What if we could inducibly create thousands of structural variants and ecDNAs in human cells and see which ones survive?



I’m excited to share our story on scrambling the human genome by combining prime editing, repetitive elements, and recombinases. A🧵 biorxiv.org/content/10.110…
The idea: Target prime editors by @davidrliu to high-copy number sequences to insert thousands of loxPsym sites. Once the genome is sprinkled with loxPsym sites, we can shuffle it at will with Cre recombinase. Taking inspiration from the Synthetic Yeast 2.0 design @SynGenome

Our story on inserting short sequences with prime editing is now online @NatureBiotech.

nature.com/articles/s4158…

So much has changed from the preprint including the discovery that 3'-flap nucleases can inhibit the insertion of long inserts. Lots to unpack 🧵 A quick recap: We wanted to understand what factors influence how well a given sequence can be inserted with prime editing. To experimentally test this, we integrated 3,604 pegRNAs into 4 target sites in three cell lines and measured their insertion rates

https://twitter.com/JonasKoeppel/status/1458765283330596870?s=20