Despite the recent massive progress in production of vertebrate genome sequencedata and large-scale efforts to completely annotate the human genome, we still havescant knowledge of the principles that built genomes in evolution, of genomearchitecture and its functional organization. This work uses bioinformatics andzebrafish transgenesis to explain a mechanism for the maintenance of long-rangeconserved synteny across vertebrate genomes and to analyze the arrangement ofunderlying gene regulation systems. Large mammal-teleost conserved chromosomalsegments contain highly conserved non-coding elements (HCNEs), their target genes,as well as phylogenetically and functionally unrelated “bystander” genes. Targetgenes are developmental and transcriptional regulatory genes with complex,temporally and spatially regulated expression patterns. Bystander genes are notspecifically under the control of the regulatory elements that drive the target genesand are usually expressed in different, less complex, patterns. Enhancer detectionreporter insertions distal to zebrafish target genes recapitulate their expressionpatterns even if located inside or beyond bystander genes. We termed thesechromosomal segments genomic regulatory blocks (GRBs). To demonstrate, that theregulatory domain of a developmental regulatory gene can extend into and beyondadjacent bystander gene transcriptional units and that these elements indeed regulatetarget genes, we tested the function of HCNEs around genes encoding transcriptionfactors, PAX6, SOX3 and SOX11 in both human and zebrafish genomes. Comparingour results with those obtained using mouse, we establish that human elements can betested reliably in zebrafish. Testing the elements form SOX11 loci further revealedsubfunctionalization after genome duplication and functional turnover as evolutionaryprocesses on the gene regulation. The genome features confirmed by this work werealso applied to provide an advance in understanding human mutations causing orpredisposing towards genetic diseases. These mutations are frequently associated tothe incorrect gene(s) coding region instead of taking the regulatory mutation in distantregulatory elements of another possible causative gene into account. We coulddemonstrate using our approach that the genes linked to diabetes by genome wide association study contain in their introns HCNEs regulating different, more distantgene functionally more probably related to the diabetes phenotype.
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