title: Dicer-processed small RNAs: rules and exceptions.
abstract: 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 Friedländer et al. [Friedländer et al., 2012, Nucleic Acids Res 40:37-52]. 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.
authors.affiliation: LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Langenberger
authors.forename: M Volkan
authors.initials: MV
authors.lastname: Çakir
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism*; D004258:DNA Polymerase III / Q000378:metabolism; D055785:Gene Knockdown Techniques; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000378:metabolism*; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D004258:DNA Polymerase III; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases