RNA–seq profiles of control and HoxC mutant mice.
RNA was extracted from the region enriched in mHotair transcripts at day 13.5, i.e. the posterior part of the fetus, including the tail, hindlimbs and the outgrowing genitalia. Plotted are mean values of 25 bp windows. (A) Transcription profiles of the four different Hox gene clusters. The positions of the genes are indicated below. (A) Expression profiles of all four Hox loci, shown with the orientation with respect to the centromers. The strong peak in the deleted HoxC cluster is a transcript induced over the second exon of Hoxc4 (non-deleted) after deletion of the cluster (see the text). (B) Examples of transcriptional variations induced by the deletion of the HoxC cluster, with some genes being slightly up-regulated (Hoxa7, Hoxb9, Hoxd10 and Wsb1), some being down-regulated (Igf2r, Slc15a2, Asb4). Hoxd13 is shown as an unaffected control gene (Hoxd13). (C) Percentage of genes either up-regulated or down-regulated in HoxC mutant animals, which were also reported to be the targets of SUZ12 in ES cells. The percentages are comparable, suggesting that capacity to recruit PRC2 may not be the main cause of the transcriptional variations observed in the HoxC mutant animals, in these tissues at this developmental time. (D) Absolute quantifications of posterior Hoxd gene transcripts and of mHotair in posterior parts of fetuses including the hindlimbs, the genital bud and the developing tail of E11.5 embryos. All values are normalized to a housekeeping gene.