Volker Boehm

Happy to see this work published! Thanks to everyone who contributed 🙏

Dusa’s study is on the cover of this month’s #CellGenomics! Check it out if you haven’t had the chance yet!

www.cell.com/issue/S2666-...

🛑Guille's @guillepalou.bsky.social no-nonsense 😉 paper is out in @springernature.com Genome Biology!

We report variable activity of the NMD pathway (mRNA QC) across tissues & individuals:

🧠less active in the nervous system & in reproductive tissues
🩸more active in digestive tract, muscle, blood

🚀 Our new paper is out @natmethods.nature.com!

Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.

🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/

wrong bioRxiv link here, sorry.

the correct link to the collaboration with Torben and Clemens is:
www.biorxiv.org/content/10.1...

The team of Prof. Dr Niels Gehring @volkerboehm.bsky.social records a comprehensive database that records systematically which genes and gene variants are directly affected by "Nonsense-mediated mRNA Decay" which opens up new avenues for RNA and genome research.
The database ➡️ nmdrht.uni-koeln.de

🥳 Congratulations from #CRC1678 to @volkerboehm.bsky.social and the Gehring lab for their publication in @cp-molcell.bsky.social on how “Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome” 🧬🧫

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome UPF1 depletion inhibits nonsense-mediated mRNA decay (NMD) and stabilizes direct target transcripts within hours. Boehm et al. use conditional protein degradation and advanced transcriptomics to map t...

Very harmonious and inspiring collaboration with Niels Gehring, @volkerboehm.bsky.social and team at Uni Köln, and colleagues at @mdc-berlin.bsky.social . Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome: Molecular Cell www.cell.com/molecular-ce...

Carien Niessen elected new Vice-Rector for Research at the University of Cologne The University Election Assembly elected Professor Dr Carien Niessen for the office of Vice-Rector for Research. The cell biologist is particularly committed to promoting excellent research at the uni...

🎉 Congratulations to our new Vice-Rector for Research, Professor Dr. Carien Niessen! 🙌

The University Council has elected Professor Niessen as Vice-Rector for Research to support the advancement of excellent research at the #UniCologne. 🎓

Read more 👇
uni.koeln/9FCEC
@cecad.bsky.social

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome UPF1 depletion inhibits nonsense-mediated mRNA decay (NMD) and stabilizes direct target transcripts within hours. Boehm et al. use conditional protein degradation and advanced transcriptomics to map the NMD-regulated human transcriptome, highlighting alternative splicing as a major NMD-activating mechanism.

Online Now: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome Online now:

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...

Figure 2. Overview of N6-methyladenosine (m6A) decay pathways. m6A acts as a destabilizing mark on mRNA.

"m6A in the coding sequence: linking deposition, translation and decay"
by Kathi Zarnack (@zarnack-group.bsky.social) & colleagues

"This review explores [m6A in] mRNA decay, with a focus on the newly discovered CDS–m6A decay (CMD) pathway..."

Read it here:
authors.elsevier.com/sd/article/S...

The latest human GENCODE releases for Human (49) and Mouse (M38), have just been released. They're available via gencodegenes.org and visible in @ensembl genome browser as part of Ensembl 115 ensembl.org

A conserved viral RNA fold enables nuclease resistance across kingdoms of life Abstract. Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence

Our study from the Steckelberg lab is out now in @narjournal.bsky.social !! We dove into a new nuclease-blocking viral #RNA structure important for viral infection, which provided evidence of similar structure-based strategies across diverse viral families. academic.oup.com/nar/article/...

Multivalent interactions with CCR4–NOT and PABPC1 determine mRNA repression efficiency by tristetraprolin - Nature Communications Deadenylation leads to mRNA decay, with PABPC1 protecting the poly(A) tail, while tristetraprolin and CCR4–NOT promote deadenylation. Here, the authors describe how these three proteins interact to re...

Delighted to present our second paper of the year. This one explores the molecular mechanism of TTP, a key post-transcriptional regulator of AU-rich mRNAs. Work led and coordinated by @filippekovic.bsky.social, in collaboration with Perry Blackshear.

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

GitHub - sbresnahan/Overdispersion-Correction-for-Alevin: Processing Salmon Alevin bootstrap replicates to account for technical uncertainty before integrating single-cell RNA-seq datasets in Seurat Processing Salmon Alevin bootstrap replicates to account for technical uncertainty before integrating single-cell RNA-seq datasets in Seurat - sbresnahan/Overdispersion-Correction-for-Alevin

In bulk RNA-seq, @plbaldoni.bsky.social et al showed that correcting overdispersion (OD) from read-to-transcript mapping ambiguity improves downstream analyses. Here I extend this to scRNA-seq using @mikelove.bsky.social et al Alevin’s bootstraps to correct per-cell OD github.com/sbresnahan/O...

A postdoc position in the Torben Heick Jensen lab, Aarhus University, Denmark: Mammalian Nuclear RNA Production and Turnover Systems - Vacancy at Aarhus University Vacancy at Department of Molecular Biology and Genetics - RNA Biology and Innovation, Aarhus University

Final call for postdoc positions in Aarhus, Denmark. Sorting of gene expression and beyond. Please get in touch for further information or apply using this link:
mbg.au.dk/en/news-and-...

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox - Nature Communications The majority of human genes can produce multiple isoforms, but studying their functional relevance requires tools to target specific isoforms. Here, the authors develop a CRISPR-based exon-exon juncti...

Excited for this to be out officially! It was a great team effort and has a lot of useful tidbits for studying isoform function. www.nature.com/articles/s41...

🚨🚨🚨

Please RT!

We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.

Deadline: 30/09/25👇

Developing serum proteomics based prediction models of disease progression in ADPKD Nature Communications - Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive cyst formation and loss of kidney function, yet prognostic biomarkers remain limited....

1/ 🧬 Exciting news! Our group just published a paper in Nature Communications on using serum proteomics to predict disease progression in #ADPKD (Autosomal Dominant Polycystic Kidney Disease) 🔬 — enhancing risk stratification beyond currently available models 🎯 rdcu.be/exbNq

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

Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay - Nature Communications Intracellular pathogens hijack host gene expression to subvert cellular processes. Here, the authors show that Legionella pneumophila’s PieF effector inhibits the human CCR4-NOT deadenylation machiner...

Happy to share the latest work on a bacterial protein that inhibits human mRNA decay machinery, in collaboration with @smlea.bsky.social #RNAsky

www.nature.com/articles/s41... Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay | Nature Communications

Freshly launched! 🚀 Check out the new CRC 1678 website 🌐
👉 crc1678.uni-koeln.de

Congratulations to our biochemistry professor Utz Fischer: he has been elected to @embo.org ! His research focuses on the macromolecular machines of the cell. 📷 Christoph Weiss www.uni-wuerzburg.de/en/news-and-...

Our latest study is now out in @narjournal.bsky.social‬: we identify a post-transcriptional bottleneck in interferon gamma signaling that hinges on proper maturation of JAK2 mRNA.
Paper: academic.oup.com/nar/article/...

🆕 publication! Cells don’t just fight infection - they fine-tune their immune response. A new study from the Versteeg lab in @narjournal.bsky.social led by Adrian Söderholm uncovers how RNA processing of JAK2 helps regulate immune signals ➡️ tinyurl.com/2py27c8u
@univie.ac.at
@meduniwien.ac.at

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

tinyurl.com/ydn6e3ac

A direct interaction between the RNA-binding proteins Staufen and Tm1-I/C in the oskar mRNA transport complex Gaber et al. identify a direct protein-protein interaction between the oskar mRNA transport particle components Staufen and Tropomyosin1-I/C. They map the interaction surface at amino acid resolution ...

If you are interested in cellular RNA transport, check out Simone Heber's first corresponding author paper: www.cell.com/cell-reports...
Very cool stuff about motor switching to get the transport direction right. Collaboration between the Ephrussi, Niessing. Hennig, Chao and Heber groups.

Lexogen Goodie Bag

Feeling grateful to have received a fun goodie bag from #Lexogen for participating in their #RNA salon survey - special shoutout for the super cool sport shirt! 🎁🧬 Big thanks to the @rhinelandrna.bsky.social‬ as well—always a pleasure to be part of this vibrant RNA community! #RNAsky

A postdoc position in the Torben Heick Jensen lab, Aarhus University, Denmark: Mammalian Nuclear RNA Production and Turnover Systems - Vacancy at Aarhus University Vacancy at Department of Molecular Biology and Genetics - RNA Biology and Innovation, Aarhus University

Postdoc positions available in the Heick Jensen lab in sunny Aarhus. Sorting of good and bad RNAs in mammalian nuclei. Please get in touch for further information and/or use the following link to apply:
mbg.au.dk/en/news-and-...