PT  - JOURNAL ARTICLE
AU  - Feng Wang
AU  - Michael J. Axtell
TI  - AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in <em>Arabidopsis thaliana</em>
AID  - 10.1101/078394
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 078394
4099  - http://biorxiv.org/content/early/2016/09/30/078394.short
4100  - http://biorxiv.org/content/early/2016/09/30/078394.full
AB  - In plants, 24 nucleotide long heterochromatic siRNAs (het-siRNAs) transcriptionally regulate gene expression by RNA-directed DNA methylation (RdDM). The biogenesis of most het-siRNAs depends on the plant-specific RNA polymerase IV (Pol IV), and ARGONAUTE4 (AGO4) is a major het-siRNA effector protein. Through genome-wide analysis of sRNA-seq data sets, we found that AGO4 is required for the accumulation of a small subset of het-siRNAs. The accumulation of AGO4-dependent het-siRNAs also requires several factors known to participate in the effector portion of the RdDM pathway, including RNA POLYMERASE V (POL V), DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and SAWADEE HOMEODOMAIN HOMOLOG 1 (SSH1). Like many AGO proteins, AGO4 is an endonuclease that can ‘slice’ RNAs. We found that a slicing-defective AGO4 was unable to fully recover AGO4-dependent het-siRNA accumulation from ago4 mutant plants. Collectively, our data suggest that AGO4-dependent siRNAs are secondary siRNAs dependent on the prior activity of the RdDM pathway at certain loci.