Figure 2

Palindrome mapping strategy. (A) Read density distribution in Chr15q21.1: 47,529,204-47,550,373 region shown as 1 kb bins. (B) qPCR analysis to monitor for palindrome enrichment and determine the directionality of the Chr15q21.1 palindrome. We calculated the amount of depletion of a specific TaqMan primer set region based on Ct value before and after GAPF protocol in both IMR-90 and MCF-7 samples. The fold enrichment is based on comparing the fold depletion among different primer sets (P1, P2, P3 and P4) relative to a single copy sequence in the genome (RAD52). The location of TaqMan primer sets P1, P2, P3 and P4 is indicated in Figure 2C. (C) Map of genomic region Chr15: 47,520,000-47,550,000 with restriction sites and primer locations. (D) Southern blot analysis. Genomic DNA IMR-90 and MCF-7 cells was digested with BamHI, BglII or NcoI. Asterisks (*) mark the rearranged bands from MCF-7 genomic DNA. (E) Snap-back (SB) southern blots of BamHI digested IMR-90 and MCF-7 DNA. Arrowhead indicates the half sized fragments after snap-back in MCF-7. (F) Inversion-PCR. Three primers all from the same strand in normal genomic DNA were used for PCR (Primers 1–3). Since primers 1 and 2 are located in the palindromic region, they can also be used as reverse primers. Because primer 3 is in the spacer, it is able to produce a PCR product with primer 1 or 3 containing the novel junction “J” as indicated in the figure.