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Corrigendum: Corrigendum: 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. September 2020 30: 1376-1; doi:10.1101/gr.270165.120
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...Pluripotent stem cells escape from senescence-associated DNA methylation changes Carmen M. Koch 1 , Kristina Reck 1 , Kaifeng Shao 2 , Qiong Lin 3 , Sylvia Joussen 1 , Patrick Ziegler 4 , Gudrun Walenda 1 , Wolf...
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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
..., a number of pan-cancer analyses have used standard RNA-sequencing (RNA-seq) data to identify 3′-UTR shortening and lengthening events across cancer types (Xia et al. 2014; Le Pera et al. 2015; Grassi et al. 2016; Feng et al. 2017; Ye et al. 2018). Although these analyses have uncovered recurrent APA events...
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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: 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
...determinants in the mammalian polyadenylation signal. Nucleic Acids Res 23: 2614–2620. doi:10.1093/nar/23.14.2614 ↵Chen M, Lyu GL, Han M, Nie HB, Shen T, Chen W, Niu YC, Song YF, Li XP, Li H, et al. 2018. 3′ UTR lengthening as a novel mechanism in regulating cellular senescence. Genome Res 28: 285–294. doi:10...
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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
...with the rest of the tissues tested, except pistil, where they were almost equal. This is an example showing that the dynamic of 3′ UTR length control could be broader than previously anticipated. To confirm the APA switching gene in different stages, we performed qRT-PCR for four 3′ UTR lengthening genes...
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Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
...diversity (Elkon et al. 2013; Tian and Manley 2017). There are different types of APA based on the location of the polyadenylation (pA) site in an mRNA, such as 3′ untranslated region APA (UTR-APA), coding region APA (CR-APA), and intronic polyadenylation (IpA) (Tian and Manley 2017). UTR-APA changes...
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