Real-time expression profiling of microRNA precursors in human cancer cell lines

Nucleic Acids Res. 2005 Sep 28;33(17):5394-403. doi: 10.1093/nar/gki863. Print 2005.


Our previous study described a real-time PCR method to quantify microRNA (miRNA) precursors using SYBR green detection [T. D. Schmittgen, J. Jiang, Q. Liu and L. Yang (2004) Nucleic Acids Res., 32, e43]. The present study adapted the assay to a 384-well format and expanded it to include primers to 222 human miRNA precursors. TaqMan minor groove binder probes were used to discriminate nearly identical members of the let-7 family of miRNA isoforms. The miRNA precursor expression was profiled in 32 human cell lines from lung, breast, colorectal, hematologic, prostate, pancreatic, and head and neck cancers. Some miRNA precursors were expressed at similar levels in many of the cell lines, while others were differentially expressed. Clustering analysis of the miRNA precursor expression data revealed that most of the cell lines clustered into their respective tissues from which each cell line was ostensibly derived. miRNA precursor expression by PCR paralleled the mature miRNA expression by northern blotting for most of the conditions studied. Our study provides PCR primer sequences to all of the known human miRNA precursors as of December 2004 and provides a database of the miRNA precursor expression in many commonly used human cancer cell lines.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Cell Line, Tumor*
  • DNA Primers
  • Fluorescent Dyes
  • Gene Expression Profiling
  • Humans
  • MicroRNAs / biosynthesis*
  • MicroRNAs / chemistry
  • Molecular Sequence Data
  • Nucleic Acid Probes
  • Polymerase Chain Reaction / methods*
  • Proteins
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism*
  • RNA, Neoplasm / biosynthesis*
  • RNA, Neoplasm / chemistry
  • Time Factors


  • DNA Primers
  • Fluorescent Dyes
  • MicroRNAs
  • Nucleic Acid Probes
  • Proteins
  • RNA Precursors
  • RNA, Neoplasm
  • mirnlet7 microRNA, human