Greg Findlay

Do reach out if interested in establishing PETRA in your system. Thanks for reading, and thanks to our generous funders for all their support. 🙏 @crick.ac.uk @erc.europa.eu

END/9

We hope PETRA’s scalability and flexibility make the method attractive to many labs studying a wide range of genes and cell types, with applications to dissecting the logic of gene regulation, discovering beneficial edits for therapies, and generating data to benchmark and refine AI models.

8/9

Correlations between PETRA expression scores and outputs of sequence-to-expression models.

Lastly, PETRA can be used to assess the performance of state-of-the-art AI models, such as Borzoi and AlphaGenome. Correlations between PETRA scores and model outputs vary highly across the four genes studied, emphasising the need to generate more data in diverse genomic contexts. 7/9

Correlation of expression scores between Jurkats and primary T cells.

Comparing variant sets between primary T cells and Jurkats reveals highly correlated effects for VAV1, but much less so for IL2RA. 6/9

Map of combinatorial MYBL2 and EGR1 motif insertions to IL2RA with expression scores for all possible combinations.

We define TF motifs that modulate expression and engineer alleles with 2+ motifs via combinatorial PE. Expression effects are largely additive. For example, some alleles with multiple MYBL2 motifs express >10-fold more IL2RA RNA. Conversely, CTCF motifs can effectively silence target genes. 5/9

Variants from the initial screen were re-tested in a smaller library for validation, confirming strong effects.

Scoring of random 6-mer insertions in large libraries is highly reproducible, with dozens of variants having relatively large effects (over 2-fold). Effects of insertions across different genes are largely context dependent, reflecting e.g. transcription factor (TF) binding site creation. 4/9

PETRA enables expression effects to be read out via amplicon sequencing of edited loci.

PETRA affords high scalability and flexibility, as no pre-engineering or elaborate assay optimisation is required. We demonstrate PETRA across four loci in Jurkat cells and two loci in primary T cells, scoring over 14,000 engineered sequences in total.

Highlights of our Results are as follows: 3/9

PETRA workflow

PETRA leverages prime editing to test variants installed downstream of target genes' transcription start sites. This allows RNA-level effects to be quantified in multiplex via amplicon sequencing of DNA and RNA, akin to the strategy of STARR-seq but with the big advantage of endogenous editing. 2/9

Our latest story is now on bioRxiv. We present PETRA, a new method for deciphering how sequence variants impact gene regulation at scale.

www.biorxiv.org/content/10.1...

This work was led by Magdalena Armas Reyes, a @crick.ac.uk PhD student until very recently. Congrats, Dr. Armas!

🧵 1/9

Variants: the typos turning loss into hope Across the 3 billion ‘letters’ of our DNA, we each carry around 6 million variations. Researchers are unravelling their effects on our lives.

We each carry around six million variations in our DNA.

Henry Scowcroft explores how scientists like @gregfindlay.bsky.social and @carovinuesa.bsky.social are helping unravel the effects of these variants, where even a small change can have a big impact on our lives.
www.crick.ac.uk/news/2025-10...

Doctoral clinical fellows The Crick's clinical PhD programme.

Just a few weeks left to apply for our clinical PhD programme.

We're looking for clinicians who are passionate about research to join the 3-year fully funded programme.

Learn more and see what positions are available ⬇️

www.crick.ac.uk/careers-and-...

Planning your afternoon poster session at #ashg25? Come say hello!

This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬

And lastly, come chat with me about Phoebe Dace's latest work on performing saturation genome editing of BRCA1 across cell types at poster 9004T, Thursday 2:30-4:30pm. Or come by just to say hi!

On Friday, @chloeterwagne.bsky.social will present:

“A scalable framework to link rare human variants to disease phenotypes using pooled prime editing”

Friday Oct 17th at 1:40pm, Rm205ABC

You can also catch up with Chloé at her poster, 5002T, Thursday 2:30-4:30

Excited to be presenting our work on "Saturation mutagenesis of 37 human splicing factor genes using pooled prime editing" later today at #ASHG2025 during the Platform Session "RNA Functions Beyond Coding Sequences" (1:30-2:30PM, Room 205ABC).

Tomorrow, October 16 at 2:00 pm,
@magdaarmas.bsky.social presents a new method:

"Modulating gene expression in human cells via high-throughput prime editing of regulatory elements"
[Rm210AB]

Hello Boston! The lab is delighted to be at #ASHG25🧬
Check out our talks over the next few days - all unpublished stories.

Kicking things off is @michaelherger.bsky.social presenting "Saturation mutagenesis of 37 human splicing factor genes with pooled prime editing". Today @2pm, Rm205abc

Also 👇

We're recruiting early career Group Leaders this autumn! I cannot think of a better place to build a lab. Come join us! 👇

Future Leaders in Biomedical Sciences: How to Apply How to apply for a Future Leaders in Biomedical Sciences Scholarship. Open to candidates of Black or mixed Black heritage only.

This year the lab is also participating in the Crick's Future Leaders in Biomedical Sciences scholarship programme, which has opened for candidates of Black or mixed Black heritage.

www.crick.ac.uk/careers-and-...

🚨 Applications to the Crick PhD programme are now open!

We are pleased to be recruiting this year. 👇

www.crick.ac.uk/careers-stud...

Doctoral clinical fellows The Crick's clinical PhD programme.

We're looking for clinicians who are passionate about research to join our 3-year fully funded clinical PhD programme. 🔬🩺

Apply by 14 November 2025. 👇

www.crick.ac.uk/careers-stud...

We now have an open post-doc position in the lab:

crick.wd3.myworkdayjobs.com/External/job...

Please apply if you have a background in functional genomics or a related field and are eager to develop methods to map variant effects at scale.

Congrats, Mike!

Many thanks!

Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!

We recently performed SGE of RNU4-2 and identified functionally impactful variants underlying a new recessive disease. Today, the team led by @rociorius.bsky.social @alexblakes.bsky.social @cassimons.bsky.social & @nickywhiffin.bsky.social provide in-depth analysis of its clinical presentation. 🧵⬇️

Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...

I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2!

tinyurl.com/3j9r56s8
@rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social

This story is the PhD work of Phoebe Dace, who has done remarkably well to bring this all together. Congrats, Phoebe! 👏
Thanks to the lab, Nicole, @lcubes.bsky.social @chloeterwagne.bsky.social and Megan), our great collaborators, and @crick.ac.uk & @cancerresearchuk.org for vital funding. 🙏 END/16

A Sankey plot of functional evidence derived for BRCA1 variants using SGE across cell lines

Rather than confounding clinical interpretation, having data from multiple models is clearly preferable. A path forward to more precisely calibrating the risk caused by individual variants is to integrate functional evidence from multiple experimental data sets generated at scale. 15/n