Strategies to identify long noncoding RNAs involved in gene regulation

Catherine Lee, Nobuaki Kikyo

Research output: Contribution to journalReview articlepeer-review

58 Scopus citations


Long noncoding RNAs (lncRNAs) have been detected in nearly every cell type and found to be fundamentally involved in many biological processes. The characterization of lncRNAs has immense potential to advance our comprehensive understanding of cellular processes and gene regulation, along with implications for the treatment of human disease. The recent ENCODE (Encyclopedia of DNA Elements) study reported 9,640 lncRNA loci in the human genome, which corresponds to around half the number of protein-coding genes. Because of this sheer number and their functional diversity, it is crucial to identify a pool of potentially relevant lncRNAs early on in a given study. In this review, we evaluate the methods for isolating lncRNAs by immunoprecipitation and review the advantages, disadvantages, and applications of three widely used approaches - microarray, tiling array, and RNA-seq - for identifying lncRNAs involved in gene regulation. We also look at ways in which data from publicly available databases such as ENCODE can support the study of lncRNAs.

Original languageEnglish (US)
Article number37
JournalCell and Bioscience
Issue number1
StatePublished - Nov 6 2012

Bibliographical note

Funding Information:
We thank Michael Franklin for critical reading of the manuscript. This work was supported by Engdahl Funds, the Office of the Vice President for Research of the University of Minnesota, and the National Institutes of Health (R01 GM098294) to N.K.


  • Immunoprecipitation
  • Long noncoding RNA
  • Microarray
  • RNA-seq
  • Tiling array


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