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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
...analysis with a much smaller PAS set based on EST sequences from multiple species (Li and Du 2013). In addition, although our sequencing data could not distinguish the two scenarios, we think, based on the biochemical data from Chen et al. (1995), pre-mRNA cleavage immediately upstream of an A residue...
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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
...Andreas J. Gruber,1 Ralf Schmidt,1 Andreas R. Gruber,1 Georges Martin,1 Souvik Ghosh,1 Manuel Belmadani,1,2 Walter Keller,1 and Mihaela Zavolan1 1Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland Alternative polyadenylation (APA) is a general mechanism...
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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
...to transcript initiation and alternative splicing. Previous EST-based analyses showed that about a half of human and rice genes and up to one-third of algal protein-coding genes undergo APA (Zhang et al. 2005; Shen et al. 2008a,b), suggesting that APA has a global role in the regulation of gene expression...
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RESEARCH: Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering
- Daniel Gautheret,
- Olivier Poirot,
- Fabrice Lopez,
- Stéphane Audic,
- and Jean-Michel Claverie
Genome Res. May 1, 1998 8: 524-530; doi:10.1101/gr.8.5.524
..., together with possible instances of tissue-specific differential polyadenylation. This study demonstrates that, besides quantitative aspects of gene expression, the distribution of alternate mRNA forms can be analyzed through EST sampling. Footnotes ↵ 1 Corresponding author. E...
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Resource: A quantitative atlas of polyadenylation in five mammals
- Adnan Derti,
- Philip Garrett-Engele,
- Kenzie D. MacIsaac,
- Richard C. Stevens,
- Shreedharan Sriram,
- Ronghua Chen,
- Carol A. Rohl,
- Jason M. Johnson,
- and Tomas Babak
Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
...previously unappreciated regulatory functions (Mercer et al. 2011). A simple and reliable method for high-throughput mapping of polyA sites is needed to help define the complete set of transcripts present in a dynamic transcriptome and to better understand the role of alternative polyadenylation. ESTs...
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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
...-evaluated and curated full-length transcriptomes.Alternative splicing (AS) and alternative polyadenylation (APA) are among the most fascinating and challenging aspects of eukaryotic transcriptomes. AS and APA are considered to be the major mechanisms of generating transcriptome complexity and thus the expansion...
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RESOURCE: Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
- Carmela Gissi and
- Graziano Pesole
Genome Res. September 2003 13: 2203-2212; Published in Advance January 1, 2003, doi:10.1101/gr.1227803
...levels. Moreover, ESTs may derive from unspliced immature mRNAs, alternative splicing and polyadenylation sites, cloning artifacts (chimerisms), and mitochondrial (mt) transcripts. Depending on tissue source and RNA extraction/fractioning methods, a remarkably high fraction of ESTs from a given c...
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LETTER: Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing
- Bin Tian,
- Zhenhua Pan,
- and Ju Youn Lee
Genome Res. February 2007 17: 156-165; Published in Advance January 8, 2007, doi:10.1101/gr.5532707
...and alternative splicing. Polyadenylation in introns can lead to conversion of an internal exon to a 3′ terminal exon, which is termed composite terminal exon, or usage of a 3′ terminal exon that is otherwise skipped, which is termed skipped terminal exon. Using cDNA/EST and genome sequences, we identified...
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Methods: ECgene: Genome-based EST clustering and gene modeling for alternative splicing
- Namshin Kim,
- Seokmin Shin,
- and Sanghyuk Lee
Genome Res. April 2005 15: 566-576; doi:10.1101/gr.3030405
...ECgene: Genome-based EST clustering and gene modeling for alternative splicing Namshin Kim 1 , 2 , Seokmin Shin 2 , and Sanghyuk Lee 1 , 3 1 Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea 2...
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Methods: The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
- Yi Xing,
- Alissa Resch,
- and Christopher Lee
Genome Res. March 2004 14: 426-441; Published in Advance February 12, 2004, doi:10.1101/gr.1304504
...deals appropriately with coupling of distinct alternative splicing events, increasing fragmentation of the input data and different types of transcript variation (such as alternative splicing, initiation, polyadenylation, and intron retention). To test the method's performance on pure fragment (EST...

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