Searching journal content for articles similar to Spies et al. 23 (12): 2078.

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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
..., Eads BD, Carlson J, Brown JB, et al. 2012. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep 1: 277–289. ↵Spies N, Burge CB, Bartel DP. 2013. 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts...
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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
...determinant of mRNA stability among eukaryotes. However, its precise contribution to overall mRNA decay and the features that modulate its efficiency are still poorly characterized. Using a combination of transcription and translation inhibitors, we were able to deconvolute mRNA decay into translation...
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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
...in alternative 3′ UTR sequences, leading to substantial differences in mRNA stability between 3′ UTR isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Furthermore, we show that mutations of U-rich motifs around the PAS often...
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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
...RNAs) play roles in diverse developmental and disease processes. Distinct miRNAs have hundreds to thousands of conserved mRNA binding sites but typically direct only modest repression via single sites. Cotargeting of individual mRNAs by different miRNAs could potentially achieve stronger and more complex...
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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
...to assign APA profiles and regulatory models. Using this approach, it is difficult to discriminate between cause (choice of a CPA site at the point of cleavage) and effect of APA (altered stability or nuclear retention of particular isoforms). To address this, we compared APA profiles of mRNA isolated from...
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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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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
..., Belgium; 6Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; 7Centro Nacional de Investigaciones Cardiovasculares CNIC, 28029 Madrid, Spain; 8Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; 9Gene Expression and mRNA Metabolism Laboratory, CSIC, IBV, 46010 Valencia...
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