Hoxd13 binds in vivo and regulates the expression of genes acting in key pathways for early limb and skeletal patterning

5′ HoxD genes are required for the correct formation of limb skeletal elements. Hoxd13, the most 5′-located HoxD gene, is important for patterning the most distal limb region, and its mutation causes human limb malformation syndromes. The mechanisms underlying the control of developmental processes by Hoxd13, and by Hox genes in general, are still elusive, due to the limited knowledge on their direct downstream target genes. We identified by ChIP-on-chip 248 known gene loci bound in vivo by Hoxd13. Genes relevant to limb patterning and skeletogenesis were further analysed. We found that Hoxd13 binds in vivo, in developing limbs, the loci of Hand2, a gene crucial to limb AP axis patterning, of Meis1 and Meis2, involved in PD patterning, of the Sfrp1, Barx1, and Fbn1 genes, involved in skeletogenesis, and of the Dach1, Bmp2, Bmp4, and Emx2 genes. We show that Hoxd13 misexpression in developing chick limbs alters the expression of the majority of these genes, supporting the conclusion that Hoxd13 directly regulates their transcription. Our results indicate that 5′ Hox proteins regulate directly both key genes for early limb AP and PD axis patterning and genes involved, at later stages, in skeletal patterning.