Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes

The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.

Automated summary

The human genome contains various noncoding transcripts that have been traditionally categorized into long or small based on their lengths. However, the functions and biological significance of most of these transcripts are still unknown. In this study, a high-throughput assay was developed to test the functionality of small noncoding RNAs (sncRNAs) by overexpressing them in human cells. Surprisingly, a significant fraction of unannotated sncRNAs were found to have biological relevance, challenging the assumption that they are merely degradation products. These findings suggest the potential existence of multiple functional sncRNAs in the small noncoding transcriptome.