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Savage Lab

@savagecatsonly.bsky.social
401 followers 215 following 35 posts

Compartmentalizing your metabolism, and y’know, CRISPR stuff. Account managed by grad students and postdocs 🤙 @ucberkeleyofficial.bsky.social @innovativegenomics.bsky.social @hhmi.bsky.social savagelab.org

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Reposted by Savage Lab
UC Berkeley MCB @berkeleymcb.bsky.social · 17/09/2026
Exciting research from the labs of MCB’s David Savage @savagecatsonly.bsky.social and Christina Listgarten, featuring MCB postdoc Maria Lukarska @marialukarska.bsky.social! 🧬🔬
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Reposted by Savage Lab
Zehan Zhou @zehanzhou.bsky.social · 05/08/2026
We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...
sciencedirect.com
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Reposted by Savage Lab
marialukarska.bsky.social @marialukarska.bsky.social · 30/07/2026
Our ProteinGuide paper is finally out! Thanks to all the co-authors @junhaobearxiong.bsky.social, @ishangaur.bsky.social, @hnisonoff.bsky.social, @loltrogge.bsky.social, @jlistgarten.bsky.social, @savagecatsonly.bsky.social! @innovativegenomics.bsky.social www.nature.com/articles/s41...
nature.com
Property guidance for protein sequence generative models with ProteinGuide - Nature Biotechnology
On-the-fly conditioning of pretrained protein generative models guides protein generation toward specific properties.
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Reposted by Savage Lab
Nature Biotechnology @natbiotech.nature.com · 29/07/2026
Property guidance for protein sequence generative models with ProteinGuide - @jlistgarten.bsky.social @savagecatsonly.bsky.social www.nature.com/articles/s41...
nature.com
Property guidance for protein sequence generative models with ProteinGuide - Nature Biotechnology
On-the-fly conditioning of pretrained protein generative models guides protein generation toward specific properties.
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Savage Lab @savagecatsonly.bsky.social · 25/07/2026
Check out our new preprint on base editors and the thread below!
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Reposted by Savage Lab
marialukarska.bsky.social @marialukarska.bsky.social · 24/07/2026
I’m happy to share our pre-print exploring the activity and specificity trade-offs in adenine base editors. Thanks to my amazing co-authors Luke Oltrogge, @hnisonoff.bsky.social, and all the other contributors @jlistgarten.bsky.social @savagecatsonly.bsky.social @innovativegenomics.bsky.social 🧵1/7
biorxiv.org
Activity and specificity trade-offs in adenine base editors
Adenine base editors (ABEs) are CRISPR effectors that introduce A-T to G-C transitions in the genome using a nucleotide deaminase fused to a Cas protein. ABEs have been evolved to have very high editi...
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Reposted by Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 08/04/2026
New preprint from Dave Savage (Savage Lab) and Yun S. Song: Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins. Read here: ow.ly/iJk950YCF8q #AI #AIresearch
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
Congrats to co-first authors @evangroover.bsky.social and David Ding, and our talented collaborators, and many thanks to Christine Queitsch, @rnanerd.bsky.social, and Jen Sheen for protoplast wisdom. We look forward to translating what we learned to stable plants! www.nature.com/articles/s41...
nature.com
Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - Nature Biotechnology
Variant mapping of sorghum promoters identifies CRISPR-accessible mutations that upregulate gene expression.
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
We show that genomic language models trained on plant genomes capture motif syntax and modestly predict the effects of hypomorphic mutations, but not hypermorphic ones. This suggests to us that problem-specific datasets like this will be essential to realize their promise.
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
The size and location of mutations are highly consequential, and shape both RNA and protein output. For example, a 57-bp deletion in the PsbS promoter induces more protein production than a 585-bp viral enhancer, showing precise edits can rival or exceed transgenic engineering!
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
A consistent ~500 bp core promoter near the TSS drives most effects, but genes differ in which mutation classes (substitutions, deletions, or insertions) boost expression. We tested thousands of insertions in this core region, uncovering motifs that strongly enhance expression.
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
Screening thousands of deletions per promoter, we map critical regulatory regions. Integrating thousands of single-base mutations pinpoints core motifs at base-pair resolution and reveals where and how promoters can be edited to change expression.
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
Crop improvement often relies on random changes to cis-regulatory DNA. With CRISPR we can target genes directly, but finding desirable edits is hard. We screen CRISPR-like mutations in PsbS, Raf1, and SBPase to find edits that achieve the same thing as transgenic overexpression.
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
Can CRISPR edits enable precise tuning of plant gene expression? We think: yes. In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.
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Reposted by Savage Lab
Nature Biotechnology @natbiotech.nature.com · 27/03/2026
Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - @savagecatsonly.bsky.social go.nature.com/3O7mDEN
go.nature.com
Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - Nature Biotechnology
Variant mapping of sorghum promoters identifies CRISPR-accessible mutations that upregulate gene expression.
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Reposted by Savage Lab
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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Reposted by Savage Lab
Zehan Zhou @zehanzhou.bsky.social · 15/01/2026
How do the ancestors of CRISPR-Cas unwind DNA and how can this lead to better genome editing? With our collaboration between @doudna-lab.bsky.social x @jacobsenucla.bsky.social x Zev Bryant's lab x @savagecatsonly.bsky.social we've uncovered the secrets behind TnpB's dynamics!
biorxiv.org
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
Together, these findings showcase the potential of engineered TnpB editors delivered via viral vectors for efficient, heritable genome editing in plants 🧬. (7/7)
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
They demonstrated enhanced activity of two engineered variants, eTnpBc (TnpB-KYLI) and eTnpBe (TnpB-VGIRL), across multiple plant species (N. benthamiana, rice🌾, and pepper🌶️).(read more: doi.org/10.1101/2025...) (6/7)
doi.org
Mutational scanning of TnpB reveals latent activity for genome editing
TnpB is a diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Due to their small size and putative evolutionary relationship to CRISPR-Cas12, TnpB enzymes hold signific...
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
These findings build on prior work by @brittneywthornton.bsky.social and @rfw.bsky.social, who engineered highly active TnpB variants by conducting and leveraging deep mutational scans of the TnpB ribonucleoprotein. (5/7)
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
These edits are transmitted to the germline without retaining the eTnpBc transgene – enabling a highly efficient path to heritable, transgene-free editing in plants in a single generation 🧬🌱 4/7) Read more: doi.org/10.64898/202...
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
In a new preprint, Nagalakshmi and Rodriguez demonstrate that an engineered, compact RNA-guided nuclease, eTnpBc (TnpB-KYLI), can be efficiently delivered via tobacco rattle virus (TRV) to achieve heritable editing efficiencies of up to 90% in Nicotiana benthamiana. (3/7)
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
Efficient delivery of genome editing reagents to plants remains a major challenge. Although viral vectors offer a promising solution, their limited cargo capacity has constrained their impact. (2/7)
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
New from Ugrappa Nagalakshmi and Jorge Rodriguez 🌱✂️– Gene editing in plants just got a lot easier! Using engineered TnpB, they demonstrate high-efficiency, heritable, transgene-free editing in plants. (1/7)
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Savage Lab @savagecatsonly.bsky.social · 05/08/2025
Congrats to our savage lab undergrads on their research and presentations in our inaugural undergrad research symposium 🎉🥳
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Reposted by Savage Lab
Doudna Lab @doudna-lab.bsky.social · 29/07/2025
‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.
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Savage Lab @savagecatsonly.bsky.social · 01/06/2025
We love generating data! But what should we do with it? We collaborated w/ the Listgarten lab on ProteinGuide - a new method for using experimental data to guide protein generative models. Congrats to @junhaobearxiong.bsky.social, @hnisonoff.bsky.social, @marialukarska.bsky.social, Ishan, & Luke! ⬇️
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Reposted by Savage Lab
brittneywthornton.bsky.social @brittneywthornton.bsky.social · 04/03/2025
Excited to share our new preprint on mutational scanning of the TnpB RNP! We identify several highly activating, single-position mutations in TnpB’s protein and reRNA. These datasets enabled us to engineer enhanced TnpB protein variants (>50x plant editing levels compared to WT).
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Reposted by Savage Lab
Ben Adler @benadler.bsky.social · 26/02/2025
It is finally out! Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)! Check it out @naturemicrobiol.bsky.social www.nature.com/articles/s41...
nature.com
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
Congrats to the whole team!! (Whole team not pictured)
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(9/9) In addition to laying the groundwork for engineering, the data could provide valuable insights into TnpB evolution and function in transposable elements. If you want to read more check out the pre-print here: www.biorxiv.org/content/10.1...
biorxiv.org
Latent activity in TnpB revealed by mutational scanning
TnpB is an evolutionarily diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Due to their small size and putative evolutionary relationship to Cas12s, TnpB holds signi...
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(8/9) They then chose 33 enriched muts across 19 AA positions & made & assayed a combinatorial protein library. 6 enriched variants were followed up on in HEK293T cells & N. benthamiana editing. All variants increased editing, with a max of 50-fold increase over WT in benthi!
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(7/9) Enrichment varied by domain - many muts in RuvC and WED were enriched, most ZnF muts were depleted, muts in the unstructured C-terminal tail were ~neutral. Additionally, positive AAs were enriched w/i the vicinity of nucleic acids, particularly near the heteroduplex
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(6/9) For the protein library, the authors made all single AA mutations and all stop codons. Surprisingly, ~20% of all mutations were enriched over WT!
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(5/9) The hinge forms a sharp bend in the reRNA in stem 2, which is hypothesized to act as a regulatory switch for TnpB. Multiple groups have shown that stem 2 truncations increase TnpB editing, and our data suggests that hinge mutations may activate TnpB by a similar mechanism
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(4/9) Starting with the reRNA– the library contained all single substitutions, 1-2 nt deletions, and larger secondary structure truncations. Many mutations were enriched over WT. Particularly, some (especially 1-2 nt dels) in the “hinge” region were highly enriched
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(3/9) In the native genomic context, TnpB’s RNA scaffold (reRNA) is encoded in the protein’s mRNA. To map the mutational landscapes of the RNP components separately, they assayed two DMS libraries for the protein and RNA in an in vivo selection for endonuclease activity in yeast
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
(2/9) TnpB is an RNA-guided endonuclease found in prokaryotic transposons. Given its compact size, complex scaffold RNA, and putative ancestral relationship to Cas12s, they thought the TnpB ribonucleoprotein would be an ideal model for DMS
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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 Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 07/02/2025
New research from IGI Investigator Dave Savage @savagecatsonly.bsky.social and first author Noam Prywes @prywes.bsky.social (pictured) details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱🧪🧬 Read more: ow.ly/t2JO50ULh10
Photo of Noam Prywes standing in from of bamboo plants
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
Check out the summary and "behind the paper" here doi.org/10.1038/d415...
doi.org
Mass testing of mutant enzymes involved in photosynthesis
Insights from a high-throughput screening assay of rubisco variants could be used to engineer improved versions of this key enzyme.
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
Small changes in sequence can have big consequences in function, and not only negatively! We hope that this data is useful to other enzyme engineers and that this result expands our view of what is possible with even small changes. (7/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
Several single AA mutations increased the CO2 affinity! Given sequence divergence and different oligomeric states of Form I & II, we were surprised to find single muts led to CO2 affinity outside of the range of Form II & at the edge of the distribution of plants and algae (6/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
Rubisco is, after all, an enzyme, so we wanted to biochemically characterize each mutation. By repeating the assay over CO2 titration, key biochemical parameters (e.g. Vmax, Kc) are estimated for each mutant! (5/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
This assay neatly identified known structural, functional, and evolutionary effects, confirming the robustness of the screen. For example, key residues in Loop 6 and the active site, are mutation-intolerant (4/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
To address this, @prywes.bsky.social et. al developed an assay to estimate the fitness of 99% of single mutations in a high-throughput E. coli screen. E. coli growth rate is linked to enzyme behavior! (3/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
As the entry-point for nearly all CO2 to the biosphere, rubisco is arguably one of the most important enzymes. Yet, Rubisco catalysis is slow. While there are 100s of biochemical measurements, our understanding of catalysis is limited by low-throughput in vitro assays (2/7)
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...
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Reposted by Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 22/01/2025
New research from IGI Investigator Dave Savage and first author Noam Prywes details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱 Read more: ow.ly/t2JO50ULh10
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