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Research: 3′ UTR lengthening as a novel mechanism in regulating cellular senescence
- Meng Chen,
- Guoliang Lyu,
- Miao Han,
- Hongbo Nie,
- Ting Shen,
- Wei Chen,
- Yichi Niu,
- Yifan Song,
- Xueping Li,
- Huan Li,
- Xinyu Chen,
- Ziyue Wang,
- Zheng Xia,
- Wei Li,
- Xiao-Li Tian,
- Chen Ding,
- Jun Gu,
- Yufang Zheng,
- Xinhua Liu,
- Jinfeng Hu,
- Gang Wei,
- Wei Tao,
- and Ting Ni
Genome Res. March 2018 28: 285-294; Published in Advance February 12, 2018, doi:10.1101/gr.224451.117
...to this work. Corresponding authors: weitao@pku.edu.cn, gwei@fudan.edu.cn, tingni@fudan.edu.cnAbstractCellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3′ untranslated regions (3′ UTRs) in messenger RNAs (m...
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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
...brain. Infernape uncovers alternative intronic PAs and 3′-UTR lengthening during cortical neurogenesis. Progenitor–neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation–differentiation axis plays...
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Research: Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
...contribute to the high levels of cotargeting in the brain. For brain-enriched miRNAs (Z-score > 2), we assessed the number of miRNA sites contained in brain-enriched 3′ UTR extension regions from Miura et al. (2013). The number of genes targeted in the 3′ UTR extension regions correlates strongly (rho = 0...
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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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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying...
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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
...) and quantified the dynamic changes in APA using the percentage of the proximal PAS usage index (PPUI). A smaller PPUI value indicates a relatively lengthened 3′ UTR. We observed that 3′ UTR length varies depending on the tissue context in mice, humans, and pigs (Figs. 2A, 6B,C). Brain tissues, particularly...
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Research: Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
- Hai-Xi Sun,
- Yan Li,
- Qi-Wen Niu,
- and Nam-Hai Chua
Genome Res. August 2017 27: 1427-1436; Published in Advance May 18, 2017, doi:10.1101/gr.218669.116
...features of plants in response to ABA and dehydration stress. In the IGVGenome Browser, we observed some mRNAs had 3′ UTR extensions in dehydration stress (Fig. 1A; Supplemental Fig. S3A). To determine whether this phenomenon was widespread, we developed a computational pipeline to identify stress...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
...premRNA processing reaction that matures primary transcripts into functional mRNA molecules. In humans, more than half of all genes containmultiple CPA sites (Tian et al. 2005), and their alternative usage is widespread. Alternative cleavage and polyadenylation (APA) can lead to regulated synthesis...
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Research: Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins
- Eric T. Wang,
- Amanda J. Ward,
- Jennifer M. Cherone,
- Jimena Giudice,
- Thomas T. Wang,
- Daniel J. Treacy,
- Nicole J. Lambert,
- Peter Freese,
- Tanvi Saxena,
- Thomas A. Cooper,
- and Christopher B. Burge
Genome Res. June 2015 25: 858-871; Published in Advance April 16, 2015, doi:10.1101/gr.184390.114
...mRNA isoforms (Fig. 4B–E) associated with CELF1 binding to 3′ UTRs provides evidence of widespread direct effects of binding on mRNA expression and identifies numerous instances of gene- and isoform-specific regulation. Evidence for CELF1-mediated regulation of alternative 3′ UTR isoforms...
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