Fig. 2. Nuclear reorganisation of the Hoxd regulatory domain in the embryo. (A) Histograms showing the 3D position of hybridisation signals for a BAC lying within the 5' flanking region (RP23-288B11, blue), a BAC covering the Lnp gene (RP24-267L11, yellow), or a Hoxd BAC (RP23-15M17, green), relative to the MMU2 CT edge in nuclei from E9.5 control tissues, tailbud or limb bud. Coloured arrowheads indicate the median location for each respective probe. n>100 loci, obtained from three embryos. (B) Mean position±s.e.m. (µm), relative to the edge of the MMU2 CT for the 5' flank (blue), Lnp (yellow) and Hoxd (green) BACs. (C) Three-dimensional DNA FISH using the Hoxd probe (red) hybridised together with a MMU2 chromosome paint (green) on DAPI counterstained nuclei of a 4 µm limb bud section from E9.5 embryo. Raw image before deconvolution. (D) Distribution of 3D interphase distances (d) in µm, measured between the Lnp and Hoxd BACs (black bars), or between the 5' flank and the Lnp BACs (white bars) in control tissues, tailbud or limb bud from E9.5 embryos. Black or white arrowheads indicate the median separation between each probe pair. In total, n>100 loci, obtained from three embryos. (E) Mean±s.e.m. interphase separation (µm), measured between Lnp and Hoxd BACs (black square), or between the 5' flank and the Lnp BAC (white squares) in control tissues, tailbud or limb bud from E9.5 embryos. (F) Three-dimensional DNA FISH with the Lnp (red) and the Hoxd (green) BACs on DAPI counterstained nuclei from E9.5 limb bud, image after deconvolution. Arrowheads point to stretched signals. (G) Histogram showing the percentage of stretched 3D FISH signals detected with the Hoxd, Lnp and 5' flank BAC probes in the control tissues, tailbud and limb bud from E9.5 embryos.