CO-FISH to measure recombination rates at minor satellite sequences. (a) A scheme of mouse minor satellite repeats and telomere repeats is shown indicating the position of the CENP-B box (bp 62–78). PNA probes are also indicated. (b) A diagram explaining the CO-FISH procedure is shown. Cells are allowed to replicate once in the presence of BrdU, giving rise to chromosomes with one BrdU-containing chromatid (dashed line). The BrdU-containing DNA strand is digested and single-stranded minor satellite probes against the lagging (red) or the leading (green) strand are hybridized to the remaining non–BrdU-labeled strand. Cen-CO-FISH labels centromeric minor satellite sequences from the lagging or leading strand. An SCE within minor satellite sequences (C-SCE) will lead to two unequal signals per chromosome after hybridization with either the leading or lagging single-stranded probes. (c) Representative Cen-CO-FISH images showing no recombination (top) or a C-SCE after hybridization with the leading and lagging minor satellite PNA probes (bottom). Bars, 1 μm.