ArticleBMC genomics2010
Detection of novel 3' untranslated region extensions with 3' expression microarrays.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- Article
- Evolution of the unspliced transcriptome.BMC evolutionary biology · 2015Article
- Alu elements shape the primate transcriptome by cis-regulation of RNA editing.Genome biology · 2014Article
- Article
- Hidden treasures in unspliced EST data.Theory in biosciences = Theorie in den Biowissenschaften · 2012Article
- Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.Genome research · 2011Article
- Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling.BMC genomics · 2011Article
- Article
- CPEB2, CPEB3 and CPEB4 are coordinately regulated by miRNAs recognizing conserved binding sites in paralog positions of their 3'-UTRs.Nucleic acids research · 2010Article
- EuroDia: a beta-cell gene expression resource.Database : the journal of biological databases and curation · 2010Article
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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
backgroundThe 3' untranslated regions (UTRs) of transcripts are not well characterized for many genes and often extend beyond the annotated regions. Since Affymetrix 3' expression arrays were designed based on expressed sequence tags, many probesets map to intergenic regions downstream of genes. We used expression information from these probesets to predict transcript extension beyond currently known boundaries.
resultsBased on our dataset encompassing expression in 22 different murine tissues, we identified 845 genes with predicted 3'UTR extensions. These extensions have a similar conservation as known 3'UTRs, which is distinctly higher than intergenic regions. We verified 8 of the predictions by PCR and found all of the predicted regions to be expressed. The method can be extended to other 3' expression microarray platforms as we demonstrate with human data. Additional confirming evidence was obtained from public paired end read data.
conclusionsWe show that many genes have 3'UTR regions extending beyond currently known gene regions and provide a method to identify such regions based on microarray expression data. Since 3' UTR contain microRNA binding sites and other stability determining regions, identification of the full length 3' UTR is important to elucidate posttranscriptional regulation.
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