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Connor Horton

@connorhorton.bsky.social
328 followers 425 following 24 posts

PhD candidate in Collins Lab at Berkeley MCB, studying mechanism and evolution of transposable elements. Formerly Fordyce Lab @ Stanford and Park Lab @ Harvard. (he/him) 🧬🏳️‍🌈

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Reposted by Connor Horton
Nick Ingolia @nickingolia.bsky.social · 29/09/2026
We are searching for a technician to work on disordered proteins and regulatory networks involved in mRNA regulation! careerspub.universityofcalifornia.edu/psc/ucb/EMPL...
careerspub.universityofcalifornia.edu
Careers
The Departments of Molecular and Cell Biology (MCB) and Integrative Biology (IB) together are among the largest academic departments at UC Berkeley. By several measures (including number of faculty and students, budget, and assigned square feet), these departments are larger than many UCB colleges and schools. The two departments represent over 186 faculty FTE (including Adjuncts, Professors of the Graduate School, active emeriti and 15 HHMI professors); 150 postdocs and other research positions; 375 graduate students; 80 department staff members; and 8 recharge centers. Financial resources include approximately $51M in annual extramural funding (which accounts for over half of the total sponsored research awards in the College of Letters & Science) and over $46M other fund sources. The department has 1,800 declared undergraduate majors (the largest majors on the Berkeley campus) and a total annual enrollment in classes of ~20,000. Department personnel are currently housed in seven buildings located in three widely separated parts of the campus.
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Reposted by Connor Horton
The Ohainle Lab @ohainlelab.bsky.social · 10/09/2026
Very excited to share the first preprint from the Ohainle Lab at UC Berkeley! www.biorxiv.org/content/10.6...
biorxiv.org
CypA is a molecular barrier to HIV emergence from Eastern chimpanzees
Of the two lineages of lentivirus that endemically infect chimpanzees, only one has served as a source of infections in hu-mans. Using HIV-CRISPR screening, we identify factors that limit the replicat...
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Connor Horton @connorhorton.bsky.social · 11/08/2026
Finally, I want to give a shout-out to Deji and Bri, the other first authors on the paper. It was such a beautiful, collaborative effort working with these two amazing scientists! Check out the paper here: www.pnas.org/doi/10.1073/... (end of thread)
pnas.org
DNA-bound avian R2 non-LTR retrotransposon protein recruits a second R2 protein for genome-protective second-strand nicking | PNAS
Animal genomes have expanded with the mobility of non-long-terminal-repeat retrotransposons. These retrotransposons initiate genome insertions usin...
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Connor Horton @connorhorton.bsky.social · 11/08/2026
We're excited about the implications of this work for understanding R2 insertion mechanism and non-LTR retrotransposons more generally! We also hope it contributes to safer, more precise engineering of gene therapy applications. A schematic of our updated model of insertion is below
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Connor Horton @connorhorton.bsky.social · 11/08/2026
These sequencing assays were performed using a new, PCR-free technique I developed called RIPPLE-seq, giving us ~100,000-fold enrichment of full-length transgene insertions and flanking target site sequence. Stay tuned for an upcoming paper describing the method in more detail 👀
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Connor Horton @connorhorton.bsky.social · 11/08/2026
As a cherry on top, we also found that our trans complementation approach (co-expressing 2nd-nick-defective R2p & DNA-binding-defective R2p) also restored more wildtype-like junctions at the rDNA target site.
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Connor Horton @connorhorton.bsky.social · 11/08/2026
Finally, we asked what are the consequences of defective 2nd strand cleavage on insertion outcomes at the sequence level. Our 2nd-nick-defective R2p variants lead to an unexpected increase in target-site duplications, requiring extensive DNA repair by the host
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Connor Horton @connorhorton.bsky.social · 11/08/2026
We next asked: could we do a "2-step" assay in cells? Could we rescue the 2nd nick-defective variants by expressing another R2p variant that can *only* nick the 2nd strand, but not nick the 1st strand or perform TPRT? Bri showed that our DNA-binding mutant (TaGuC) could rescue PRINT defects in trans
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Connor Horton @connorhorton.bsky.social · 11/08/2026
We wondered whether defects in 2nd strand nicking would have effects on transgene insertion by PRINT in cells. Equipped with these mutants, Bri showed that defects in 2nd nicking activity resulted in lower insertion efficiency, demonstrating a role for 2nd nick in retrotransposition in cells
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Connor Horton @connorhorton.bsky.social · 11/08/2026
Anthony and Deji next screened dozens of mutants biochemically and found separation-of-function variants which are wildtype-like in 1st strand nicking, but near-dead for 2nd strand nicking. In the 2-step assay, 2nd nick was detected when these variants were added 1st, not 2nd
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Connor Horton @connorhorton.bsky.social · 11/08/2026
Deji developed a 2-step cleavage assay. First, add endonuclease-dead protein to "pre-bind" target site. Next, add endonuclease-competent protein and monitor 2nd-strand nicking. Critically, our DNA-binding mutant (TaGuC) is able to nick the 2nd strand, suggesting recruitment by pre-bound EN-dead R2p
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Connor Horton @connorhorton.bsky.social · 11/08/2026
I'm excited to share our work providing the first complete mechanistic picture of how R2 proteins nick the second strand, out today in @pnas.org! ✂️🧬 This step in retrotransposition has long been mysterious, but crucial for understanding R2's. Check it out: www.pnas.org/doi/10.1073/... A thread 🧵:
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Reposted by Connor Horton
Nozhat @nozhathassan.bsky.social · 02/05/2026
After a long time finding reviewers, my paper on the evolution of R2 retrotransposons is out! This project was in collaboration with my amazing co-authors Bri and Anthony from the Collins lab. 🐢🐦‍⬛ Big thanks to my team, especially my supervisor Dave Adelson! #TEsky link.springer.com/article/10.1...
link.springer.com
Lineage-specific evolution, structural diversity, and activity of R2 retrotransposons in animals - Genome Biology
Background Retrotransposons play outsized roles in the evolution of gene regulation, genome function, and disease pathogenesis, and more recently they have sparked interest as instruments for new gene...
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Reposted by Connor Horton
Nature Biotechnology @natbiotech.nature.com · 11/03/2026
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - @savagecatsonly.bsky.social go.nature.com/4loaOGn
go.nature.com
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - Nature Biotechnology
TnpB endonucleases are engineered for improved genome editing.
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Connor Horton @connorhorton.bsky.social · 03/07/2025
Congrats Grace, Max, and team! We in the Collins lab are looking forward to diving into the paper!
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Reposted by Connor Horton
Akanksha Thawani, PhD @akankshathawani.bsky.social · 23/06/2025
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
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Reposted by Connor Horton
cryoEM papers @cryoempapers.bsky.social · 21/06/2025
Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking pubmed.ncbi.nlm.nih.gov/40540573/ #cryoEM
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Reposted by Connor Horton
Max Kozlov @maxkozlov.bsky.social · 16/06/2025
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."
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Reposted by Connor Horton
Nozhat @nozhathassan.bsky.social · 14/05/2025
A big chunk of my PhD work with the Collins lab is now on bioRxiv!
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Reposted by Connor Horton
Polly Fordyce @pollyfordyce.bsky.social · 12/05/2025
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)
berkeleystanfordnextgensymposium.com
Stanford.Berkeley.UCSF Next Generation Faculty Symposium
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Reposted by Connor Horton
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10/05/2025
Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals www.biorxiv.org/content/10.1101/202…
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Reposted by Connor Horton
UC Berkeley MCB @berkeleymcb.bsky.social · 29/04/2025
Congrats to MCB's Kathy Collins on her election to the National Academy of Sciences! 👏🎉https://www.nasonline.org/news/2025-nas-election/
Kathleen Collins elected to the National Academy of Sciences
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Reposted by Connor Horton
Ollie Rando @epididymosome.bsky.social · 28/04/2025
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
elifesciences.org
Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR
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Connor Horton @connorhorton.bsky.social · 25/04/2025
This is so cool! Congrats Emily!!
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Reposted by Connor Horton
Innovative Genomics Institute @innovativegenomics.bsky.social · 08/03/2025
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!
Jennifer Doudna speaking at Stand Up for Science in Berkeleycrowd at Stand Up for Science in Berkeleycrowd at Stand Up for Science in Berkeleycrowd at Stand Up for Science in Berkeley
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Reposted by Connor Horton
Savage Lab @savagecatsonly.bsky.social · 26/02/2025
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)
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Reposted by Connor Horton
Stanford Department of Bioengineering @bioe-stanford.bsky.social · 04/02/2025
🚀 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
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Reposted by Connor Horton
Vikram Paralkar @paralkarlab.bsky.social · 05/02/2025
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....
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Connor Horton @connorhorton.bsky.social · 28/12/2024
My favorite!!
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Reposted by Connor Horton
Polly Fordyce @pollyfordyce.bsky.social · 13/12/2024
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....
onlinelibrary.wiley.com
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...
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Reposted by Connor Horton
Greg Priest @gregpriest.bsky.social · 01/02/2024
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
science.org
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.
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Reposted by Connor Horton
Eric Topol @erictopol.bsky.social · 06/12/2023
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
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Reposted by Connor Horton
Liana Lareau @lianafaye.bsky.social · 29/11/2023
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...
biorxiv.org
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
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Reposted by Connor Horton
Di Jiang @dijiang319.bsky.social · 03/10/2023
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
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James Fraser @fraserlab.com · 04/10/2023
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!
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
biorxiv.org
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
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
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)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
Short tandem repeats (STRs) are enriched in eukaryotic regulatory elements and are known to alter gene expression. STR polymorphisms have also been associated with schizophrenia, Crohn's disease, and autism.   But the underlying mechanism has remained mysterious! (2/11)
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Connor Horton @connorhorton.bsky.social · 21/09/2023
Check out our paper and the accompanying perspective by Kuhlman published today in Science about the surprising role of short tandem repeats in regulating eukaryotic transcription! www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... A thread (1/11):
science.org
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
Transcription factors directly bind repetitive sequences that need not resemble known motifs.
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