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3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.

Loredana Le Pera1, Mariagiovanna Mazzapioda2, Anna Tramontano3

  • 1Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.

Bioinformatics (Oxford, England)
|January 25, 2015
PubMed
Summary

3USS identifies novel alternative 3' untranslated regions (UTRs) in RNA sequencing data. This tool helps researchers discover new regulatory elements affecting gene expression by analyzing variations in 3'UTR length.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Protein-coding genes can produce mRNA 3'UTR sequences of varying lengths due to alternative polyadenylation sites.
  • These length variations can lead to the loss or gain of regulatory elements, impacting mRNA stability, localization, and translation efficiency.

Purpose of the Study:

  • To develop a web-server, 3USS, for the automated identification of alternative 3'UTRs.
  • To provide researchers with a tool to detect 3'UTRs not present in existing databases.

Main Methods:

  • The 3USS web-server analyzes RNA sequencing data to identify alternative 3'UTRs.
  • It compares sequences against a reference transcriptome to detect shorter or longer variants.
  • The tool can also identify common and specific alternative 3'UTRs when data from two related samples are uploaded.

Main Results:

  • 3USS automatically identifies alternative 3'UTRs, including those not annotated in current databases.
  • It enables the comparison of alternative 3'UTRs between related samples, highlighting commonalities and differences.

Conclusions:

  • 3USS offers a valuable resource for experimentalists to discover novel alternative 3'UTRs.
  • The tool enhances standard RNA-seq analysis by providing insights into regulatory element variations and their potential impact on gene expression.