Fig. 2

Transcript profiles at the HoxD locus in both control (Wt) and del(attP-Rel5)d9lac-mutant limb buds. a, b Normalized RNA-seq profiles of control (Wt) and mutant proximal (a) and distal (b) limb cells. Values from forward (red) and reverse (blue) strands are merged into the same graph. The positions of various genes and of Island3 are shown below. The dashed rectangles depict the del(attP-Rel5)d9lac deletion. The isolated signal around Hoxd9 in the second tracks in a and b arises from the Hoxd9/lacZ reporter transgene present in the mutant line. The scale is set such that changes in non-coding regions can be better observed. n = 3. c WISH of Island3 eRNA in both del(attP-Rel5)d9lac and wild-type E12.5 forelimbs. qPCR values (mean ± SD) are shown on the top of each image. n = 6 for Wt and n = 4 for del(attP-Rel5)d9lac. d Schemes of the various deleted regions of the mutant lines used in a to e. e qPCR of Island3 eRNAs in E12.5 distal limb cells in two distinct partial deletions of the 5′-TAD. The mutant lines used were del(SB1-Atf2) (n = 4) and del(Rel1-Rel5) (n = 9), both balanced by the del(Rel5-Atf2) allele (where Island3 is deleted, abbreviated by Δ in the legend). Results were compared to del(Rel5-Atf2)/+ samples as controls (white bar, n=12). Bars show mean ± SD. Welch’s t test **p = 0.0026 and ***p < 0.0001