🧵 8/8 Huge shoutout to the amazing four labs of our collaboration: @doudna-lab.bsky.social @jacobsenucla.bsky.social Zev Bryant's lab and @savagecatsonly.bsky.social, my world-class co-first authors Irenka Saffarian-Deemyad @honglue.bsky.social and Trevor Weiss and our amazing co-authors!!!
🧵 7/8 From this, we think that Ymu1 TnpB genome editing occurs in a stepwise basis and can be stabilized at each distinct stage! As long as you modulate individual checkpoints, you can make a highly efficient and compact genome editor 🧪
🧵6/8 Pre-unwinding the DNA helped WT Ymu1 get over the kinetic barriers in cleavage, but didn't do much for Ymu1-WFR! Good genome editing maps onto strong unwinding abilities 🧬
🧵5/8 The ability of the mutations in Ymu1-WFR to stabilize Ymu1 unwinding is much like how negative supercoiling stabilizes the unwound states of Ymu1 as well- both protein mutations and DNA supercoiling share a similar energetic landscape ⛰️
🧵 4/8 In WT Ymu1 TnpB, the protein mostly stays at the C state, occassionally going to the I and O states. With a single mutation, the I state is stabilized and with all three mutations, I and O states are both strongly stabilized💪
🧵 3/8 The improvement in efficiency comes from Ymu1-WFR strongly stabilizing the protein's ability to bind and unwind DNA. We uncovered that Ymu1 TnpB DNA binding transitions between a closed duplex state (C), a half-unwound intermediate state (I), and a fully unwound open state (O)
🧵2/8 The reduced efficiency can be significantly improved with certain mutations (H4W, L304F, V305R) and stacking all three makes a TnpB that is a significantly better editor in plants and in vitro (Ymu1-WFR) 🌱
🧵 1/8 Ymu1 TnpB is from the same family tree as CRISPR-Cas but is significantly smaller, making it of interest in delivery. However, they are not particularly effective genome editors 😔
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!
New preprint 👉Doudna x Bryant x Jacobsen x Savage collaboration!
Work led by @zehanzhou.bsky.social, I. Saffarian-Deemyad, @honglue.bsky.social, T. Weiss
We dissect how stepwise DNA unwinding gates TnpB genome editing, revealing how unwound DNA states enhance cleavage
www.biorxiv.org/content/10.6...
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Excited to share our new preprint co-led by @jnoms.bsky.social!
Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.
1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs.
Full story here:
www.biorxiv.org/content/10.1...
Our paper is finally out in Molecular Cell! 🚀 We uncover why PAM-relaxed Cas9 variants like SpRY are inefficient — they get kinetically trapped during target engagement. Mechanistic insights like this are key to engineering smarter, faster genome editors. Huge thanks to the team! #CRISPR #editing🔬🧬
Glad to welcome Democratic Vice Chair
@tedlieu.bsky.social to CA-12 today.
We toured labs at @ucberkeleyofficial.bsky.social and discussed how the Trump administration's attacks on
NIH funding endangers decades of leading research and scientific work.
