Figure S4: Pol IV 21-22 nt siRNAs are enriched in AGO1 from Arabidopsis RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

sRNA accumulation from different loci is shown in total, AGO1-IP or negative control mock-IP samples in wt Col inflorescence tissue. A) High enrichment of all miRNAs in AGO1-IP vs mock-IP. B) and C) Positive controls miR166 and miR171 [45] show high enrichment of specific mature miRNA in AGO1. D) miRNA 390a is known to be incoporated specifically into AGO7 and not AGO1 [45,46] and is shown here as a negative control demonstrating no enrichment of mature miRNA in AGO1-IP vs mock. E) Only a subset of 24 nt sRNA from Pol IV 24 nt clusters are incorporated into AGO1-IP (AGO1-IP/total < 0.2) but the ones that do are enriched compared to mock (AGO1-IP- /mock IP > 2). and F) 21-22 nt sRNAs from Pol IV 21-22 nt clusters show genome-wide enrichment into AGO1 (AGO1-IP/total > 2) like all miRNAs in A. AGO1-IP/mock enrichment (>3) is not as high as miRNAs but higher than the negative control miR390a. Together these data demonstrate that Pol IV-dependent 21-22 nt sRNAs are incorporated into AGO1.