Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
Fig 2
Greatly expanded annotations of human and mouse mirtrons.
(A) Numbers of splicing-derived miRNAs in human and mouse, categorized as conventional, 5'-tailed, 3'-tailed, and two-tailed mirtrons. Most of the miRNAs newly annotated in this study were 5'-tailed mirtrons, reflecting their status as the dominant mirtron class in human and mouse. (B) Few mirtrons were annotated from small RNA data in both mouse and human, and only a subset of these were constrained in primary sequence. (C, D) Human and mouse mirtrons are generally modestly expressed, but were annotated to higher levels of evidence than hundreds of human and mouse miRNAs in the miRBase registry (i.e. that have <50 reads in the aggregate data analyzed in this study). Most mirtrons were supported by evidence from Ago-IP datasets (red bars). (E, F) Cumulative distribution function (CDF) plots of enrichment of canonical miRNAs and mirtron-derived miRNAs in Ago complexes. (E) Analysis of human small RNAs. Rat RmC was used as control IP; since Ago4 is not expressed in HeLa cells, it effectively serves as another control IP. Canonical miRNAs were enriched in Ago1-3-IP data as well as input RNA (which is mostly composed of Ago-bound miRNAs), relative to control IP data. Mirtron-derived small RNAs showed similar Ago-IP enrichment, except that they also exhibited enrichment between Ago1-3-IP and input RNA libraries. (F) Analysis of mouse small RNAs shows similar enrichment of canonical miRNAs and mirtron-derived small RNAs in Ago1 and Ago2 complexes relative to control IgG complex.