ArticleNucleic acids research2007
Beyond the 3' end: experimental validation of extended transcript isoforms.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 19 citations in OpenAlex.
- Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes.PloS one · 2016Article
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
- IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons.The Journal of comparative neurology · 2014Article
- Genome-wide analysis of long noncoding RNA stability.Genome research · 2012Article
- A novel function of Tis11b/BRF1 as a regulator of Dll4 mRNA 3'-end processing.Molecular biology of the cell · 2011Article
- Poly(A) signals located near the 5' end of genes are silenced by a general mechanism that prevents premature 3'-end processing.Molecular and cellular biology · 2011Article
- Non-coding RNA transcripts: sensors of neuronal stress, modulators of synaptic plasticity, and agents of change in the onset of Alzheimer's disease.Neuroscience letters · 2009Review
- Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation.Nucleic acids research · 2009Article
- Identification of gene 3' ends by automated EST cluster analysis.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.Genome research · 2008Article
- Article
- Specific expression of long noncoding RNAs in the mouse brain.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High throughput EST and full-length cDNA sequencing have revealed extensive variations at the 3' ends of mammalian transcripts. Whether all of these changes are biologically meaningful has been the subject of controversy, as such, results may reflect in part transcription or polyadenylation leakage. We selected here a set of tandem poly(A) sites predicted from EST/cDNA sequence analysis that (i) are conserved between human and mouse, (ii) produce alternative 3' isoforms with unusual size features and (iii) are not documented in current genome databases, and we submitted these sites to experimental validation in mouse tissues. Out of 86 tested poly(A) sites from 44 genes, 84 were individually confirmed using a specially devised RT-PCR strategy. We then focused on validating the exon structure between distant tandem poly(A) sites separated by over 3 kb, and between stop codons and alternative poly(A) sites located at 4.5 kb or more, using a long-distance RT-PCR strategy. In most cases, long transcripts spanning the whole poly(A)-poly(A) or stop-poly(A) distance were detected, confirming that tandem sites were part of the same transcription unit. Given the apparent conservation of these long alternative 3' ends, different regulatory functions can be foreseen, depending on the location where transcription starts.
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