Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs.

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Authors
Valli, Adrian A 
Santos, Bruno ACM 
Hnatova, Silvia 
Bassett, Andrew R 
Molnar, Attila 
Abstract

We describe here a forward genetic screen to investigate the biogenesis, mode of action, and biological function of miRNA-mediated RNA silencing in the model algal species,Chlamydomonas reinhardtii Among the mutants from this screen, there were three at Dicer-like 3 that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell into several classes including transposon- and repeat-derived siRNAs as in higher plants. The DCL3-dependent miRNAs differ from those of higher plants, however, in that many of them are derived from mRNAs or from the introns of pre-mRNAs. Transcriptome analysis of the wild-type and dcl3 mutant strains revealed a further difference from higher plants in that the sRNAs are rarely negative switches of mRNA accumulation. The few transcripts that were more abundant in dcl3 mutant strains than in wild-type cells were not due to sRNA-targeted RNA degradation but to direct DCL3 cleavage of miRNA and siRNA precursor structures embedded in the untranslated (and translated) regions of the mRNAs. Our analysis reveals that the miRNA-mediated RNA silencing in C. reinhardtii differs from that of higher plants and informs about the evolution and function of this pathway in eukaryotes.

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Keywords
Chlamydomonas reinhardtii, Chromosome Mapping, Gene Expression Regulation, Plant, Introns, MicroRNAs, Mutation, RNA Interference, Ribonuclease III, Untranslated Regions
Journal Title
Genome Res
Conference Name
Journal ISSN
1088-9051
1549-5469
Volume Title
26
Publisher
Cold Spring Harbor Laboratory
Sponsorship
Wellcome Trust (096082/Z/11/Z)
European Research Council (340642)
Work in the Baulcombe laboratory is supported by the Balzan Prize award and the ERC Advanced Investigator Grant ERC-2013-AdG 340642 TRIBE. AAV was supported by a Marie-Curie fellowship (PIEF-GA-2010-276037). BYC was supported by an EMBL long-term postdoctoral fellowship and a Sir Henry Wellcome Fellowship (096082). DCB is the Royal Society Edward Penley Abraham Research Professor.