B30011

ChIP assays were performed as previously described (Fang et al., 2015) . Briefly, 10-day-old Col-0 and ago1-36 seedlings (about 1.5 g), without or with hormone and stress treatments, were cross-linked in 1% formaldehyde for 20 min. Then the nuclei were isolated and resuspended in high salt nuclear lysis buffer (20 mM Tris-HCl, pH 7.5, 500 mM NaCl, 4 mM MgCl 2 , 0.2% NP-40, 5 mM DTT, and Roche protease inhibitor cocktail). Chromatin was sonicated to an average size of 200-500 bp using the Bioruptor (Diagenode). After centrifugation at 16,000 g for 10 min, the supernatant was diluted 5-fold with dilution buffer (20 mM Tris-HCl, pH 7.5, 4 mM MgCl 2 , 0.2% NP-40). AGO1 (Qi et al., 2005) , myc (Abcam, ab32), Pol II (Abcam, ab817), Pol II Ser2P (Abcam, ab24758), or Pol II Ser5P antibody (Abcam, ab24759) was used to immunoprecipitate the protein-DNA complex. Rabbit IgG (Abmart, B30011) or mouse IgG (Abmart, B30010) was used as a negative antibody control for IP. After reverse cross-linking, digestion by proteinase K, the enriched DNA was purified for library construction for Illumina sequencing or for qPCR. The primers are listed in Table S6.