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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
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
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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
...that the cis-regulatory elements mediating S. cerevisiae polyadenylation can be quite degenerate. However, no study has been carried out to systematically examine the relative importance of signal variants. Our deep learning models PolyaClassifer and PolyaStrength provided unprecedented insights...
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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
...polyadenylation sites (IPAs). ALE–IPA has been shown to alter neuronal mRNA localization (Taliaferro et al. 2016) and polarize neuronal functions (Yap et al. 2016). Increasing evidence has linked variations in PA usage to human trait-associated genetic loci (Mittleman et al. 2020; Li et al. 2021b). Thus, PAs...
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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
...to characterize sample-specific APA using the corresponding RNA-seq data, but suffered from high error rate on both polyadenylation site (PAS) identification and quantification of PAS usage (PAU), and bias toward 3′ untranslated regions. Here we developed a tool for APA identification and quantification (APAIQ...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...–1056. doi:10.1111/j.1474-9726.2010.00631.x ↵Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36. ↵Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. 2000. Patterns of variant polyadenylation...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
....feigin@roswellpark.orgAbstractAlternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3′-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA...
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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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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
...37:W202–W208. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. 2000. Patterns of variant polyadenylation signal usage in human genes. Genome Res 10: 1001–1010. Boss PK, Bastow RM, Mylne JS, Dean C. 2004. Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
..., Rutgers University, New Brunswick, New Jersey 08901, USA Corresponding author: btian@rutgers.eduAbstractCleavage and polyadenylation is essential for 3′ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to m...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...of sequence content and isoform patterns. Although individual read pairs show high similarity, we find differences in (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation site (poly(A)-site) assignment, and (4) exon–intron structures. Overall, 25% of read pairs disagree on either TSS...
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