An expanded reference catalog of translated open reading frames for biomedical research Abstract. Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidenc

From @johnprensner.bsky.social & coll. in @narjournal.bsky.social #NARDataResourcesAndAnalyses publication | An expanded reference catalog of translated open reading frames for biomedical research | #ncORFs #RiboSeq #Bioinformatics #Database #OpenScience 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/article/...

An expanded reference catalog of translated open reading frames for biomedical research Abstract. Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidenc

*MANUSCRIPT ALERT*

Today the TransCODE / GENCODE Phase II catalog of #RiboSeq ORFs came out in @narjournal.bsky.social

Check out the most authoritative resource for #DarkProteome discovery.

1/

academic.oup.com/nar/article/...

In this review we highlight how bridging single-molecule imaging and genome-wide Ribo-Seq experiments can shed light on complex mRNA translation dynamics across scales. #Translation #RiboSeq @tim-stasevich.bsky.social bit.ly/3LQ08Dc

Systematic Analysis of C-Termini of Small Open Reading Frame-Encoded Peptides in Human Cancer Cell Lines The C-termini often regulate protein biological functions through specific structures or modifications. Small open reading frame-encoded peptides (SEPs) make up a novel class of gene expression products that participate in various biological activities. Their C-termini have also been found to affect their function, but the polymorphism of SEPs’ C-termini has not yet been systematically elucidated. Using C-terminal proteomics, we identified 3636 C-terminal peptides from 2168 proteins in three human cancer cell lines, including 3364 peptides from 1901 classical proteins and 272 peptides from 267 SEPs. Approximately 20% of all of the identified C-terminal peptides had been reported in previous studies, originating from mRNA alternative splicing or protease cleavage, while more than 85% of the C-terminal peptides from SEPs were novel. Bioinformatics analysis revealed that most new SEP C-termini are likely produced by protease cleavage by the KLK, MMP, and CAT protease families. Others without accurately predicted hydrolysis sites may originate from alternative splicing or protein trimming. The intact and hydrolysis products of some SEPs were verified by immunoblotting. Some cleavage occurs in the predicted domain, which might affect SEPs’ function. This study enriches the SEP sequence information, provides experimental evidence for SEP in vivo processing, and supports the subsequent functional analysis of SEP.

Systematic analysis of C-termini of small open reading frame-encoded peptides.

#Riboseq
#proteomics
#darkproteome

pubs.acs.org/doi/10.1021/...

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, still very little is known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from the closely related species Arabidopsis halleri, A. lyrata and A. thaliana and characterized genome-wide patterns of translation across them. Synteny analysis revealed 211 Open Reading Frames (ORFs) that have emerged de novo within the Arabidopsis genus and already exhibit signs of active translation. Most of these de novo translated ORFs were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved Coding DNA Sequences (CDS), and their GC content increased with phylogenetic conservation. While most of them were located in intergenic regions and are thus newly discovered, 34 were previously annotated as CDS in at least one genome, and are promising putative genes. Our results demonstrate the abundance of translation events outside of conserved CDS, and their role as starting material for the emergence of novel genes in plants. ### Competing Interest Statement The authors have declared no competing interest. Université de Lille, https://ror.org/0546v5182

🧬 What does the starting material from which genes could emerge #denovo look like?
🌱 We used #RiboSeq to investigate the landscape of translated de novo ORFs in 3 #Arabidopsis species, and how they might be linked to gene birth!

📝 Check out our preprint here:
doi.org/10.1101/2025...

🔬 Recap – Protein Synthesis & Translational Control 2025 @embl.org
We showcased our technologies Ribo-tRNAseq & HT-RiboSeq (RiboWich), connected with brilliant scientists & had inspiring conversations 🤩 Thanks to all who joined us in Heidelberg!
#ribosome #tRNA #EMBLProtein #riboseq

The Summer School is almost here! 🔬 Samples ready, welcome kits prepared, vials aliquoted... we can’t wait to teach you all about Ribo-Seq Multiplexing 🤩 Are you ready? Learn more 👉 zurl.co/rpaHT

#RiboSeq #ribosome #multiplexing #summerschool

The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data. #GeneExpression #RiboSeq #Visualization #Bioinformatics @genomeresearch.bsky.social
genome.cshlp.org/content/earl...

How does G3BP1 impact cell motility? 🧬
Using RiboLace Ribo-Seq, Boraas et al. reveal G3BP1 regulates focal adhesion dynamics independently of translation.
A new take on RNA-binding proteins in motion!
Read more 👉 zurl.co/P5ksd
#RiboSeq #RNA #CellBiology

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Last chance to sign up for the #GordonResearchConference on #Microproteins. Join us to learn about all things #DarkProteome / #RiboSeq!

Poster awards are still available for trainees! Get your abstracts in by July 20!!!

#Proteomics
#RNASky
#GENESky
#Bioinformatics

www.grc.org/decoding-mic...

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ONE WEEK LEFT TO SIGN UP FOR the GRC on #Microproteins.

Students, trainees, and scientists interested in #darkproteome, #proteomics, #riboseq, #microproteins, #smORFs will not want to miss this.

Submit an abstract now and be eligible for a poster award!

www.grc.org/decoding-mic...

☀️ Summer + science = the perfect combo!
Few spots left for our Ribo-Seq Multiplexing Workshop in Italy
🔬 Hands-on training, processing of provided samples & expert insights
⏰ Don’t miss out! Sign up now: zurl.co/S5AHP
#RiboSeq #Workshop #RNA #summerschool

An overview of defining all ncORFs and the Primary set of ncORFs with enriched features.

We take the output of 9 prominent #Riboseq analyses and systematically map them to #GENCODE v45. We develop two concepts for your use:
- Comprehensive set: all high-quality #ncORFs
- Primary set: #ncORFs with metrics similar to protein-coding genes.

An expanded reference catalog of translated open reading frames for biomedical research Non-canonical (i.e., unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidence of their translation, limiting their incorporation into biomedical research. To address this, in 2022, we initiated the TransCODE consortium and built the first community-driven consensus catalog of human ncORFs, which was openly distributed to the research community via Ensembl-GENCODE. While this catalog represented a starting point for reference ncORF annotation, major technical and scientific issues remained. In particular, this initial catalogue had no standardized framework to judge the evidence of translation for individual ncORFs. Here, we present an expanded and refined catalog of the human reference annotation of ncORFs. By incorporating more datasets and by lifting constraints on ORF length and start-codon, we define a comprehensive set of 28,359 ncORFs that is nearly four times the size of the previous catalog. Furthermore, to aid users who wish to work with ncORFs with the strongest and most reproducible signals of translation, we utilized a data-driven framework (i.e. translation signature scores) to assess the accumulated evidence for any individual ncORF. Using this approach, we derive a subset of 7,888 ncORFs with translation evidence on par with canonical protein-coding genes, which we refer to as the Primary set. This set can serve as a reliable reference for downstream analyses and validation, with a particular emphasis on high quality. Overall, this update reflects continual community-driven efforts to make ncORFs accessible and actionable to the broader research public and further iterations of the catalog will continue to expand and refine this resource. ### Competing Interest Statement J.R.P. has received research honoraria from Novartis Biosciences and Quantum-Si, and is a paid consultant for ProFound Therapeutics. J.L.A. is an advisor to Microneedle Solutions. G.M. is co-founder and CSO of OHMX.bio. P.F. is a member of the scientific advisory board of Infinitopes. A.-R. C. is a member of the advisory board of ProFound Therapeutics. P.V.B. is a cofounder and shareholder of Eirnabio Ltd.

Are you looking to study the #darkproteome but don't know where to start?

Never fear, we've got your back.

Here, we share the latest catalog for #RiboSeq #ORFs.

Thanks to Sonia Chothani and @jruizorera.bsky.social for leading!

🧪
💻 + 🧬
#GENESky
#bioinformatics

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

dry seeds stall ribosomes at start codons — with Kozak-like motifs calling the shots
hydration triggers a sharp translational shift
a gorgeous map of ribosome positioning during germination made by Prof. Leónie Bentsink and team
doi.org/10.1101/2025...
#riboseq #seedbiology #translationalcontrol

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Looking to come to the #GordonConference on #Microproteins / #DarkProteome, but missed the abstract deadline?

NO WORRIES. Late breaking abstracts are now accepted until July 20. Be eligible for a #BestPoster award!

#RNAsky
#Genomics
#Bioinformatics
#Proteomics
#RiboSeq

www.grc.org/decoding-mic...

🎉 Catch Immagina this June at these 3 events!
📍 Shwachman-Diamond Syndrome Congress, Cincinnati (June 5–8)
📍 RBSCDB Spring Meeting, Liège (June 6)
📍 RiboMod2025, Bologna (June 12–13)

#RNA #RiboSeq #Translatomics #tRNA #ribosome

#alternativetranslation #cancer #scc #ribosomequalitycontrol #ribosome #skin #usp10 #g3bp1 #rnf10 #ubiquitin #turboID #silac #massspectrometry #proteomics #riboseq #eIF2A #translation #mRNA

What if the key to your system lies in the tRNAs your ribosomes actually use? 🔬
Meet Ribo-tRNAseq: the first kit to isolate and sequence actively translating tRNAs—fast, easy, and insightful.
Learn more: zurl.co/cFoM5
#tRNA #RiboSeq #Translatomics

That’s a wrap on the 19th Microsymposium on RNA Biology in Vienna! 🧬✨ @imbavienna.bsky.social
Big thanks to all who stopped by—and congrats to Anastasia Polikarpova, winner of our quiz prize and proud new owner of an Immagina backpack! 🎒
#RNA #MicrosymposiumRNA #RiboSeq

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ALERT: Time to turn your research to the #darkproteome.

The deadline is approaching for abstracts for the AMAZING Gordon Research Conference on 🔎 #microproteins.

Sign up now while space is available!

#RiboSeq
#RNASky
#Cancer
#Genomics
#Bioinformatics
#Proteomics

www.grc.org/decoding-mic...

☀️ Science meets summer in Italy!
Join our 4th workshop “Multiplexing it” to master ribosome profiling w/ the RiboLace Multiplexing kit. Less input, less handling—more data!

🔗Learn more and register here: zurl.co/GZ1PF
#RiboSeq #SummerWorkshop #ribosome

We combined RNA-seq, Ribo-seq, tRNA quantification, and proteomics to study BCAA starvation.
💥 Valine codon stalling creates elongation bottlenecks.
🧩 Codon identity, tRNA dynamics, and amino acid levels shape translation and protein output.
#RiboSeq #Translation #tRNA #MolecularBiology #BCAA

Congrats @simonelsasser.bsky.social and so excited to see this work in print!

#genomics
#bioinformatics
#RNAsky
🔎 #microproteins
🧬 💻
#RiboSeq
#ncORFs

Where else will you get access to the leaders and best in #RiboSeq, #Immunopeptidomics, and the #DarkProteome?

It's a once-a-year chance to get into this new field and don't miss out!

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Sign up now and don't miss out! The 2025 Gordon Research Conference on #Microproteins is here for registration: bit.ly/3EGGntM

Submit your application in the next 2 months and you are eligible for a short talk and/or a scholarship!!!

#RiboSeq
🔎 microproteins
#genomics
#bioinformatics
🧬 💻
#RNAsky

Using #RiboSeq we were able to identify new alternative coding sequences (ARFs) in the HIV genome. More importantly we were able to show that some peptides from these ARFs trigger an immune response. A lot remains to do to understand their biological functions and their therapeutic interests.

Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling - Nature Communications Here, using ribosomal profiling, the authors characterize the translatome of HIV-1 revealing tens of alternative open reading frames (ARF) that encode conserved viral antigens and show that ARF-derive...

I am very pleased to share with you this fantastic work done in in collaboration with Arnaud Moris’steam. It has been a very pleasant collaboration and a fantastic project done at the #I2BC. #microproteine #riboseq #HIV www.nature.com/articles/s41...

Deep learning to decode sites of RNA translation in normal and cancerous tissues - Nature Communications RNA translation is a core cell process that is deregulated in cancer. Here, the authors show that a machine learning approach, RiboTIE, can reconstruct RNA translation in cancer and non-cancer cells. ...

Looking to see how #RiboSeq can improve your cancer research?

Check out how we've been developing new methods to study #medulloblastoma and other forms of #childhoodcancer.

Out in @naturecomms.bsky.social now. Thanks to Jim Clauwaert and Gerben Menschaert as well!

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

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ONLY 200 days until the GRC on #microproteins launches!

Sign up now for the landmark event in the scientific field.

Don't miss this chance to meet all of the leaders in #RiboSeq, #RNA, #Proteomics, #Translation!

#genomics
#bioinformatics
🧬 💻
🔎 microproteins
#RNAsky

www.grc.org/decoding-mic...