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When you are 6 hours ahead of your lab to submit jobs! :)

dnaPipeTE from @clementgoubert directly performing TE detection, classification, and quantification from unassembled short reads link.springer.com/protocol/10. #genomics #genome #genetics

RT @NASA_Orion
We've completed our return powered flyby burn and are heading home!

RT @JN_Wells
Excited to finally be able to share some new work on the evolution of zinc finger genes!
biorxiv.org/content/10.1101/20
Zinc finger genes are a deeply conserved family of eukaryotic transcription factors. But in animals, the copy number of these genes has exploded 💥 (1/10)

Transposable elements drive the evolution of metazoan zinc finger genes

Cys2-His2 Zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that the targeting and repression of lineage-specific transposable elements (TEs) plays a major role in the diversification of the Kruppel-associated box ZNF (KZNF) subfamily, which predominates in tetrapod genomes. At present, it is unknown whether this function and co-evolutionary relationship is unique to KZNFs, or a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver in the diversification of ZNFs in animals. Sampling from more than 4000 animal genome assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution, both within and between major taxonomic groups. Using computational predictions, we show that ZNFs preferentially bind TEs in a diverse set of representative animal species. We further investigate one of the most expansive ZNF subfamilies found in cyprinid fish, which are characterized by a conserved domain we dubbed the Fish N-terminal Zinc-finger associated (FiNZ) domain. FiNZ-ZNFs have dramatically expanded in several fish species, including the zebrafish in which we predict ~700 FiNZ-ZNF genes. Almost all are located on the long arm of chromosome 4, and recent duplicates are evolving adaptively under positive selection. Like mammalian KZNFs, the bulk of zebrafish FiNZ-ZNFs are expressed in waves at the onset of zygotic genome activation. Blocking FiNZ-ZNF translation using morpholinos during early zebrafish embryogenesis results in a global de-repression of young, transcriptionally active TEs, likely driven by the failure to establish heterochromatin over these elements. Together, these data suggest that ZNF diversification has been intimately connected to TE expansion throughout animal evolution and that families of ZNFs have been deployed independently in fish and mammals to repress TEs during early embryogenesis. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org

Big big big thanks to @guilbourque for the sustained support the last two year! Such a great group full of talents! 🎉👏✌️

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Next, the amazing @groza_cristian describe a approach to detect and genotype insertions, which is the foundation of our new tool GraffiTE! 3/4 link.springer.com/protocol/10. github.com/cgroza/GraffiTE

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With the brilliant @xunchen85, we describe the use of short-reads methods to detect insertion polymorphism against a reference genome link.springer.com/protocol/10. 2/4

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Big thanks to @BrancoLab and @deMendoza_Alex for putting this amazing resource together 🎉! And kudos to @xunchen85 and @groza_cristian for their amazing contributions... 👇 1/4
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RT @BrancoLab
Enjoyed (well... maybe not the nitty gritty editing) putting together this TE methods book with @deMendoza_Alex. If you're a aficionado or wanna-be, look out for its release in the New Year. link.springer.com/book/10.1007
twitter.com/BrancoLab/status/1

RT @joinmastodon
Mastodon has just passed over 2 million active monthly users, a new record! People are voting with their feet. The future of social media doesn't have to belong to a billionaire, it can be in the hands of its users.

#Mastodon features that #Twitter doesn’t have:

* Temporary muting (e.g. for a day)
* Self-verified URLs in the profile
* Hiding spoilers etc. via content warnings
* URLs must start with protocols (fewer false positives, e.g. in code).
* Everyone can edit posts (in v4+).
* No ads (which doesn’t come for free = donate if you can afford it)

More obscure: I like that you can search for post URLs to “transfer” them between accounts.

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