Definition of key terms. (a) The genomic regulatory block model and its possible evolutionary fate after whole genome duplication. Many HCNEs act as long-range regulators of target genes, while having no effect on bystander genes. The target gene is kept in both zebrafish copies of the loci, along with HCNEs, whereas bystander genes are differentially lost. (b) Tag clusters (TCs) are defined as overlapping CAGE tags (red horizontal arrows). Each distinct CAGE tag start corresponds to a CTSS. CTSSs are shown as vertical bars in the bottom track with the height of each bar corresponding to the number of CAGE tags for that CTSS.