Deep annotation of mouse iso-miR and iso-moR variation

With a dataset of more than 600 million small RNAs from mouse hippocampal and staged sets of cells that underwent reprogramming to induced pluripotent stem cells, we annotated the stem–loop precursors of known mouse miRNAs were annotated to identify moRs, loops, non-preferred strands, and guide strands. Products from both strands are readily detectable for most miRNAs. Some miRNAs switched the preferred strand between cell types. We detected significant variation among isomiRs; however, the terminal nucleotide of the dominant isomiR aligned with the dominant off-set sequence suggesting that Drosha cleavage generates most miRNA reads without terminal modification. Among the terminal modifications detected, most were non-templated mono- or di-nucleotide additions to the 3’ end. Based on the relative enrichment or depletion of certain nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading. We identified those miRNAs with abundant secondary isomiRs, which could regulate different sets of targets and detected miRNAs that switched the dominant isomiRs among samples. Sequence variation of the two strands at their cleavage sites and showed higher fidelity of Drosha than Dicer. These studies demonstrate multiple patterns of miRNA processing and considerable versatility in miRNA target selection.