• miRNA;
  • microarray;
  • Notch;
  • Hedgehog;
  • cyclopamine;
  • DAPT


microRNAs (miRNAs) are small (∼22 nucleotide) non-coding RNAs that regulate gene expression at the post-transcriptional level, typically by inhibiting translation. The genes encoding these small RNAs are estimated to comprise approximately 2–3% of animal genomes yet potentially regulate a majority of protein-coding genes including those involved in cell specification and development. A key remaining question is to identify target mRNAs regulated by microRNAs. As a means to identify potential targets, we designed a sensitive microarray to analyze global miRNA expression patterns at twelve developmental stages in zebrafish. Further, we conducted arrays on zebrafish embryos treated with small molecule inhibitors of the Hedgehog and Notch signaling pathways to enable identification of differentially expressed miRNAs that target genes controlling key developmental pathways during early embryogenesis. Developmental Dynamics 236:2172–2180, 2007. © 2007 Wiley-Liss, Inc.