Connor Horton

Congrats Grace, Max, and team! We in the Collins lab are looking forward to diving into the paper!

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

Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking pubmed.ncbi.nlm.nih.gov/40540573/ #cryoEM

An NIH staffer reacts to today's ruling:
"I'm looking forward to the day that we are so slammed with work trying to reinstate everything that we had to terminate illegally — I'll work 24/7 to make that happen if I can."

A big chunk of my PhD work with the Collins lab is now on bioRxiv!

Stanford.Berkeley.UCSF Next Generation Faculty Symposium

Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)

Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals https://www.biorxiv.org/content/10.1101/2025.05.05.652312v1

Kathleen Collins elected to the National Academy of Sciences

Congrats to MCB's Kathy Collins on her election to the National Academy of Sciences! 👏🎉https://www.nasonline.org/news/2025-nas-election/

Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR

It is finally (FINALLY) out! We characterized Kathy Collin's super cool OTTR protocol for tRNA and tRF cloning, showing that it is comparable (mim-tRNA-seq, maybe nano-tRNA -seq and LIDAR) or superior (everything else) to the best protocols in the literature.

elifesciences.org/articles/77616

This is so cool! Congrats Emily!!

Jennifer Doudna speaking at Stand Up for Science in Berkeley

crowd at Stand Up for Science in Berkeley

crowd at Stand Up for Science in Berkeley

crowd at Stand Up for Science in Berkeley

Thanks to out @ucberkeleyofficial.bsky.social community for joining us at Stand Up For Science! @jenniferdoudna.bsky.social spoke about how NIH funding supported her PhD & NSF funding supported her development of #CRISPR genome editing. Federal funding is needed for life-saving science!

What's better than 1 deep mutational scanning (DMS) library? 2! In a new pre-print @brittneywthornton.bsky.social and @rfw.bsky.social et al. map the mutational landscape of ISDra2 TnpB protein and reRNA and leverage these datasets to engineer highly active variants (1/9)

🚀 Meet Eliel Akinbami, a Stanford BioE PhD student in @pollyfordyce.bsky.social Lab! Their research has led to HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a groundbreaking technique that condenses years of enzyme research work into just weeks. 🔬 @stanford-chemh.bsky.social #stanfordbioe

I was stunned by this work from Kathleen Collins' lab (Berkeley) when I heard her present this at a FASEB meeting!

What a crazy innovative idea: Adapting the R2 retrotransposon to efficiently insert any custom transgene directly into RIBOSOMAL DNA ARRAYS! 🤯🤯🤯

The applications are endless....

My favorite!!

FACS‐Sortable Triple Emulsion Picoreactors for Screening Reactions in Biphasic Environments Biphasic reactions can enhance reactions where the catalyst and substrate have different solvent preferences. This study optimizes triple emulsion picoreactors that encapsulate a biphasic solvent env...

Many industrially-important reactions (e.g. lipase-catalyzed biofuel production) involve substrates poorly soluble in water. How can we screen enzymes for these reactions? Samuel Thompson invented a new 'triple emulsion' platform for biphasic screening (1/n):
onlinelibrary.wiley.com/doi/full/10....

Changing fitness effects of mutations through long-term bacterial evolution Predictable and parallel changes occur in the fitness effects of mutations in Escherichia coli over 50,000 generations.

A new LTEE paper is out. They don't use the term "adjacent possible," but the idea is there.

As populations accumulated mutations, "some evolutionary paths that were inaccessible to the ancestor became accessible to the evolving populations, while others were closed off."

🦋🦫🌱🐋🧪 #philsci #evobio

A big step forward in the science of aging: organ-specific tracking via plasma proteins
www.nature.com/articles/s41...
20% of people assessed had accelerated aging in 1 organ, 1.7% multi-organ

Codon optimality modulates protein output by tuning translation initiation bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...

Short tandem repeats (STRs) are common in eukaryotic genomes. Horton et al. in Science show transcription factors (TFs) directly bind STRs by a additive model - low-affinity bindings amount to large effects suggesting STRs tune TF binding and regulate gene expression bit.ly/add1250 bit.ly/adk2055

I see this all the time - you don't need to wait for a journal to ask you to review - JUST REVIEW THE PREPRINT and post your review!

We do it all the time: fraserlab.com/reviews

The majority of the time, a journal asks us to include the review in their process AFTER we post!

And biggest thanks of all to Polly @pollyfordyce.bsky.social who saw the promise of this project from the beginning and believed in me every step of the way! I learned so much from you! (11/11)

This project would not have been possible without the awesome interdisciplinary team! Amr Alexandari, Michael Hayes, Emil Marklund, Julia Schaepe, Arjun Aditham, Peter Suzuki, Nilay Shah, Avanti Shrikumar, Ariel Afek, Raluca Gordan, Will Greenleaf, Julia Zeitlinger, and @anshulkundaje.bsky.social

STRs are a case study in the importance of sequence context and low-affinity binding! We hope our work inspires others to think beyond TF motifs! (9/11)

By analyzing published protein-binding microarray data, we predict that 90% of eukaryotic TFs bind at least one type of STR above background, suggesting that STRs (which are enriched in enhancers!) function as regulatory sequences. (8/11)

Kinetic measurements and modeling work from Emil Marklund and Julia Schaepe show that STRs primarily alter apparent association rates (k_on), perhaps affecting TF target search. (7/11)

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in v... bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Teaming up with Amr Alexandari in @anshulkundaje.bsky.social's lab, we trained neural net models on ChIP-seq data to show that the same repeats altering in vitro binding alter TF occupancy in cells.
 
Check out www.biorxiv.org/content/10.1... for more! (6/11)

What part of the TF is responsible for recognizing STRs? We made truncation mutants and single-residue substitutions of TFs and show that the DNA-binding domain directly recognizes STRs. (5/11)

Using partition function models from statistical mechanics, we show that STRs are low-affinity sites that maximize the number of binding microstates.
 
And we can apply these models to vastly improve binding predictions for any arbitrary TF and DNA sequence! (4/11)

Using high-throughput microfluidic binding assays, we showed that STRs can alter transcription factor binding affinities to a surprisingly large degree, up to 70-fold!
 
And here's the weird part: the STRs don't need to resemble high-affinity motifs to affect binding. (3/11)