Fyodor Urnov

A New, ‘Adorable’ Deep-Sea Fish Swims Into View

How incredibly gracious and sweet they named the vehicle "Doc Ricketts."
"Canary Row" is one of my favorite books of all time and this story warmed my heart.
Plus the fish is totes adorbs.
www.nytimes.com/2025/09/08/s...

David Baltimore, Nobel-Winning Molecular Biologist, Dies at 87

Of David's countless accomplishments is the important work that Matt Porteus did in his lab on early-stage genome editing with engineered nucleases (pubmed 12730593).
He and Matt both speak about this in the documentary "Human Nature."
A true titan.
www.nytimes.com/2025/09/07/s...

Potent and uniform fetal hemoglobin induction via base editing - Nature Genetics A comparison of fetal hemoglobin gene editing strategies using human sickle cell disease donor cells and in vivo transplantation finds that adenine base editing of the –175A>G site in the γ-globin ...

I will switch out of "dripping with scathing sarcasm" mode and cite a lovely paper by David, Shengdar, Mitch, et al - one of many such papers - where this technically trivial experiment is done.
www.nature.com/articles/s41...

Multiple overlapping binding sites determine transcription factor occupancy - Nature A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

If only, if ONLY there was some method to change these newly discovered TF binding "motifs" at endogenous gene regulatory regions to see if ANY of this new phenomenology has ANYTHING to do with actual gene regulation...
1. PHE PHE SER.
2. SER MET HIS.
www.nature.com/articles/s41...

"Epigenetics: the way genes learn from experience" (Mikula BC, Genetics 140-379; 1985).
Here it is, folks - an atlas of human genes learning from experience.
Holy Waddington.
www.researchsquare.com/article/rs-7...

In Brief: A new center in San Francisco will offer tailor-made CRISPR therapies to cure children with rare diseases www.nature.com/articles/s41...

Fellow editors - nota bene 10x!

PSA:
if you're not a mouse person you may enjoy knowing that mouse Sca1 (the hematopoiesis marker) is not encoded by Sca1 (spinocerebellar ataxia 1) but rather Ly6a.
I mean, OF COURSE it is. What else could it be?
I'm an hg38 person and below is a self-portrait while I was figuring this out.

A dogged reporter takes on a mysterious cabal in 'The Diary of Lies' Philip Miller's sinister thriller is set in a Great Britain that's lost its bearings. But even when she's terrified, fictional journalist Shona Sandison will always risk everything to get the story.

F1.1 (Taz Urnov) acquired and edited this gem for Soho Press.
www.npr.org/2025/08/13/n...

Around back then I became an ace at dispensing with it 500 ul PB into 20 qiagen columns without splashing chaotrope all over the bench.

+1
My students have a digital one and my reaction is - why?

'CRISPR Cures' center launches with $20M to make customized gene editing therapies Scientists seeking to make personalized gene editing therapies a reality for more people have launched a new initiative to develop cures for the rarest of diseases left behind by drug companies.

A new CRISPR Cures center, fuded by $20M from @chanzuckerberg.bsky.social and led by @urnov.bsky.social, will create 8 custom therapies for patients in the next 3 years.
“Our goal is to aggressively walk the walk of CRISPR platformization,” Urnov told me. @endpts.com endpoints.news/crispr-cures...

"Quaternary kissing loops"👌

Baby KJ looking alert and healthy

Thanks to the BBC's The Inquiry program for great conversations with IGI's @jenniferdoudna.bsky.social @doudna-lab.bsky.social and @urnov.bsky.social about Baby KJ, #CRISPR on-demand, and the future of personalized medicine!

Listen here: www.bbc.com/audio/play/w...

Photo credit: TODAY

Paul Wade was my patient and gracious mentor in Alan Wolffe’s lab (‘97-99). He did gorgeous work back then and continues to do so.

This is v helpful.
I'd love to know how many genes are like Car2.
Five percent? Ten percent?
Because looping is everywhere, and so-called TADs as well, but if 5% of the genes actually depend on looping for their control - well, this means the vast majority of looping is gene-control irrelevant.

I missed this paper - this is an important finding - will read. Thank you!

At Vijay's suggestion I looked at your paper (Hansen et al).
So would you say Cas2 is the poster child for cohesin-mediated loop essentiality in gene control? B/c clearly for Sox2 it's not true. What other genes like Car2 are this well-characterized wrt this dependency?

Stefan, I agree with you completely.
Is there evidence that eliminating cohesin-mediated looping affects HBA expression in adult human erythropoiesis?
(apologies if I missed it)
I am fine with local looping that's cohesin-independent as instructive to transcription.

Precisely.

I mean, you kill looping and transcription goes - whatevs.
This is a major epistemological challenge.

You realize this is a Sangamo paper by my colleagues when I was there? 🤓
What can be showed to happen does not mean happens naturally. 🤓

Anton, my first grad school rotation in 1990 was on the serum albumin enhancer. 🤓

Um.
You kill looping and transcription mostly ignores that.
This has been shown over and over again.
Other than that my initial statement is mostly wrong.

Could you kindly share the definitive references? 🙏

Thank you.
Until those data exist my original posting stands, imho.

I hear you.
You’re making a classic post hoc ergo propter hoc argument, right?

YouTube video by U.S. Food and Drug Administration FDA Roundtable on Cell and Gene Therapy

IGI's @urnov.bsky.social today at the #FDA Roundtable on Cell & Gene Therapy. Grateful for an opportunity to share more about using #CRISPR on demand to treat rare diseases!

Watch here: www.youtube.com/watch?v=0qDh...

🧬

Alan Wolffe taught me to think of chromatin-based processes as either instructive or permissive.
Looping is which of these?

Physicists create 'the world's smallest violin' using nanotechnology Physicists at Loughborough University have used cutting-edge nanotechnology to create what they believe may be "the world's smallest violin," which is small enough to fit within the width of a human h...

I have written a concerto for it.
phys.org/news/2025-06...