Congratulations to Aykut Shen, one of my first PhD students, who has successfully passed his viva yesterday. Many thanks to examiners @conradn.bsky.social and @adamcribbs.bsky.social and co-supervisor/collaborator. @whaerty.bsky.social. @nrpdtp.bsky.social @biouea.bsky.social

How do RNA molecules shape genome regulation in the nervous system? (AKAY_U26CASE) | Doctoral Training Partnership This PhD project will investigate how RNA modifications influence the activity of topoisomerase I (TOP1), a crucial enzyme that regulates DNA supercoiling during replication and transcription. Using C...

New BBSRC funded PhD opportunity in my group with Inspiralis Ltd and @conradn.bsky.social. If you are interested in RNA - protein interactions and RNA modifications check the details below for how to apply. @nrpdtp.bsky.social @biouea.bsky.social @earlhaminst.bsky.social tinyurl.com/bdzvn4dr

This is a cool observation from @bartellab.bsky.social about what happens when polyA binding protein is limiting during viral infection

Decoding Spliceosome Dynamics through Computation and Experiment RNA splicing is orchestrated by a complex and exceptionally dynamic RNA–protein machine, called the spliceosome. Stepwise, large-scale structural and compositional remodeling of the spliceosome enable...

Our new review entitled 'Decoding Spliceosome Dynamics through Computation and Experiment' has been published on Chemical Reviews @pubs.acs.org Congrats to @pokorna.bsky.social, Sebastian Fica and Jana Aupic! pubs.acs.org/doi/10.1021/...

Collective challenges need collective solutions. Happy to share the insights we've gained from the way our cells handle this: www.nature.com/articles/s41... and its summary www.crick.ac.uk/news/2025-09....

Whose papers have an edge at Science? In unusual study, journal looks in the mirror Confidential data show being in the U.S., at a prestigious institution, and in a large team all may help

Whose papers have an edge at Science? In unusual study, journal looks in the mirror | Science | AAAS via @jeffreybrainard.bsky.social www.science.org/content/arti...

Please share & RSVP to join the November 25th webinar!
Hear from the 2025 Philip N. Benfey Arabidopsis Community Lifetime Achievement Awardees! bit.ly/naascawards
@plantevolution.bsky.social

Molecular basis of polyadenylated RNA fate determination in the nucleus Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs, that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, including prote...

How do cells sort which RNAs to keep or destroy? New preprint from THJ, Brenneke and Plaschka labs shows that export and decay machineries (TREX2/PAXT) both recognise UAP56-bound RNAs. Whether they’re exported or degraded depends on where in the nucleus this happens.
www.biorxiv.org/content/10.1...

Why does the m6A writer complex require so many proteins? Post-transcriptional gene regulation through m6A deposition is dysregulated in many diseases and is catalyzed by a multi-protein writer complex. This Unsolved Mystery investigates why the writer compl...

Post-transcriptional #GeneRegulation through #m6A deposition is dysregulated in many diseases. Samie Jaffrey &co investigate why the m6A writer complex requires multiple subunits and what roles its individual proteins might have in m6A regulation. 🧪
plos.io/3VjfjWI

It’s great to see this story out. Congratulations!

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...

Excited to share some new work from our group - www.biorxiv.org/content/10.1...

A great collaboration with @kurianlab.bsky.social that began with how an RBP (QKI) controls cardiomyocyte function, and led to uncovering a unique mechanism of direct interaction with U6 & the tri-snRNP at weak 5'SS

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...

Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...

Very interesting paper from @kaiserlab.bsky.social!

This is an amazing opportunity to join the plant sciences faculty in the Oxford Department of Biology!

I am so impressed with the quality and collegiality of these colleagues. I’m not on the committee, but I’m happy to answer questions as I can.

Isoform-level profiling of m6A epitranscriptomic signatures in human brain Direct RNA-seq in brain reveals RNA isoform and region-specific m6A modifications, highlighting their role in gene regulation.

Our paper using Oxford #Nanopore direct RNA sequencing to identify m6A modifications on RNA isoforms in human brain is now out in Science Advances. 🧪
www.science.org/doi/10.1126/...

My lab's very first manuscripts are out!!!!

- We identified nearly 60 conserved RNA structures in plastids #chloroplast #RNA
- We found that transcriptional response to warm temperatures in whole seedling is confounded by response at organ level #thermomorphogenesis

Link to both preprints below

🤔...

The ten dollar proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers www.biorxiv.org/cont...

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#proteomics #prot-preprint

This is definitely worth reading

🚀 Our latest AlphaFold video is out! Find out how you can discover hidden domains in your AlphaFold models using Jalview's PAE-focused cluster analysis.

▶️ Watch the full video here: www.youtube.com/watch?v=pQC8...

Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

www.nature.com/articles/s41...

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

1/

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Neutrophils are k...

Happy to share our latest preprint doing low cell number (mini-bulk) and single cell #proteomics on tumour associated neutrophils from human glioblastoma where we find multiple functional states that would be invisible to scRNAseq, some showing pro-tumoural states with potential therapeutic value

U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays - Nature Communications Massively parallel reporter assays (MPRAs) are powerful technologies for measuring the impact of non-coding sequences on gene expression. Here, the authors demonstrate that MPRA reporters often underg...

Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences.

www.nature.com/articles/s41...

[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.

@hhu.de @crg.eu @embl.org @impvienna.bsky.social

Finally out!
I’m thrilled to share our new paper (Wolin et al., Cell 2025).

This paper describes SPIDR, a high-throughput method for mapping RBP binding sites.

By combining #SPIDR with #cryoEM, we identified the exact binding site of LARP1 within the #mRNA channel of the 40S ribosomal subunit.

Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique...

New preprint! We solve a mystery you didn't know existed. Mitotic cells lack new transcription but require ongoing translation. Interphase mRNA half life is only 2-4 hrs. So how do cells arrest in mitosis for hours without depleting their transcriptomes?

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

Home

Hi #RNAsky, #ChromatinSky!
It is a pleasure to announce that the @ox.ac.uk RNA & transcription club is now on Bluesky. Follow us to stay in touch with everything RNA and transcription from gene regulation to disease. Join us here: rna.web.ox.ac.uk/home

We’re excited to share a new CRISPR-Cas12 genome editing system, highly efficient across multiple brown algae species!

Brown algae transformation has been challenging despite many thoughtful approaches over the years.

We hope this one is kelpful 🌿😅
🔗 doi.org/10.1101/2025...
#CRISPR #Algae

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field?

That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience

A 🧵 1/n

m6A in the coding sequence: linking deposition, translation, and decay N6-methyladenosine (m6A) is the most abundant internal modification in mRNA and plays a crucial role in regulating mRNA turnover. This review explores the characteristics of m6A sites in the coding se...

🚨Check out our brand new review on m6a in the CDS!🚨

m6A in the coding sequence: linking deposition, translation, and decay: Trends in Genetics www.cell.com/trends/genet...

Excited to share our latest work! We found transcription factor SPT6 and phosphorylated Pol II CTD help recruit U1 snRNP to elongating Pol II, allowing efficient co-transcriptional splicing.

Glad to be featured in the Editors’ Highlights!

www.nature.com/articles/s41...

#splicing #cryoEM