A noncanonical Pol III-dependent, Microprocessor-independent biogenesis pathway generates a germline enriched miRNA family

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression and play critical roles in development and differentiation. In canonical miRNA biogenesis, primary miRNAs are transcribed from intergenic loci or intronic regions by RNA polymerase II, sequentially cleaved by the Microprocessor complex and Dicer, and resulting mature miRNAs are loaded into Argonaute to repress target mRNAs. A minority of miRNAs are generated via noncanonical biogenesis pathways that bypass the Microprocessor and/or Dicer. Here, we describe a new Pol III-dependent, Microprocessor-independent, and Dicer-dependent biogenesis pathway exemplified by the mir-1829 family in C. elegans. The mir-1829 family is germline enriched and resides in unusually long introns of three host genes that have no apparent overlapping functions. Using multiple approaches, we determined that the mir-1829 family is derived from independent Pol III transcripts with consistent transcription start sites. Unlike other Pol III-dependent miRNAs, the mir-1829 family small RNAs are the dominant species derived from their loci, rather than fragments of a larger functional noncoding RNA. We extend these findings, identifying additional Pol III-transcribed and noncanonical miRNAs in C. elegans and human datasets. These young, noncanonical miRNAs may represent an early snapshot in the evolution of de novo miRNA genes.