In addition to protein coding sequence, the organism genome contains a 
significant amount of regulatory DNA. Comparative genomics reveals that the 
organism genomes of vertebrates, tunicate, cephalochordate, flies, and nematodes 
contain cis-regulatory elements with highly conserved non-coding elements 
(CNEs). CNEs that cluster around trans-dev genes are part of core gene 
regulatory networks (GRNs), and usually, they can act as transcriptional 
enhancers. In this review, we described the identification of CNEs and 
summarized their key properties across the metazoans, and then discussed the 
evolution of CNEs after large-scale genome duplication events and the role of 
CNEs in the evolution of ani-mal body plan.