a Relative enrichment analysis by R-ChIP from wild-type or transiently transformed plants. WT: wild-type plants; TT: transiently transformed plants.The relative enrichment was calculated as 2 −(ΔCT 1−ΔCT 2). ΔCT 1: The Ct of the studied (isolated) DNA subtracted from the Ct of the internal control DNA in the products of R-ChIP. ΔCT 2: The Ct of DNA of studied (isolated) subtracted from the Ct of the internal control DNA in the input sample. The promoter region of AtCAT3 used for the qPCR evaluation was site 1 and is shown in in Fig. 7l and Supplementary Data 4. The promoter of AtActin3 (which is far away from the promoter of AtCAT3) was used as the internal control. Three replicates (sample size of 500 seedlings) were performed (n = 3 experiments). Error bar indicates standard deviations of the mean measurements. Asterisks indicate highly significant difference between two samples (**P < 0.01, t-test). b SDS-PAGE analysis of the proteins captured using R-ChIP. Lanes 1–3: the proteins isolated from wild-type plants from three biological replicates, respectively. Lanes 4–6: the proteins isolated from transient transformed plants from three biological replicates, respectively. The proteins were stained with silver nitrate.