Genome-wide mapping of Hoxa11 and Hoxa13 binding sites in the limb bud

Hox genes control domain specific cartilage pattern formation along the proximodistal axis. Hoxa11 and Hoxd11 (Hox11) show overlapping expression in the mesenchyme of the zeugopod and regulate cartilage growth and differentiation. Hoxa13 and Hoxd13 (Hox13) are expressed in the autopodal mesenchyme and are crucial for the autopodal cartilage patterning. Since both Hox11 and Hox13 are involved in the limb cartilage development, they may share the target genes. To identify common target genes among the Hoxa11 and Hoxa13, we performed ChIP-Seq analysis using specific antibody. Overall design: Soluble chromatin was prepared from mouse limb bud and the Hox binding DNA was recovered by immune-precipitation. Then the enriched sequence was determined by NGS analysis.