The human genome encodes a multitude of novel miRNAs

Human cells generate a vast complexity of noncoding RNAs, the "RNA dark matter," which includes a vast small RNA (sRNA) transcriptome. The biogenesis, biological relevance, and mechanisms of action of most of these transcripts remain unknown, and they are widely assumed to represent degradation products. Here, we aimed to functionally characterize human sRNA transcriptome by attempting to answer the following question-can a significant number of novel sRNAs correspond to novel members of known classes, specifically, microRNAs (miRNAs)? By developing and validating a miRNA discovery pipeline, we show that at least 2726 novel canonical miRNAs, majority of which represent novel miRNA families, exist in just one human cell line compared to just 1914 known miRNA loci. Moreover, potentially tens of thousands of miRNAs remain to be discovered. Strikingly, many novel miRNAs map to exons of protein-coding genes emphasizing a complex and interleaved architecture of the genome. The existence of so many novel members of a functional class of sRNAs suggest that the human sRNA transcriptome harbors a multitude of novel regulatory molecules. Overall, these results suggest that we are at the very beginning of understanding the true functional complexity of the sRNA component of the "RNA dark matter."