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Reposted by Gordon Simpson

Alper Akay @alperakay.bsky.social · 1d

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

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Reposted by Gordon Simpson

Alper Akay @alperakay.bsky.social · 3d

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

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...

biodtp.norwichresearchpark.ac.uk

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Reposted by Gordon Simpson

Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 1d

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

David Bartel's Lab @bartellab.bsky.social · 2d

Check out the latest work from our lab, led by Arash Latifkar @ara-latifkar.bsky.social , www.biorxiv.org/content/10.1...

mRNA poly(A)-tail length is a battleground for coronavirus–host competition

Most eukaryotic mRNAs contain a poly(A) tail, which in post-embryonic cells enhances their stability. Many cytoplasmic RNA viruses also harbor poly(A) tails on their genomic RNA and mRNAs. Here, we re...

www.biorxiv.org

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Reposted by Gordon Simpson

Alessandra Magistrato @magistratolab.bsky.social · 2d

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/...

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...

pubs.acs.org

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Reposted by Gordon Simpson

Ule Lab @ulelab.bsky.social · 22d

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....

This link will take you to a page that’s not on LinkedIn

lnkd.in

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Reposted by Gordon Simpson

Charles Piller @charlespiller.bsky.social · 22d

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...

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

www.science.org

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Reposted by Gordon Simpson

North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · 23d

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

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Reposted by Gordon Simpson

William Garland @willgarland.bsky.social · 29d

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...

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...

www.biorxiv.org

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Reposted by Gordon Simpson

PLOS Biology @plosbiology.org · Sep 16

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

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...

plos.io

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Reposted by Gordon Simpson

Alper Akay @alperakay.bsky.social · Sep 10

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

Guifeng Wei @guifengwei.bsky.social · Sep 9

Thrilled to share our new Brockdorff lab paper at NSMB: we show that the primary role of m6A RNA modification on Xist is to promote RNA degradation. Xist turnover is mediated by the NEXT complex, not PAXT, and is independent of the m6A reader YTHDC1. www.nature.com/articles/s41...

m6A and the NEXT complex direct Xist RNA turnover and X-inactivation dynamics - Nature Structural & Molecular Biology

Wei et al. show that the primary function of m6A on the nuclear long noncoding RNA Xist, a master regulator of X inactivation, is to promote RNA degradation. Xist turnover is mediated by the nuclear e...

www.nature.com

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Reposted by Gordon Simpson

Eric Van Nostrand Lab @ BCM @evannostrandlab.bsky.social · Sep 8

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, ...

www.biorxiv.org

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Reposted by Gordon Simpson

Kurianlab @kurianlab.bsky.social · Sep 8

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...

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, ...

www.biorxiv.org

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Reposted by Gordon Simpson

Alper Akay @alperakay.bsky.social · Aug 27

Very interesting paper from @kaiserlab.bsky.social!

RNA Society Journal @rnajournal.bsky.social · Aug 27

Spatiotemporal NAIL-MS analysis shows that ALKBH5 does not affect global m6A turnover in human mRNA across subcellular compartments under standard growth conditions bit.ly/4lvVtC6

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Reposted by Gordon Simpson

Rebecca Mosher @rm0sher.bsky.social · Aug 25

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.

Lars Østergaard @larsostergaard.bsky.social · Aug 25

👉 my.corehr.com/pls/uoxrecru...
Join us and be part of shaping the future of #plantscience at Oxford as we move to the new Life and Mind Building lifeandmind.web.ox.ac.uk/home (recognised for its potential to change the World edition.cnn.com/2025/01/01/s...) @biology.ox.ac.uk www.biology.ox.ac.uk

'

my.corehr.com

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Reposted by Gordon Simpson

Mike Clark @michaelbclark.bsky.social · Aug 12

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/...

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.

www.science.org

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Reposted by Gordon Simpson

Rodrigo Reis @rodrigoreislab.com · Aug 25

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

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Reposted by Gordon Simpson

PastelBio @pastelbio.bsky.social · Aug 1

🤔...

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

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Reposted by Gordon Simpson

Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · Aug 1

This is definitely worth reading

Katrina Miller @katrinamillerphd.bsky.social · Jul 31

Mary K Gaillard, a theorist who had a knack for telling experimental physicists where to look, died in her home on May 23 at 86.

Dr. Gaillard was an unpaid scientist at CERN for more than a decade, & the first woman physicist hired & tenured at Berkeley:

www.nytimes.com/2025/07/31/s...

Mary K. Gaillard, 86, Physicist Who Probed the Subatomic Universe, Dies

www.nytimes.com

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Reposted by Gordon Simpson

Jalview @jalview.bsky.social · Aug 1

🚀 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...

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Reposted by Gordon Simpson

Sorek Lab @soreklab.bsky.social · Jul 30

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

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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...

www.nature.com

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Reposted by Gordon Simpson

Alejandro Brenes @ajbrenes.com · Jul 27

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

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...

www.biorxiv.org

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Reposted by Gordon Simpson

DjuranovicLab at Brown University RNA Center @djuranoviclab.bsky.social · Jul 25

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...

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...

www.nature.com

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Reposted by Gordon Simpson

Samarendra Pani @samarendra-pani.bsky.social · Jul 24

[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

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Reposted by Gordon Simpson

Jay Brito Querido @jbquerido.bsky.social · Jul 22

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.

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Reposted by Gordon Simpson

Iain Cheeseman @iaincheeseman.bsky.social · Jul 23

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...

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...

www.biorxiv.org

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