Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

Abstract

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.

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

“…Teleost genomes contain four clusters (12) given the extra genome duplication at the base of their lineage. Thus, Six genes' genomic organization remained strongly conserved, likely reflecting the presence of strong cis-regulatory constraints (11). Using high-resolution circular chromosome conformation capture (4C-seq) on zebrafish embryos, we identified genomic contacts of different genes located along the chromatin region encompasing the six3a-six2a cluster (Fig.…”

“…Six homeobox genes, essential for the development of many embryonic structures, comprise three subfamilies-Six1/2, Six3/6, and Six4/5-tandemly arrayed in tight genomic clusters strongly conserved in several animal phyla (11). As a consequence of ancestral whole genome duplications, most vertebrate genomes contain two paralogous copies of the Six cluster: one containing Six2 and Six3 and the other Six1, Six4 and Six6.…”

The Proto-MHC of Placozoans, a Region Specialized in Cellular Stress and Ubiquitination/Proteasome Pathways

“…Large gene deserts with enhancers acting over long distances are mostly found in vertebrate genomes, whereas invertebrate metazoans generally have local regulatory controls of expression (60). However, it has been proposed that locked genomic regulatory blocks (GRBs) defined by key developmental transcription factors and their distal enhancers provide an explanation for the maintenance of long-range conserved synteny across vertebrate and invertebrate genomes (61,62). It is proposed that bystander genes be trapped in the GRBs and thus form conserved syntenic blocks of genes (61,62).…”

Enhancer turnover and conserved regulatory function in vertebrate evolution

“…In addition, although some examples of rigid enhancer organization exist [2,3], the order of TFBSs on a given enhancer can be quite flexible [4]. Finally, enhancers act at a distance and can even be embedded within neighbouring loci [5][6][7][8][9], indicating a large degree of positional freedom of enhancers in relation to the genes they control. Thus, while new protein coding genes mostly appear by duplication of pre-existing genes [10], DNA sequences within an enhancer can change quickly over evolutionary time and new enhancers can appear in new locations and replace ancient ones.…”