The order of genes in eukaryotic genomes has generally been assumed to be 
neutral, since gene order is largely scrambled over evolutionary time. Only a 
handful of exceptional examples are known, typically involving deeply conserved 
clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we 
report the first systematic survey of microsynteny conservation across 
metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of 
unrelated genes that have remained tightly physically linked in diverse lineages 
across over 600 million years of evolution. Integrating sequence conservation, 
gene expression data, gene function, epigenetic marks, and other genomic 
features, we provide extensive evidence that many conserved ancient linkages 
involve (1) the coordinated transcription of neighboring genes, or (2) genomic 
regulatory blocks (GRBs) in which transcriptional enhancers controlling 
developmental genes are contained within nearby bystander genes. In addition, we 
generated ChIP-seq data for key histone modifications in zebrafish embryos, 
which provided further evidence of putative GRBs in embryonic development. 
Finally, using chromosome conformation capture (3C) assays and stable transgenic 
experiments, we demonstrate that enhancers within bystander genes drive the 
expression of genes such as Otx and Islet, critical regulators of central 
nervous system development across bilaterians. These results suggest that 
ancient genomic functional associations are far more common than previously 
thought-involving ∼12% of the ancestral bilaterian genome-and that 
cis-regulatory constraints are crucial in determining metazoan genome 
architecture.