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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...) Numbers of genes with different numbers of the identified PAS.We performed RNA 3′ end-seq (QuantSeq 3′ mRNA-seq, Lexogen) on four cell lines, including K562, HepG2, THLE2, and SNU398, to comprehensively characterize the expressed/used PAS in these four samples, respectively. To avoid internal primming...
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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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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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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
...of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA ↵3 These authors contributed equally to this work. Corresponding author: jsanfor2@ucsc.eduAbstractAlternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms, leading to transcripts with distinct...
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Method: Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
- Cédric Howald,
- Andrea Tanzer,
- Jacqueline Chrast,
- Felix Kokocinski,
- Thomas Derrien,
- Nathalie Walters,
- Jose M. Gonzalez,
- Adam Frankish,
- Bronwen L. Aken,
- Thibaut Hourlier,
- Jan-Hinnerk Vogel,
- Simon White,
- Stephen Searle,
- Jennifer Harrow,
- Tim J. Hubbard,
- Roderic Guigó,
- and Alexandre Reymond
Genome Res. September 2012 22: 1698-1710; doi:10.1101/gr.134478.111
...by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA) as described in Washietl et al. (2007). Aliquots (two of 12.5 mL) of up to 4700 independent amplification reactions were pooled together respecting the tissue origin and purified with the QIAquick PCR...
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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
...initiation, tRNA processing, mRNA processing, and regulation of RNA polII transcription, as well as pathways related to immune system and response to cytokine (Supplemental Fig. S8B; Supplemental Table S1). Significantly down-regulated transcripts are enriched for ribosomal proteins, protein ubiquitination...
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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
..., Lianne Boeglin2, Sudha Chivukula2, Anusha Dias2, Tod Strugnell2, Fernando Ulloa Montoya3, Vikram Agarwal2, Ziv Bar-Joseph1 and Sven Jager1 1Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA; 2mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA; 3mRNA Center of Excellence, Sanofi...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...Genomics Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA ↵4 Present address: Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA Corresponding author: jarriber@ucsc.eduAbstractPremature stop codon–containing mRNAs can produce...
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Research: Promoter architecture determines cotranslational regulation of mRNA
- Lorena Espinar,
- Miquel Àngel Schikora Tamarit,
- Júlia Domingo,
- and Lucas B. Carey
Genome Res. April 2018 28: 509-518; Published in Advance March 22, 2018, doi:10.1101/gr.230458.117
...-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34: 525–527. ↵Bregman A, Avraham-Kelbert M, Barkai O, Duek L, Guterman A, Choder M. 2011. Promoter elements regulate cytoplasmic mRNA decay. Cell 147: 1473–1483. ↵Carey LB, van Dijk D, Sloot PMA, Kaandorp JA, Segal E. 2013. Promoter sequence determines...
REVIEW: Quantitative PCR and RT-PCR in virology.
- M Clementi,
- S Menzo,
- P Bagnarelli,
- A Manzin,
- A Valenza,
- and P E Varaldo
Genome Res. February 1993 2: 191-196; doi:10.1101/gr.2.3.191
...directly using qualitative RT-PCR methods that allow qualitative detection of specific viral mRNAs, as in the cases of HIV-1 (13-1s) and HBV infections. (16,17) Third, because PCR amplification supplies templates pure enough to be an- alyzed directly using standard sequenc- ing protocols, this method...
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