We report evidence for a mechanism for the maintenance of long-range conserved 
synteny across vertebrate genomes. We found the largest mammal-teleost conserved 
chromosomal segments to be spanned by highly conserved noncoding elements 
(HCNEs), their developmental regulatory target genes, and phylogenetically and 
functionally unrelated "bystander" genes. Bystander genes are not specifically 
under the control of the regulatory elements that drive the target genes and are 
expressed in patterns that are different from those of the target genes. 
Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, 
rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the 
expression patterns of these genes even if located inside or beyond bystander 
genes, suggesting that the regulatory domain of a developmental regulatory gene 
can extend into and beyond adjacent transcriptional units. We termed these 
chromosomal segments genomic regulatory blocks (GRBs). After whole genome 
duplication in teleosts, GRBs, including HCNEs and target genes, were often 
maintained in both copies, while bystander genes were typically lost from one 
GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy 
GRBs of higher vertebrates intact. We show that loss of bystander genes and 
other mutational events suffered by duplicated GRBs in teleost genomes permits 
target gene identification and HCNE/target gene assignment. These findings 
explain the absence of evolutionary breakpoints from large vertebrate 
chromosomal segments and will aid in the recognition of position effect 
mutations within human GRBs.