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Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods Computational methods to discover and quantify isoforms with alternative untranslated regions

Szkop, KJ; Nobeli, I; (2017) Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods Computational methods to discover and quantify isoforms with alternative untranslated regions. BioEssays , 39 (12) , Article 1700090. 10.1002/bies.201700090. Green open access

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Abstract

In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly‐adenylation events in high‐throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly‐adenylation sites has been revealed by sequencing methods focused on the ends of transcripts, the application of these methods is not yet widely adopted by the community. We suggest 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. We review these methods here, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal.

Type: Article
Title: Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods Computational methods to discover and quantify isoforms with alternative untranslated regions
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/bies.201700090
Publisher version: https://doi.org/10.1002/bies.201700090
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, Biology, Life Sciences & Biomedicine - Other Topics, alternative poly-adenylation, alternative transcription start site, RNA-seq, untranslated region, RNA POLYADENYLATION SITES, GENOME-WIDE DETECTION, CHANGE-POINT MODEL, MESSENGER-RNAS, 3' UTRS, DIFFERENTIAL EXPRESSION, POLY(A) SITES, CAP ANALYSIS, START SITES, SEQ
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10073356
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