R-ChIP signal at annotated genes is lower in SETX-depleted cells and correlates with overall transcript level. (A and B) Wild-type or SETX KO U2OS cells expressing catalytically inactive RNaseH were used to perform R-ChIP with quantification by qPCR at the SNPRN and beta-actin loci (A) or two regions within the rDNA IGS (B). Three biological replicates were analyzed for each condition with Flag antibody (+Ab) as well as in the absence of antibody (−Ab). * indicates P < 0.05 or *P < 0.005 by two-sample unpaired t test. (C) R-ChIP signal from two biological replicates was quantified for each annotated gene in the promoter region (1,000 nt upstream of transcription start through 500 nt downstream) and plotted against transcript level for the gene in U2OS wild-type and SETX knock-out cell lines as indicated. Genes were grouped into bins according to transcript abundance in each cell line with the average R-ChIP signal and corresponding transcript abundance level shown.