Total RNA was extracted with RNEasy kit (Qiagen) for RNA-seq. For each ChIP-Seq and ChIA-PET, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined Protein G Dynabeads prebound with appropriate antibodies at 4C overnight. Beads were collected with magnet and washed 5 or 8x. For ChIP-seq, chromatin was eluted with TE+1%SDS at 65C for 10 minutes. Crosslinks were reversed at 65C overnight then chromatin was purified with PCR cleanup kit (Qiagen). For ChIA-PET, chromatin was end-repaired, ligated to ChIA-PET adaptors, and the 5’ ends of the adaptors was phosphorylated. Chromatin was eluted as described above, followed by ligation of chromatin complexes and reversal of crosslinking (65C overnight). DNA was purified with phenol:chloroform extraction and ethanol precipitation. ChIP-seq libraries were constructed with the standard procedure included with the Illumina ChIP-Seq kit but paired-end adaptors (PE-102-1001) were used instead of those provided in the kit. For multiplexed samples, Illumina Multiplexing adapters and primers (PE-400-1001) were used. RNA-seq Iibraries were constructed with the standard procedure included with the Illumina TruSeq RNA Sample Preparation kit. ChIA-PET libraries were constructed with Illumina paired-end adaptors (PE-102-1001) and the protocol outlined in Fullwood, et al. 2010 (PMID:20069536)