miRNA length variation during macrophage stimulation confounds the interpretation of results: implications for miRNA quantification by RT-qPCR

Katherine A. Pillman, Gregory J. Goodall, Cameron P. Bracken, Michael P. Gantier

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)


Most microRNAs (miRNAs) are expressed as a mix of length isoforms (referred to as isomiRs). IsomiR stoichiometry can be differentially impacted upon cell stimulation, as recently evidenced by our group in the context of immune responses induced by type-I interferon (IFN). Here, we revisit published RNA-seq data sets of human and mouse macrophages stimulated with bacterial products at the isomiR level. We demonstrate that for several miRNAs, macrophage stimulation induces changes in isomiR stoichiometry. Critically, we find that changes in miRNA expression can be misinterpreted when miRNAs are quantified by RT-qPCR, as primers directed against canonical miRNA sequences may not equally target the different isomiRs that are regulated endogenously. Beyond the case of phagocyte stimulation, our analyses reinforce the concept that analysis of miRNA expression at the isoform level should become standard practice.

Original languageEnglish
Pages (from-to)232-238
Number of pages7
JournalRna-A Publication of the Rna Society
Issue number2
Publication statusPublished - 1 Feb 2019


  • Bacterial infection
  • Interferon
  • IsomiR
  • LPS
  • Macrophages
  • MicroRNA isoform
  • RT-qPCR miRNA assays

Cite this