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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
...are less well understood. Here, we directly measure spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA sequencing. This allows us to calculate mRNA half-lives within specific cell types...
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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
...). Translation-dependent decay (TDD) pathways were originally identified and studied as the means by which cells rid themselves of aberrant mRNAs (e.g., those containing premature termination codons in the case of nonsense mediated decay [NMD] and truncated or prematurely polyadenylated mRNAs in the case...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...across distantly related species.In eukaryotes, the 3′-ends of mRNAs are cotranscriptionally generated by a two-step catalytic process: endonucleolytic cleavage followed by poly(A) tail synthesis (Richard and Manley 2009). Cleavage and polyadenylation happens through the recruitment of processing factors...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...depletion of SMC-3 and WAPL-1 resulted in striking changes in cohesin binding and the Hi-C contacts forming fountains, but not on RNA Pol II binding or mRNA levels measured by ChIP-seq and mRNA-seq, respectively (Fig. 8). In a recent preprint, TEV-mediated cleavage of two cohesin kleisin subunits over...
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Research: Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay
- Jessica A. Hurt,
- Alex D. Robertson,
- and Christopher B. Burge
Genome Res. October 2013 23: 1636-1650; Published in Advance June 13, 2013, doi:10.1101/gr.157354.113
...Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay Jessica A. Hurt , Alex D. Robertson and Christopher B. Burge 1 Department of Biology, Massachusetts Institute of Technology, Cambridge...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...), but our long RNA-seq mappings could also be consistent with TR transcription in C. elegans being a byproduct of mRNA transcription.View larger version: In this window In a new window Figure 6. Transcription from a tandem repeat in various tissue types. This shows an alignment of long RNA-seq reads...
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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
...–367. ↵Kim YK, Furic L, Desgroseillers L, Maquat LE. 2005. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′UTRs so as to elicit mRNA decay. Cell 120: 195–208. ↵Kurosaki T, Maquat LE. 2016. Nonsense-mediated mRNA decay in humans at a glance. J Cell Sci 129: 461–467. ↵Kurosaki T, Li W, Hoque M, Popp MW...
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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
...2019; Zhang et al. 2021). Finally, recognition of a polyadenylation signal (PAS) by the RNA cleavage complex initiates cleavage and polyadenylation (addition of a poly(A) tail) to form the 3′ end of the mRNA molecule (Tian and Manley 2016). Each of these events—transcription initiation, pre-mRNA...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...26G-RNAs require Dicer but derive from an atypical RNA duplex and are produced exclusively antisense to their messenger RNA (mRNA) templates. To identify canonical siRNAs in C. elegans, we first characterized the siRNAs produced via the exogenous RNA interference (RNAi) pathway. During RNAi, ds...
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Resource: The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting
- Hannah S. Steber,
- Christina Gallante,
- Shannon O'Brien,
- Po-Lin Chiu,
- and Marco Mangone
Genome Res. December 2019 29: 2104-2116; Published in Advance November 19, 2019, doi:10.1101/gr.254839.119
...high-quality 3′-UTR data mapped at single-base ultraresolution for 23,084 3′-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this data set to study and probe principles of mRNA cleavage and polyadenylation in C. elegans...
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