Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls

Huifen Cao, Claes Wahlestedt, Philipp Kapranov

Research output: Contribution to journalReview articlepeer-review

44 Scopus citations


The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.

Original languageEnglish (US)
Pages (from-to)704-721
Number of pages18
JournalTrends in Genetics
Issue number9
StatePublished - Sep 2018


  • challenges to lncRNA annotation
  • functional annotation of lncRNAs
  • integrative approach to lncRNA annotation
  • lncRNAs
  • methods to analyze lncRNA function
  • unique features of lncRNAs

ASJC Scopus subject areas

  • Genetics


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