SRA

Canonically, Arabidopsis RNA Polymerase IV (Pol IV) is known to produce heterochromatic small RNAs (typically 23-24 nucleotide in length) that maintain silencing of transposable elements (TEs). In contrast, when TEs are transcriptionally activated and produce Pol II transcripts, these transcripts are degraded into 21-22 nt small RNAs (sRNAs) known to participate in post transcriptional gene silencing. Recently, it was reported that Pol IV can also produce 21-22 nt sRNAs in pollen. We investigated the mechanism of Pol IV dependent 21-22 nt sRNAs and show that this mechanism is not specific to pollen. Additionally, we show that these 21-22 nt sRNAs can participate in RNA-directed DNA methylation, are incorporated into ARGONAUTE 1 (AGO1) and may guide AGO1 to cleave genic mRNAs to regulate their expression. Overall design: Examination of total small RNA accumulation in wild-type Columbia and eight mutants. AGO1 protein was immunoprecipitated and small RNAs incorporated in AGO1 was sequenced in wild-type Columbia and pol IV mutant. Whole genome methylC-seq was performed for two mutants.