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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
....ricci@ens-lyon.org, melissa.moore@umassmed.eduAbstractmRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...) upstream of the uORF stop codon (orange dashed line) suggests that multiple ribosomes stack in this region. Accumulation of the PARE-seq reads (highlighted by pink dashed lines) occurs at 13 nt upstream of the corresponding Ribo-seq peaks, supporting cotranslational mRNA decay in this region. The shift...
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...) ribosomes. For this purpose, we set up a run-off experiment and determined the ratio between polysome-associated and monosome-associated mRNAs following harringtonine treatment. Control (shGFP) and shTRAP1 HeLa cells were treated for 2 min with harringtonine and fractionated, and the number of transcripts...
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Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...levels: RNA transcript, open reading frames (ORFs), and finally protein sequences (Reixachs-Solé and Eyras 2022). The complex interplay between the changes occurring to AS variants and their ORF and protein products is hard to characterize and quantify. Changes in mRNA sequence may lead to nonlinear...
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Method: Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
- Mai Sun,
- Björn Schwalb,
- Daniel Schulz,
- Nicole Pirkl,
- Stefanie Etzold,
- Laurent Larivière,
- Kerstin C. Maier,
- Martin Seizl,
- Achim Tresch,
- and Patrick Cramer
Genome Res. July 2012 22: 1350-1359; Published in Advance March 30, 2012, doi:10.1101/gr.130161.111
...data (Fig. 3A). This new normalization method allows rate estimation from labeled and total quantities alone (Methods). Our published median half-life for Sc mRNAs (Miller et al. 2011) enabled determination of the median Sp half-life relative to Sc (Supplemental Fig. S2). We measured growth curves...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...proteins). The ABC neighborhood (Fig. 4A) of the PriOmics-CIG model comprises in total 19 peptides from 12 different proteins, in which the tryptic peptide at the protein N terminus of PDLIM1 ([1Ac]-TTQQIDLQPGPWGFR) was acetylated after cotranslational cleavage of the N-terminal methionine by methionine...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...secondary structures in lncRNA.G4s form in certain guanine-rich regions through the self-assembly of guanines into planar quartets, which are stacked into a three-dimensional structure. G4 formation can alter gene expression by inhibiting initiation complex binding at mRNA transcripts, recruiting splicing...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...and, hence, to reduction of the time spent by ribosomes on each mRNA, thereby increasing the pool of free ribosomes available in the cell, which ultimately allows a higher cellular growth rate (Bulmer 1991). Second, the usage of synonymous codons decoded by the most abundant tRNAs increases...
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Research: Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets
- Michael Stadler,
- Karen Artiles,
- Julia Pak,
- and Andrew Fire
Genome Res. December 2012 22: 2418-2426; Published in Advance August 1, 2012, doi:10.1101/gr.136515.111
...(Wang et al. 2008), inducing premature ribosome drop-off (e.g., Petersen et al. 2006), or co-translational or peri-translational proteolysis (Nottrott et al. 2006). Considerable evidence has also accumulated to indicate that target mRNA deadenylation and subsequent degradation can be an important...
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Research: A novel translational control mechanism involving RNA structures within coding sequences
- Jennifer Jungfleisch,
- Danny D. Nedialkova,
- Ivan Dotu,
- Katherine E. Sloan,
- Neus Martinez-Bosch,
- Lukas Brüning,
- Emanuele Raineri,
- Pilar Navarro,
- Markus T. Bohnsack,
- Sebastian A. Leidel,
- and Juana Díez
Genome Res. January 2017 27: 95-106; Published in Advance November 7, 2016, doi:10.1101/gr.209015.116
...primarily membrane and secreted proteins Specific mRNA features might allow coregulation of functionally related proteins. To determine whether themRNAs translationally regulated by Dhh1 are functionally linked, we performed Gene Ontology (GO) analysis (Fig. 5E,F). Genes translationally activated byDhh1...

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