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Dicer-processed small RNAs: Rules and exceptions

: Langenberger, David; Cakir, M. Volkan; Hoffmann, Steve; Stadler, Peter F.


Journal of experimental zoology. Part B, Molecular and developmental evolution 320B (2013), Nr.1, S.35-46
ISSN: 0022-104X
ISSN: 1552-5007
ISSN: 1552-5015
Deutsche Forschungsgemeinschaft DFG
SPP 1258; STA 850/7-2
Fraunhofer IZI ()

Canonical microRNAs are excised from their hairpin-shaped precursors by Dicer. In order to find possible exceptions to this rule and to identify additional substrates for Dicer processing we re-evaluate the small RNA sequencing data of the Dicer knockdown experiment in MCF-7 cells orignally published by Friedlander et al. [Friedlander et al., 2012, Nucleic Acids Res 40:3752]. While the well-known non-Dicer mir-451 is not sufficiently expressed in these experiments, there are several additional Dicer-independent microRNAs, among them the important tumor supressor mir-663a. We recover previously described examples of non-miRNA Dicer substrates such as tRNA-Gln and several snoRNAs. Interestingly, sdRNAs derived from box C/D snoRNAs are Dicer-independent, while those derived from box H/ACA snoRNAs are often Dicer dependent. Several pol-III transcripts, in particular the vault RNAs and the great ape specific snaRs are processed by Dicer, while the small RNAs originating from Y RNAs seem to be Dicer independent.