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Impact of two RNaseIII-like protein on the small RNA repertoire

ABSTRACT: RNaseIII enzymes catalyze the cleavage of double stranded RNA (dsRNA) and have diverse functions in RNA maturation. Arabidopsis RNASE THREE LIKE2 (RTL2) carries one RNaseIII and two dsRNA-binding (DRB) domains, and is the unique Arabidopsis RNAse III enzyme resembling the budding yeast siRNA-producing Dcr1 enzyme. Here we show that RTL2 modulates the production of siRNAs, and that this activity depends on both RNaseIII and DRB domains. However, RTL2 mode of action differs from that of Dcr1. Indeed, whereas Dcr1 directly cleaves dsRNAs into 23-nt siRNAs, RTL2 likely cleaves dsRNAs into molecules longer than siRNAs, which are subsequently processed by the DCL enzymes. Depending on the dsRNA considered, RTL2-mediated maturation either improves (RTL2- dependent loci) or reduces the efficiency of DCL processing (RTL2-sensitive loci). Because the vast majority of plant small RNAs are 24-nt siRNAs that guide DNA methylation at transposons and intergenic regions, RTL2 depletion mostly modifies DNA methylation in these regions. Nevertheless, 13% of the siRNA-producing loci affected by RTL2 depletion correspond to protein coding genes. We show that changes in 24-nt siRNA levels also affect DNA methylation levels at such loci, and inversely correlate with mRNA steady-state levels, thus implicating RTL2 in the control of protein-coding gene expression.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE71782 | GEO | 2015/10/01

SECONDARY ACCESSION(S): PRJNA292074

REPOSITORIES: GEO

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