Chris Fell

nature.comReprogramming site-specific retrotransposon activity to new DNA sites - NatureA study of retrotransposon activity repurposes a retroelement called R2Tocc to create a programmable system called STITCHR that enables diverse genome edits including efficient, scarless large pa...

So excited to share our new paper out today in @nature.com. We repurposed R2 retrotransposons to create STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions 🧵 www.nature.com/articles/s41...

cell.comStructure and engineering of the large serine recombinase Bxb1 for gene integrationSoma et al. present cryo-EM structures of the large serine recombinase Bxb1 bound to attP and attB substrates and provide mechanistic insights into attP/attB recognition, synaptic complex formation, a...

8 June

🚨 Today we report cryo-EM structures of the Bxb1 integrase complexed with its attB/attP DNA substrates before, during and after recombination. Using these structures, we engineer Bxb1 mutants with improved recombination efficiencies and altered sequence recognition properties. Check it out! ⬇️

8 June

@cp-molcell.bsky.social

@maxewilkinson.bsky.social

8 June

This is the result of a great and ongoing collaboration with the Nishimasu lab. Thanks a bunch to all authors

Chris Fell reposted

Max Wilkinson

3 July 2025

If you like transposons... If you you love genome editing... Or if you just like random bird animations, we have the paper for you! We (@kedmonds.bsky.social et al) are happy to share our work turning a songbird retrotransposon into a genome editing tool. 🐣 (1/n)

Chris Fell reposted

Addgene

@addgene.bsky.social

10 Apr 2025

STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions. Plasmids here www.addgene.org/browse/artic...

addgene.orgAddgene: Reprogramming site-specific retrotransposon activity to new DNA sites.

Chris Fell@cfell.bsky.social

This was a really fun project which I’m excited is finally out. There were some unique challenges on the way, including learning how to Southern blot to address a reviewer’s concern. The blot got buried in the supplemental, but it took me months, so here it is in all its glory

Lastly, I’m very thankful of my excellent co-first authors Lukas Villiger, Justin Lim, Masa Hiraizumi, and mentors Omar and Jonathan. We are so grateful for our fantastic ongoing collaborations with Hiroshi Nishimasu. Thanks to all co-authors for their invaluable contributions!

STITCHR can insert whatever is between its homology arms. We can efficiently install a diverse range of edits, including substitutions, deletions and large insertions of at least 12.7kb with high fidelity

There’s much more data in the paper, so please check it out! We also showed insertion by delivering RNA templates, insertion in different cell types, in vitro characterization of STITCHR, mapping of nicking sites, PacBio sequencing of long insertions, offtarget mapping and more

We found the architecture of the RNA cargo to be critical. The 3’ UTR is dispensable in cells, however, the homology arms and a small section of the 5’ UTR are essential, including a short sequence homologous to its natural 28S insertion site.

We tested a panel of R2s for their ability to perform scarless insertion at AAVS1, identifying R2Tocc as our best orthologue due to high on-target insertion and low 28S insertion. After screening sgRNA panels and homology arms, we could insert efficiently at multiple genomic loci

To understand cargo constraints, we permuted R2Tg’s RNA template, deleting and/or re-ordering the UTR and homology arm architecture. Interestingly, deletion of the UTRs internal to the homology arms were still functional and resulted in scarless cargo insertion!

Swapping out homology arms for NOLC1 sequences led to the natural reprogramming of R2Tg, inserting a GFP at NOLC1, which was improved with nCas9-assited retargeting. We called this system Site-specific Target-primed Insertion via Targeted CRISPR Homing of Retroelements (STITCHR).

We were interested in whether R2s could be reprogrammed in cells. We searched the natural world, uncovering 8,248 orthologues and their site preferences. Excitingly, we discovered instances of R2s acquiring novel insertion sites during evolution, a natural form of reprogramming!

nature.comHarnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci - Nature BiotechnologyTransgenes are inserted into human cells by 2-RNA delivery of a retroelement protein and template.

We selected a diverse set of R2s and tested if they could insert non-natural cargoes at their natural sites in human cells. We identified an R2 from the zebra finch Taeniopygia guttata (R2Tg) with high insertion activity in cells and in vitro.

Impressive work from the Collins lab and others demonstrated the repurposing of R2s for all-RNA insertion of transgenes at human safe harbour loci, an exciting therapeutic application! www.nature.com/articles/s41...

science.orgStructure of the R2 non-LTR retrotransposon initiating target-primed reverse transcriptionA retrotransposon structure elucidates the principles of target DNA selection and self-RNA recognition.

Additionally, fascinating work from the Zhang lab reported the structure of Bombyx mori R2 and showed that in principle R2s could be reprogrammed, at least in vitro. www.science.org/doi/10.1126/...

In the AbuGoot lab, we were intrigued by the R2 retrotransposon class of mobile genetic elements. Foundational work by Thomas Eikbush and colleagues showed a Target-Primed Reverse Transcription mechanism of insertion, priming with RNA homology arms.