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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
...maturation rather than a consequence of decay.The model is based on a detailed long-read sequencing–based molecular analysis of the polyadenylation, cleavage, and capping status of mRNA molecules produced from approximately two dozen endogenous C. elegans NMD-target genes. We expect that a similar model...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...exon, altering only the 3′ UTR sequence while leaving the protein-coding sequence unchanged. Because the 3′ UTR contains many essential regulatory elements—such as microRNA and RNA-binding protein (RBP) binding sites—variation in 3′ UTR length can modulate target mRNA function, stability...
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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
...for mammalian genes. It remains unknown if the polyadenylation events occurring across a cleavage zone represent poly(A) site microheterogeneity or the utilization of separate alternative poly(A) sites. Both heterogeneous cleavage and alternative polyadenylation (APA) can generate mRNAs with different 3′ UTRs...
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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
...for destabilization and translational inhibition (Chekulaeva and Filipowicz 2009). Our cell type–specific mRNA half-life measurements also allowed us to examine the decay of known miRNA targets. C. elegans genes encoding subunits of the vacuolar adenosine triphosphatase (V-ATPase) complex, which controls...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...: 10,461,689–10,461,701. TargetScan predicts a high context score percentile of 79.00, suggesting the site as a favorable target. By evaluating miRNA binding to the mRNA before and after the mutation, Mimosa predicts a classification of one, and TargetNet predicts a probability of ∼0.84 for both cases...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...studies as well as new therapeutic angles to target eukaryotic pathogens.Cleavage and polyadenylation (CPA) are key steps in eukaryotic mRNA maturation, specifying the 3′ end of the transcript and the addition of the poly(A) tail. Required for the proper expression of nearly all mRNAs, the site of pre-mRNA...
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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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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
...μg total RNA, using the ZYMO RNA Clean & Concentrator-5 kit (Zymo R1015). The rRNA-depleted RNA (5 μL) was then mixed with 1 μL 50 pmol Universal miRNA cloning linker (NEB S1315S; 5′ rAppCTGTAGGCACCATCAAT–NH2 3′) at 65°C for 5 min, and then ligated using T4 RNA Ligase 2, truncated KQ (NEB M0373S...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
...; Srivastava et al. 2018). This molecular effect connects to various post-transcriptional regulations, including alteration of mRNA stability, the gain or loss of miRNA, and/or RNA-binding protein targets (Mayr 2017). By -wide calculation of the weighted 3′-UTR length of genes, we found that 3′ UTR lengthening...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
...to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.For ∼70% of human genes, differential polyadenylation alters the 3′ untranslated regions (3′ UTRs) that may regulate mRNA metabolism and protein expression (Derti et al. 2012; Tian...
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