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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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APAatlas: decoding alternative polyadenylation across human tissues.

Wei Hong1, Hang Ruan1, Zhao Zhang1

  • 1Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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|October 6, 2019
PubMed
Summary

Alternative polyadenylation (APA) creates different mRNA versions affecting gene regulation. We mapped APA events in 53 human tissues, creating the APAatlas database for research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Alternative polyadenylation (APA) is a key RNA processing event influencing gene expression by generating mRNA isoforms with varying 3' untranslated region (3'UTR) lengths.
  • APA plays a critical role in post-transcriptional gene regulation, impacting mRNA translation, stability, and localization, and demonstrates significant tissue-specific patterns.
  • A comprehensive database detailing APA events across numerous human normal tissues was lacking, hindering research into its functional roles.

Purpose of the Study:

  • To systematically identify and analyze alternative polyadenylation (APA) events across a wide range of human tissues.
  • To develop a centralized, user-friendly database (APAatlas) for accessing and exploring APA event data.
  • To facilitate research into the functional implications and regulatory mechanisms of APA in human tissues.

Main Methods:

  • Utilized RNA-sequencing (RNA-seq) data from the Genotype-Tissue Expression (GTEx) project, encompassing 9475 samples from 53 human tissues.
  • Systematically identified and characterized APA events within these diverse tissue samples.
  • Developed and curated the APAatlas database, providing tools for searching, browsing, and downloading APA-related information.

Main Results:

  • Successfully identified a large number of APA events across 53 distinct human tissues.
  • Examined the associations between APA events and various biological traits, as well as gene expression patterns across tissues.
  • Launched APAatlas, a publicly accessible database offering comprehensive APA data for human tissues.

Conclusions:

  • The comprehensive mapping of APA events and the creation of APAatlas provide a valuable resource for the scientific community.
  • APAatlas enables researchers to investigate the functional significance and regulatory roles of APA events in human health and disease.
  • This work significantly advances the understanding of post-transcriptional regulation mediated by APA in a tissue-specific context.