High-throughput characterization of primary microRNA transcripts

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations


Proper control of microRNA (miRNA) expression is critical for normal development and physiology, while abnormal miRNA expression is a common feature of many diseases. Dissecting mechanisms of miRNA regulation, however, is complicated by the generally poor annotation of miRNA primary transcripts (pri-miRNAs). Although some miRNAs are processed from well-defined protein coding genes, the majority of pri-miRNAs are poorly characterized noncoding RNAs, with incomplete annotation of promoters, splice sites, and polyadenylation signals. Due to the efficiency of DROSHA processing, the abundance of pri-miRNAs is very low at steady state, thereby complicating the elucidation of pri-miRNA structures. Here we describe a strategy to enrich intact pri-miRNAs and improve their coverage in RNA sequencing (RNA-seq) experiments. In addition, we outline a computational approach for reconstruction of pri-miRNA structures. This pipeline begins with raw RNA-seq reads and concludes with publication-ready visualization of pri-miRNA annotations. Together, these approaches allow the user to define and explore miRNA gene structures in a cell-type or organism of interest.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages9
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • microRNA
  • pri-miRNA
  • Primary transcript
  • RNA-seq
  • Transcriptome assembly

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Chang, T. C., & Mendell, J. T. (2018). High-throughput characterization of primary microRNA transcripts. In Methods in Molecular Biology (pp. 1-9). (Methods in Molecular Biology; Vol. 1823). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8624-8_1