Significance
MicroRNAs (miRNAs) have important functions in development and cell physiology. The vast majority of mature miRNAs are produced from primary transcripts of microRNAs (pri-miRNAs) by a multi-step pathway. The first step, cleavage of pri-miRNAs by the Microprocessor complex, is highly regulated but technically challenging to study. We have developed a robust method that faithfully measures pri-miRNA processing efficiency in live cells. Using this assay, we establish an essential function of heme in miRNA maturation, a provocative idea suggested by previous biochemical studies. Our study reveals a previously unknown cellular function of this central biological cofactor, linking metal ion biology with the regulation of noncoding RNAs. Our method should be widely useful for studying RNA processing in biology and diseases.