qPCR of DNA isolated by ChIP using anti-c-myc-MuB antibody after induction of Mu replication. (a) Location of DNA segments within and outside the Mu prophage. The Mu insertion is in malF, whose direction of transcription on the E. coli genome is indicated by arrows. The L0 region spans 45 to 328 bp from the beginning of att R, whereas the R0 region spans 89 to 343 bp from the beginning of att L. L1 to L25 and R1 to R25 indicate approximate distance in kb from the Mu ends. Mu1 to Mu7 amplify the following regions in bp, the numbering starting at 1 on the att L. Mu1: 1 to 350; Mu2: 2,650 to 3,021; Mu3: 9,915 to 10,245; Mu4: 17,641 to 17,983; Mu5: 26,419 to 26,790; Mu6: 34,223 to 34,660; Mu7: 36,421 to 36,717. See Additional file 3 for primer sequences. (b) MuB binding to regions indicated in A in three Mu lysogen strains: SJG3, SJG3 Δfis and SJG3 Δhns. Real-time PCR reactions of ChIP samples and Mu copy number estimates were performed as described in Methods. MuB binding to hot (yidP), cold (rfaS) and average (ahpF) Mu insertion target genes in E. coli was monitored in parallel (see Figure 1). The log2 BBP values are the Ct difference between ChIP and mock samples for each segment. The data are an average of nine experiments: three independent biological repeats, each with three independent technical repeats. BBP = MuB binding preference.