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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
..., such as cdsBERT (Hallee et al. 2023), addresses the issue of codon awareness for a protein language model.To address these limitations, we developed CodonBERT, an LLM that extends the BERT model and applies it to the language of mRNAs. CodonBERT uses a multihead attention transformer architecture framework...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...of active marks (H3K27ac) (Fig. 2; Meshorer et al. 2006; Bonev et al. 2017; Liu et al. 2023). These effects are thought to result in overall increased compaction of chromatin transcription, as embryonic stem cells (ESCs) exhibit globally elevated levels of mRNA, which decreases alongside chromatin...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...Corresponding author: jmurr@pennmedicine.upenn.eduAbstractDuring embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS technologies for RNA-based applications, including concerns about low coverage, high...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...in the CDS can also influence the fate of mRNAs. For example, the RBP ELAVL1 stabilizes target mRNAs by binding to AU-rich elements (AREs) within the CDS, preventing their degradation. Conversely, RBPs like ZFP36 can promote mRNA degradation by binding to AREs in coding regions, leading to mRNA decay (Otsuka...
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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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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
..., both the new level of transcript abundance and the speed of the transition (responsiveness) depend on RNA kinetic rates. In the most straightforward case, differential expression—the regulation of the cellular abundance of premature (P) and mature (M) RNA species—derives from changes in the rate of RNA...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...), there is a paucity of quantitative models that integrate the various elements to predict mRNA deadenylation, degradation, and RBP binding. Thus, it is still poorly understood how sequence composition influences mRNA stability, how the sequence context affects the regulatory potential of each motif, what...
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Method: Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
- Matteo J. Marzi,
- Francesco Ghini,
- Benedetta Cerruti,
- Stefano de Pretis,
- Paola Bonetti,
- Chiara Giacomelli,
- Marcin M. Gorski,
- Theresia Kress,
- Mattia Pelizzola,
- Heiko Muller,
- Bruno Amati,
- and Francesco Nicassio
Genome Res. April 2016 26: 554-565; Published in Advance January 28, 2016, doi:10.1101/gr.198788.115
...al. 2011 ; Neilsen et al. 2012 ; Ruegger and Grosshans 2012 ; Lee et al. 2014 ). A target-dependent mechanism has also been identified, in which turnover is mediated by the interaction of miRNAs with their mRNA targets, promoting miRNA unloading from AGO and degradation ( Baccarini et al. 2011...
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Research: A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells
- Naoto Imamachi,
- Kazi Abdus Salam,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. March 2017 27: 407-418; Published in Advance December 9, 2016, doi:10.1101/gr.206060.116
...helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3′ untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify...

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