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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
...underwent alternative polyadenylation. In two cases, sub1 and clp1, an ovary-specific short 39 UTR isoform accumulated, and in four others, papolb, pcf11, cstf3, and pabpn1, the APA determined the identity of the last exon of the transcript, thereby affecting the coding sequence (Fig. 3C; Supplemental Fig...
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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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LETTER: A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing
- Rodger B. Voelker and
- J. Andrew Berglund
Genome Res. July 2007 17: 1023-1033; Published in Advance May 24, 2007, doi:10.1101/gr.6017807
...A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing Rodger B. Voelker and J. Andrew Berglund 1 Institute of Molecular Biology, University...
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LETTER: Patterns of Variant Polyadenylation Signal Usage in Human Genes
- Emmanuel Beaudoing,
- Susan Freier,
- Jacqueline R. Wyatt,
- Jean-Michel Claverie,
- and Daniel Gautheret
Genome Res. July 1, 2000 10: 1001-1010; doi:10.1101/gr.10.7.1001
...) database, dbEST ( Boguski et al. 1993 ), which contains highly redundant partial cDNAs, especially from the 3′ UTRs, is a rich source of information on mRNA 3′ ends. Analyzing clustered EST sequences, we previously identified multiple cases of alternate polyadenylation in mRNA ( Gautheret et al. 1998...
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Methods: Gene and alternative splicing annotation with AIR
- Liliana Florea,
- Valentina Di Francesco,
- Jason Miller,
- Russell Turner,
- Alison Yao,
- Michael Harris,
- Brian Walenz,
- Clark Mobarry,
- Gennady V. Merkulov,
- Rosane Charlab,
- Ian Dew,
- Zuoming Deng,
- Sorin Istrail,
- Peter Li,
- and Granger Sutton
Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405
.... For instance, it cannot represent certain isoforms with alternative 5′ or 3′ ends in which one form is subsumed by the other. Post-processing of the gene's tails based on EST clone information to identify potential polyadenylation sites with programs such as PASS ( Kan et al. 2001 ) could partially overcome...
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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
.... The trends in mouse are almost the same as in human. The extent of alternative splicing is slightly decreased, probably due to the smaller size of the EST database. The rat shows much less AS events, and the average number of isoforms does not increase by including less reliable transcripts, which is due...
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Research: DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
- Joel H. Graber,
- Fathima I. Nazeer,
- Pei-chun Yeh,
- Jason N. Kuehner,
- Sneha Borikar,
- Derick Hoskinson,
- and Claire L. Moore
Genome Res. October 2013 23: 1690-1703; Published in Advance June 20, 2013, doi:10.1101/gr.144964.112
...stages of gene expression. One gene regulatory mechanism used by eukaryotes is selection among alternative transcript isoforms that differ in polyadenylation [poly(A)] sites, resulting in changes either to the coding sequence or to portions of the 3′ UTR that govern translation, stability...
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Resource: Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
- LaDeana W. Hillier,
- Valerie Reinke,
- Philip Green,
- Martin Hirst,
- Marco A. Marra,
- and Robert H. Waterston
Genome Res. April 2009 19: 657-666; Published in Advance January 30, 2009, doi:10.1101/gr.088112.108
...to zero, the model is terminated. The tool then evaluates the ends to see if the termination points correspond to transplice or polyadenylation sites and regions of strand bias. By using all splice junctions in a region it is also able to generate alternative splice forms, but of course the short reads do...
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METHODS: d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences
- John Burke,
- Dan Davison,
- and Winston Hide
Genome Res. November 1, 1999 9: 1135-1142; doi:10.1101/gr.9.11.1135
....A. ( 1998 ) The Merck Gene Index Browser: An extensible data integration system for gene finding, gene characterization and EST data mining. Bioinformatics 14 : 2 – 13 . ↵ Gautheret D. , Poirot O. , Lopez F. , Audic S. , Claverie J.M. ( 1998 ) Alternative polyadenylation in human mRNAs: A large...
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Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
- Jingfeng Li,
- Keiko Akagi,
- Yongjun Hu,
- Anna L. Trivett,
- Christopher J.W. Hlynialuk,
- Deborah A. Swing,
- Natalia Volfovsky,
- Tamara C. Morgan,
- Yelena Golubeva,
- Robert M. Stephens,
- David E. Smith,
- and David E. Symer
Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
...; and (bottom) IAPEY2 elements. (Dark blue) Integrants present in one strain; (light blue) two strains; (purple) three; (light pink) four; (orange) five; (red) all six. (Bottom) Mouse chromosomes 1–19, X, and Y (alternating shading). Genome Research 871 www..org Transcriptional variation due to polymorphic ERVs...

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