Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF

MicroRNAs are ∼22-nucleotide RNAs processed from primary transcripts and exported from the nucleus to repress gene expression by base-pairing to mRNAs. Surprisingly, we find that the highest levels of RNA Polymerase II (Pol II) at human microRNA genes are within the ribosomal gene repeat arrays (rDNAs). Alignment of public nascent transcript data to the hs1 human genome assembly reveals a 50-nucleotide transcript for both miR-1275 and miR-6724, which exits from the nucleus with exceptional rapidity. We show that the miR-1275/miR-6724 transcription unit is closely flanked by CCCTC-binding factor (CTCF) within a <400-bp span of the rDNA spacer promoter. MiR-1275/miR-6724 and microRNA precursors expressed from the 5’ External Transcribed Spacer (5’ETS) are exported independently of known RNA processing activities and are detected in exosomes and as circulating cancer biomarkers. We propose that Pol II-generated rDNA spacer promoter and 5’ETS microRNA genes have evolved for general regulatory functions in recipient cells.