Introns in UTRs: Why we should stop ignoring them

@article{Bicknell2012IntronsIU,
  title={Introns in UTRs: Why we should stop ignoring them},
  author={Alicia A. Bicknell and Can Cenik and Hon Nian Chua and Frederick P. Roth and Melissa J. Moore},
  journal={BioEssays},
  year={2012},
  volume={34}
}
Although introns in 5′‐ and 3′‐untranslated regions (UTRs) are found in many protein coding genes, rarely are they considered distinctive entities with specific functions. Indeed, mammalian transcripts with 3′‐UTR introns are often assumed nonfunctional because they are subject to elimination by nonsense‐mediated decay (NMD). Nonetheless, recent findings indicate that 5′‐ and 3′‐UTR intron status is of significant functional consequence for the regulation of mammalian genes. Therefore these… Expand
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Intron retention in mRNA: No longer nonsense
TLDR
Until recently, retention of introns in mature mRNAs has been regarded as a consequence of mis‐splicing, but recent advances in next‐generation sequencing technologies have enabled the detection of numerous transcripts that retain introns. Expand
A position-specific 3′UTR sequence that accelerates mRNA decay
TLDR
A genome-wide analysis of the impact of this new regulatory pathway showed that the most active motifs are located within the 5′ and 3′-terminal portions of 3′UTRs, whereas elements in the center tend to be inactive. Expand
Stop codon-proximal 3′UTR introns in vertebrates can elicit EJC-dependent Nonsense-Mediated mRNA Decay
TLDR
This work shows that genes with stop codon-proximal 3′UIs encode a new class of EJC-regulated NMD targets with critical roles during vertebrate development. Expand
The exon–intron gene structure upstream of the initiation codon predicts translation efficiency
TLDR
The uORF, in combination with leader EEJ, predicts lower expression for nearly one-third of eukaryotic proteins. Expand
TAPAS: tool for alternative polyadenylation site analysis
TLDR
A new tool, called TAPAS, is proposed, which can deal with more than more than two APA sites in a gene as well as APA Sites that occur before the last exon and outperforms the existing tools for APA site detection or shortening/lengthening analysis significantly. Expand
Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates
TLDR
Several features of 5′UTRs, such as GC content variation, hairpin structure conservation or5′UTR segmentation, are shown, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research. Expand
Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3′UTR Introns
TLDR
It is demonstrated conclusively that NMD, EJC, and CBC factors have essential roles in controlling mRNA stability and that, based on differential requirements for these factors, there are branched mechanisms for NMD. Expand
Spliceosomal introns in the 5′ untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression
TLDR
The results indicated that gene expression dependent on a 5′UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution. Expand
Genome-Wide Identification and Characterization of UTR-Introns of Citrus sinensis
TLDR
This is the first report about the UIS in sweet orange from genome-wide level, which could provide evidence for further understanding of the role of UIs in gene expression regulation. Expand
Untranslated Parts of Genes Interpreted: Making Heads or Tails of High‐Throughput Transcriptomic Data via Computational Methods
TLDR
It is suggested that computational methods applied to standard high‐throughput technologies are a useful, albeit less accurate, alternative to the expertise‐demanding 5′ and 3′ sequencing and they are the only option for analysing legacy transcriptomic data. Expand
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