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Quantification of non-coding RNA target localization diversity and its application in cancers

Lixin Cheng1, Kwong-Sak Leung1

  • 1Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.

Journal of Molecular Cell Biology
|February 2, 2018
PubMed

Insights

We developed ncTALENT to measure non-coding RNA (ncRNA) target localization diversity. High diversity in ncRNA targets is linked to cancer and impacts clinical prognosis.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Subcellular localization is crucial for RNA and protein function.
  • Protein interaction localization diversity is studied, but ncRNA target protein localization diversity is not.
  • Understanding ncRNA target localization is vital, especially in cancer.

Purpose of the Study:

  • To develop a novel algorithm, ncTALENT, to quantify ncRNA target localization diversity.
  • To investigate the characteristics of target localization diversity in long non-coding RNAs (lncRNAs).
  • To explore the association between lncRNA target localization diversity and cancer.

Main Methods:

  • Developed the non-coding RNA target localization coefficient (ncTALENT) algorithm.
  • Utilized ncRNA-protein interaction and protein subcellular localization data.
  • Analyzed lncRNAs across different biotypes and in various cancer contexts.

Main Results:

  • ncTALENT quantifies how diversely ncRNA targets are distributed across subcellular locations.
  • Target localization diversity is a key characteristic of lncRNAs.
  • lncRNAs implicated in cancer, differentially expressed cancer lncRNAs, and those with multiple cancer targets exhibit higher diversity.
  • lncRNA target localization diversity is associated with clinical prognosis in gastric cancer.

Conclusions:

  • ncTALENT provides a novel metric for assessing ncRNA target localization diversity.
  • Target localization diversity is an intrinsic feature of lncRNAs with implications in cancer.
  • This diversity is linked to cancer development and patient outcomes, particularly in gastric cancer.

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