question: Describe the involvement of conserved noncoding sequences in the regulation of Hox genes.
answer: Comparisons of noncoding sequences of the elephant shark and human Hox clusters have identified a large number of conserved noncoding elements (CNEs), which represent putative cis-regulatory elements that may be involved in the regulation of Hox genes.  The b-paralogs of the duplicated fugu Hox clusters are virtually devoid of unique ancient CNEs.  Elephant shark and human Hox clusters have lost fewer ancient CNEs. If these ancient CNEs are indeed enhancers directing tissue-specific expression of Hox genes, divergence of their sequences in vertebrate lineages might have led to altered expression patterns and presumably the functions of their associated Hox genes.  When compared, the amphioxus Hox cluster with the human HoxA, HoxB, HoxC, and HoxD clusters were found to have several conserved noncoding regions, both in intergenic and intronic regions. This suggests that the regulation of Hox genes is highly conserved across chordates, consistent with the similar Hox expression patterns in vertebrates and amphioxus.