation of F-box genes is out now on @molbioevol.bsky.social. 🎉

paper here:
academic.oup.com/mbe/article/...

Check my previous, but still up-to-date 🧵 to read the highlights. #TEsky #evosky #Celegans

Our May issue is live!

Yukihide Tomari et al outline repression mechanisms for transposons (which “jump” through the genome like monkeys [see cover]). Meanwhile, Sarah Signor et al dive into the evolution of one of these mechanisms: the piRNA system.

More here!
www.cell.com/trends/genet...

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n

Human de novo mutation rates from a four-generation pedigree reference - Nature Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set t...

This is a very cool article. They did T2T (high depth, low error) sequencing on genomes from FOUR generations of a family. 🧵

"Human de novo mutation rates from a four-generation pedigree reference"

www.nature.com/articles/s41...

In this study, Hermant et al. describe the evolution of the retrotransposon MERVL and its cis-regulatory transcription factor binding motifs, highlighting the phyloregulatory adaptation at play during early embryogenesis.

Learn more here:
➡️ tinyurl.com/gd352270

Cryptic infection of a giant virus in a unicellular green alga Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe a 617 kbp integrated giant viral element in the model green alga C...

Cryptic infection of a giant virus in a unicellular green alga | Science www.science.org/doi/10.1126/...

A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.

A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...

The mobile genome: genetic and physiological impacts of transposable elements

Do you have transposon-related research cooking, with some cool results you are exciting to share? Start thinking about registering to #EMBOMobileGenome workshop! Nov 4-7 2025 in Heidelberg. One of the historical TE meetings, with a diverse and welcoming community. www.embl.org/about/info/c...
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Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇

I am thrilled to share our story online at @cellpress.bsky.social . Big thanks to all authors: Zhiping, Bill, @lubanlab.bsky.social, Keith & bluesky-less!

authors.elsevier.com/c/1kjdaL7PXu...

How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA

More below 👇

Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis www.biorxiv.org/content/10.1101/2025.03....

Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?

This looks quite cool, latest paper from Frank Johannes on somatic mutations in trees:

Branching architecture limits the rate of somatic mutation accumulation in trees
doi.org/10.1101/2025...

Transposable elements may enhance antiviral resistance in HIV-1 elite controllers - Genome Biology Background Less than 0.5% of people living with HIV-1 are elite controllers (ECs)—individuals who maintain undetectable plasma viremia without antiretroviral therapy, despite having replication-compet...

Feels awkward but necessary to celebrate scientific progress in this imperiled time for US biomedical research.

Proud of our latest paper out today exploring the role of transposable elements in antiviral resistance to HIV 🦠

genomebiology.biomedcentral.com/articles/10....
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In this new Feature Review, Yukihide Tomari and colleagues examine repression mechanisms that silence transposons and discuss the dynamic coevolution of transposons and host defenses in animals.

Read for FREE till April 11th:

authors.elsevier.com/a/1keCScQbJF...

SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro - Nature A biochemical system recapitulates the hallmarks of meiotic double-strand break formation, with mouse SPO11 catalysing break formation in the absence of any partners and remaining covalently atta...

🥳Just published @nature.com. Over 25 years after the discovery of SPO11 as the enzyme responsible for initiating meiotic recombination, we finally succeeded in reconstituting its DNA cleavage activity.🧵
www.nature.com/articles/s41...