An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!

  • Hsiao-Lin V. Wang
  • Julia A. Chekanova
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)


The discovery of pervasive transcription in eukaryotic genomes provided one of many surprising (and perhaps most surprising) findings of the genomic era and led to the uncovering of a large number of previously unstudied transcriptional events. This pervasive transcription leads to the production of large numbers of noncoding RNAs (ncRNAs) and thus opened the window to study these diverse, abundant transcripts of unclear relevance and unknown function. Since that discovery, recent advances in high-throughput sequencing technologies have identified a large collection of ncRNAs, from microRNAs to long noncoding RNAs (lncRNAs). Subsequent discoveries have shown that many lncRNAs play important roles in various eukaryotic processes; these discoveries have profoundly altered our understanding of the regulation of eukaryotic gene expression. Although the identification of ncRNAs has become a standard experimental approach, the functional characterization of these diverse ncRNAs remains a major challenge. In this chapter, we highlight recent progress in the methods to identify lncRNAs and the techniques to study the molecular function of these lncRNAs and the application of these techniques to the study of plant lncRNAs.

Key words

High-throughput methods RNA methods Noncoding RNAs lncRNAs Plant lncRNAs RNA secondary structures RNA interactions 


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Copyright information

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

Authors and Affiliations

  • Hsiao-Lin V. Wang
    • 1
    • 2
  • Julia A. Chekanova
    • 1
  1. 1.Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanningChina
  2. 2.Present address: Department of BiologyEmory UniversityAtlantaUSA

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