Chromosome conformation capture (3C) mapping of long-range chromatin interactions in the Kcnq1 region in neonatal tissues. (A) Genomic organization of the Kcnq1 region scanned in this study, spanning 387 kb. Dark boxes in the Kcnq1 gene are exons. Arrows show direction of transcription; maternal-specific and paternal-specific expression is indicated above and below the line. Reactivated Kcnq1 expression is depicted as a red arrow. Vertical bars indicate only the Afl III/Nco I restriction sites analyzed in this study, with the fragments assayed by the variable primers for contact with the Kcnq1 promoter numbered. White arrowhead indicates the anchor primer at the Kcnq1 promoter. Graphical representation is not to scale. (B,C) Relative crosslinking frequency of regions interacting with the Kcnq1 promoter, with association values plotted on the y-axis. Distances in kb relative to the Kcnq1 promoter are plotted along the x-axis (not to scale). Each value is derived from three independent samples and the standard error is indicated. Hatched vertical line represents the anchor position. High crosslinking frequencies with the anchor fragment indicate close proximity. (B) 3C map of neonatal heart and brain. (C) Reciprocal 3C analysis of heart-specific interactions in the Kcnq1 region by anchoring the PCR reactions at fragment 12 (intron 1).