henriqueswill.bsky.social

Type I CRISPR-Cas immunity primes type III spacer acquisition CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often c…

Ever wondered why some bacteria have multiple CRISPR-Cas systems? Our new study led by Leah Smith shows how type I CRISPR systems can promote the acquisition and retention of new spacers into a co-occuring type III system. www.sciencedirect.com/science/arti...

a cartoon drawing of a cat flying through space ALT: a cartoon drawing of a cat flying through space

We finish this manuscript with more questions than we started with... a good sign! 🤓

What are these capsids transporting? Which cells release them?? Where do they go???👾🧑‍🚀

So, stay tuned: even in the tiny fly brain, these mechanisms might reveal how similar processes operate in our own. 🧠✨

📢 Fresh off the press! Our article on Arc is out in @currentbiology.bsky.social:
www.cell.com/current-biol...

🧶 Full thread on our discoveries here: bsky.app/profile/thec...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

piRNAs are essential for transposon silencing in the animal germline.
But how do hosts trap transposon sequences in genomic loci that help establish a piRNA response?

Looking at a natural transposon invasion, Baptiste Rafanel and Kirsten Senti made some remarkable observations.

The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals - PubMed Selfish genetic elements comprise significant fractions of mammalian genomes. In rare instances, host genomes domesticate segments of these elements for function. Using a complete human genome assembl...

Definitely interested! I study the evolutionary outcomes of genetic conflicts by examining how viral-like genes have been domesticated for host functions. Would be thrilled to talk about this work: pubmed.ncbi.nlm.nih.gov/38507667/

Possible Horizontal Transfer of Drosophila Genes by the Mite Proctolaelaps regalis There is strong inferential evidence for recent horizontal gene transfer of the P (mobile) element to Drosophila melanogaster from a species of the Drosophila willistoni group. One potential vector of...

I need you, and I can't stress this enough, to read this paper by Margaret Kidwell et al. on horizontal transfer of P elements from mites to flies and back...from *1991*: www.science.org/doi/10.1126/...

Bacterial Schlafens mediate anti-phage defense Human Schlafen proteins restrict viral replication by cleaving tRNA, thereby suppressing protein synthesis. Although the ribonuclease domain of Schlafen proteins is conserved across all domains of lif...

First preprint from the Nemudryi Lab! 🍾

In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages.

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

Temperate phages enhance host fitness via RNA-guided flagellar remodeling Bacterial flagella drive motility and chemotaxis while also playing critical roles in host-pathogen interactions, as their oligomeric subunit, flagellin, is specifically recognized by the mammalian im...

#phagesky

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

Gene regulatory networks and essential transcription factors for de novo-originated genes Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Pls. share widely

Calling all transposon fans & lovers of genetic innovation

MOBILE GENOME welcomes you in Heidelberg, Nov. 4–7 2025

→ Vibrant & friendly community
→ Cutting-edge talks from mechanisms to physiology
→ Plenty of surprises (TEs never stop innovating)

submit abstract by July 29

YouTube video by Université Côte d'Azur White Board #1 : L'histoire des gènes sauteurs

Connaissez-vous l'histoire des gènes sauteurs ?🧬
Dans cette vidéo, Gaël Cristofari, chercheur ( #UniCA, @cnrs.fr, @inserm.fr) explique de manière claire et illustrée comment ces gènes se déplacent et quel rôle essentiel ils jouent dans notre génétique.
➡️https://youtu.be/twtOhB-TPJk?feature=shared

📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!

We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.

Found 3 new families targeting immune signaling!

Vertebrate retrotransposons are the future of gene therapy. But how do they insert their genes? 🔥🔥

Thrilled to share our new work now published with Kathy Collins, @nogaleslab.bsky.social @berkeleymcb.bsky.social where we investigate this with #cryoEM & biochemistry in 🧪 and cells! #RNAsky #TEsky

An E. coli cell being lysed by bacteriophages

🚨New paper!

A prophage-encoded sRNA limits lytic phage infection in adherent-invasive E. coli.

Huge thanks to members of the Round Lab, @duerkoplab.bsky.social, Wiedenheft Lab, and phage legend Sherwood Casjens.

#microsky 🦠🧫🧪🧬

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

In @elife.bsky.social: Effective population size does not explain long-term variation in genome size and transposable element content in animals doi.org/10.7554/eLif...

This is the revised version of our manuscript, which will become the final published version !

Thanks to all the co-authors for their work and input on the manuscript. @asantiagofrangos.bsky.social @lainahall.bsky.social

It's an exciting time to be studying CRISPR adaptation - check out related work in the type II-A system by @giedriussasnauskas.bsky.social:
www.biorxiv.org/content/10.1...

and also:
www.biorxiv.org/content/10.1...

Full integration requires two sequential transesterification reactions. Focusing on the CRISPR repeat, we learned that the CRISPR repeat is distorted at key conserved purine-pyrimidine steps as it passes from the first transesterification site to the second.

We next added short fragments of foreign DNA with and without a protospacer adjacent motif (PAM), to understand why the PAM blocks integration into the CRISPR array.

We learned that foreign DNA length alters the complex stability, and that adding 2 bp makes all the difference.

Cas1-2/3 integrase bound to foreign DNA. The foreign DNA fragment binds to the positively charged channel. The propeller arms formed by the Cas3 lobes rotate out, creating a dogbone shape that exposes three additional DNA-binding channels.

We next determined the structure of the complex formed by adding a short foreign DNA fragment to Cas1-2/3. Foreign DNA binding triggers dramatic conformational changes that expose new DNA binding surfaces necessary for homing the integrase to the CRISPR locus.

Intriguingly, we saw that in this DNA-unbound conformation, a short loop in the Cas3 RecA1 domain covers the nuclease active site, much like a latched gate.

Comparing Cas3 in this OFF state to a previously nuclease ON state reveals the gate swings open when the nuclease is active.

cryoEM structures of the Cas1-2/3 integrase. The heterohexamer assembles into a four-bladed propeller, with one face lined with positively charged residues.

We wanted to understand how this fantastic genomic knot assembles, so we set out to determine multiple structures of the Cas1-2/3 complex at distinct stages of CRISPR adaptation.

In the absence of DNA, Cas1-2/3 forms a prominent, positively charged channel on one face of the complex.

Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays - Nature Structural & Molecular Biology Here, using cryo-EM, the authors show how Cas1–Cas2/3 and integration host factor, by means of a U-shaped bend that traps the invading DNA and a loop that positions it for the integrase, regulate inte...

Cas1 and Cas2 are the hallmark proteins of CRISPR immunity. However, in the type I-F CRISPR system, Cas2 is fused to Cas3, a helicase/nuclease.

Previously, @asantiagofrangos.bsky.social showed Cas1-2/3 bends the CRISPR leader for site-specific integration: doi.org/10.1038/s415...

A schematic of a bacterial cell being infected by a phage, with the Cas operon and CRISPR locus detailed. The Cas1-2/3 integrase adopts distinct conformations during the capture, delivery, and integration of a short fragment of the phage DNA.

New preprint from the Wiedenheft lab!

We used #cryoEM to show how a type I-F #CRISPR integrase captures, delivers, and integrates foreign DNA.
www.biorxiv.org/content/10.1...

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs.
Full story here:
www.biorxiv.org/content/10.1...

HMMER is the bedrock of genomic annotation globally, and now its funding is terminated for no reason.

@cryptogenomicon.bsky.social is now on bsky:

1/10 Today in @science.org in collaboration with
the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

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

Barbara McClintock proposed – over 40 years ago – that transposable element activity could be a response to stress, and I think that we are still only beginning to understand how right she was.