John McCormick

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...
🧵1/3

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...
1/3

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 https://www.biorxiv.org/content/10.1101/2025.03.07.641981v1

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....
🧵1/n

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...

An RNA Splicing System that Excises Transposons from Animal mRNAs All genomes harbor mobile genetic parasites called transposable elements (TEs). Here we describe a system, which we term SOS splicing, that protects C. elegans and human genes from DNA transposon-medi...

One of the coolest and most novel findings I’ve seen in years. This is why I work in worms. To find things no one even really knew to look for. Like a conserved system that splices transposons out of mRNAs to prevent otherwise lethal insertions in essential genes! - www.biorxiv.org/content/10.1...

Antero-posterior patterning in the brittle star Amphipholis squamata and the evolution of body plans across echinoderms https://www.biorxiv.org/content/10.1101/2025.02.13.638179v1

Congrats Peiwei! 🥳
All the more awesomely fitting given Larry Sandler’s discovery of segregation distorter and meiotic drive!

This is batshit mad.Things that spread between bacteria by hijacking phage tails
"These subcellular entities then interact with phage tails from various species, forming chimeric particles that inject DNA into different bacterial species depending on the tail present"
www.biorxiv.org/content/10.1...

The KRAB-Zinc Finger protein ZKSCAN3 represses enhancers via embedded retrotransposons Gene cis -regulatory sequences are increasingly recognised as containing “domesticated” transposable elements that impact their function. The KRAB Zinc Finger Protein (KZFP) family of transcription fa...

Our new #preprint has:
✅ A KRAB Zinc Finger (the SCAN domain-containing kind)
✅ #transposon sequences (the SINE kind)
✅ #epigenetic regulation (the #enhancer kind)
✅ lineage specification (the neural kind)
❌ and NO heterochromatin!

All by PhD student Daniel Moore 🚀

www.biorxiv.org/content/10.1...

If you have been affected by the fires in LA, or are concerned about your ability to keep precious Drosophila strains going during the latest funding crisis, we will host your strains as a backup. Please email me.

Please amplify. If you are also able to host fly strains, add your name as well.

If you’re a federal govt employee targeted for leave or termination on the basis of your DEI work, please file an EEO (Equal Employment Opportunity) complaint & retain legal counsel.

I’m a former NIH PI. Happy to refer you to a law firm that has successfully sued the govt many times!

Pls repost 🙏❤️

over the moon to share the news that I got selected as a
@hhmi.bsky.social HHMI Hanna Gray Fellow 😄 super humbled to join this wonderful community to learn and grow and do cool science!! 🔬🧪🧬 also thanks to so many of my mentors and friends who have supported me along the way 🙏 #HannaGrayFellows

An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility Retrotransposons, multi-copy sequences that propagate via copy-and-paste mechanisms involving an RNA intermediate, occupy large portions of all eukaryotic genomes. A great majority of their manifold c...

To kick start the New Year, I'm delighted to share the lab's first preprint - now online:
biorxiv.org/cgi/content/...

See below for a couple of highlights👇
Any feedback is welcome!
"TEsky"

HAPPY NEW YEAR to everyone! 🥂