ncRNA Editing: Functional Characterization and Computational Resources

  • Giovanni NigitaEmail author
  • Gioacchino P. Marceca
  • Luisa Tomasello
  • Rosario Distefano
  • Federica Calore
  • Dario Veneziano
  • Giulia Romano
  • Serge Patrick Nana-Sinkam
  • Mario Acunzo
  • Carlo M. Croce
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)


Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.

Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.

In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.

Key words

A-to-I RNA editing ncRNA editing 3′UTR Introns miRNA lncRNA Bioinformatics NGS 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Giovanni Nigita
    • 1
    Email author
  • Gioacchino P. Marceca
    • 1
    • 2
  • Luisa Tomasello
    • 1
  • Rosario Distefano
    • 1
  • Federica Calore
    • 1
  • Dario Veneziano
    • 1
  • Giulia Romano
    • 3
  • Serge Patrick Nana-Sinkam
    • 3
  • Mario Acunzo
    • 3
  • Carlo M. Croce
    • 1
  1. 1.Department of Cancer Biology and Genetics, Comprehensive Cancer CenterThe Ohio State UniversityColumbusUSA
  2. 2.Department of Clinical and Experimental MedicineUniversity of CataniaCataniaItaly
  3. 3.Division of Pulmonary Diseases and Critical Care MedicineVirginia Commonwealth UniversityRichmondUSA

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