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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
...-cell atlas of pigs by adding a layer of posttranscriptional regulation to the existing gene expression data, highlighting the significant role of cell type–specific 3′ UTR lengths in cell commitment and complex trait regulation.Alternative polyadenylation (APA) refers to the process by which pre-mRNA adds...
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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
...Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain Bowei Kang1, Yalan Yang1, Kaining Hu1, Xiangbin Ruan1, Yi-Lin Liu2, Pinky Lee1, Jasper Lee1, Jingshu Wang2 and Xiaochang Zhang1,3 1Department of Human Genetics, The University of Chicago, Chicago...
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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
.... Corresponding authors: xin.gao@kaust.edu.sa, chenw@sustech.edu.cn, zb.picb@gmail.comAbstractAlternative polyadenylation (APA) enables a gene to generate multiple transcripts with different 3′ ends, which is dynamic across different cell types or conditions. Many computational methods have been developed...
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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
...this atlas of decay rates, we investigated the contribution of mRNA decay toward specific gene expression patterns across developmental stages and cell types, as well as how differential mRNA degradation may be regulated.ResultsTranscription inhibition by actinomycin D allows mRNA decay measurements in C...
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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
....1101/gr.224451.117 ↵Derti A, Garrett-Engele P, MacIsaac KD, Stevens RC, Sriram S, Chen RH, Rohl CA, Johnson JM, Babak T. 2012. A quantitative atlas of polyadenylation in five mammals. Genome Res 22: 1173–1183. doi:10.1101/gr.132563.111 ↵Elkon R, Ugalde AP, Agami R. 2013. Alternative cleavage...
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Method: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression
- Yipeng Gao,
- Lei Li,
- Christopher I. Amos,
- and Wei Li
Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
...Yipeng Gao1,2, Lei Li3, Christopher I. Amos2 and Wei Li3 1Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; 3Division of Computational Biomedicine...
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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
...: 2755–2766. Danckwardt S, HentzeMW, Kulozik AE. 2008. 3′ endmRNAprocessing:molecularmechanisms and implications for health and disease. EMBO J 27: 482–498. Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T. 2012. A quantitative atlas of polyadenylation...
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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
....Cleavage and polyadenylation is an essential step for 3′ end maturation of almost all mRNAs in eukaryotes (Shi and Manley 2015; Proudfoot 2016). The site of cleavage, also known as poly(A) site (PAS), is defined by surrounding sequence motifs, which vary in different phylogenic groups (Tian and Graber 2012). In mammals...
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Research: Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency
- Yonggui Fu,
- Liutao Chen,
- Chengyong Chen,
- Yutong Ge,
- Mingjing Kang,
- Zili Song,
- Jingwen Li,
- Yuchao Feng,
- Zhanfeng Huo,
- Guopei He,
- Mengmeng Hou,
- Shangwu Chen,
- and Anlong Xu
Genome Res. November 2018 28: 1656-1663; Published in Advance September 18, 2018, doi:10.1101/gr.231506.117
..., Rohl CA, Johnson JM, Babak T. 2012. A quantitative atlas of polyadenylation in five mammals. Genome Res 22: 1173–1183. ↵Di Giammartino DC, Nishida K, Manley JL. 2011. Mechanisms and consequences of alternative polyadenylation. Mol Cell 43: 853–866. ↵Elkon R, Ugalde AP, Agami R. 2013. Alternative...
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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
...(U) Of the human andmouse 3′ end processing sites from our poly(A) atlases, 76% and 75%, respectively, possessed a conserved poly(A) signal in their 60 nt upstream region. That ∼25% did notmay support the hypothesis that pre-mRNA cleavage and polyadenylation do not absolutely require a poly(A) signal (Venkataraman...
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