title: Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides.
abstract: Endogenous short RNAs (esRNAs) play diverse roles in eukaryotes and usually are produced from double-stranded RNA (dsRNA) by Dicer. esRNAs are grouped into different classes based on biogenesis and function but not all classes are present in all three eukaryotic kingdoms. The esRNA register of fungi is poorly described compared to other eukaryotes and it is not clear what esRNA classes are present in this kingdom and whether they regulate the expression of protein coding genes. However, evidence that some dicer mutant fungi display altered phenotypes suggests that esRNAs play an important role in fungi. Here, we show that the basal fungus Mucor circinelloides produces new classes of esRNAs that map to exons and regulate the expression of many protein coding genes. The largest class of these exonic-siRNAs (ex-siRNAs) are generated by RNA-dependent RNA Polymerase 1 (RdRP1) and dicer-like 2 (DCL2) and target the mRNAs of protein coding genes from which they were produced. Our results expand the range of esRNAs in eukaryotes and reveal a new role for esRNAs in fungi.
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors.forename: Francisco Esteban
authors.initials: FE
authors.lastname: Nicolas
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Juan P
authors.initials: JP
authors.lastname: de Haro
authors.forename: Silvia
authors.initials: S
authors.lastname: Calo
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: Santiago
authors.initials: S
authors.lastname: Torres-Martínez
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Ruiz-Vázquez
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
mesh_terms: D005091:Exons; D015966:Gene Expression Regulation, Fungal; D020071:Interspersed Repetitive Sequences; D035683:MicroRNAs / Q000235:genetics; D009089:Mucor / Q000201:enzymology / Q000235:genetics*; D009154:Mutation; D012331:RNA, Fungal / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000096:biosynthesis; D022661:RNA, Untranslated / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012331:RNA, Fungal; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; D012324:RNA-Dependent RNA Polymerase; D043244:Ribonuclease III