Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

Abstract

Animal genomes possess highly conserved cis-regulatory sequences that are often found near genes that regulate transcription and development. Researchers have proposed that the strong conservation of these sequences may affect the evolution of the surrounding genome, both by repressing rearrangement, and possibly by promoting duplicate gene retention. Conflicting data, however, have made the validity of these propositions unclear. Here, we use a new computational method to identify phylogenetically conserved noncoding elements (PCNEs) in a manner that is not biased by rearrangement and duplication. This method is powerful enough to identify more than a thousand PCNEs that have been conserved between vertebrates and the basal chordate amphioxus. We test 42 of our PCNEs in transgenic zebrafish assays-including examples from vertebrates and amphioxus-and find that the majority are functional enhancers. We find that PCNEs are enriched around genes with ancient synteny conservation, and that this association is strongest for extragenic PCNEs, suggesting that cis-regulatory interdigitation plays a key role in repressing genome rearrangement. Next, we classify mouse and zebrafish genes according to association with PCNEs, synteny conservation, duplication history, and presence in bidirectional promoter pairs, and use these data to cluster gene functions into a series of distinct evolutionary patterns. These results demonstrate that subfunctionalization of conserved cis-regulation has not been the primary determinate of gene duplicate retention in vertebrates. Instead, the data support the gene balance hypothesis, which proposes that duplicate retention has been driven by selection against dosage imbalances in genes with many protein connections.

Whole-genome duplication in teleost fishes and its evolutionary consequences

“…Hufton et al even propose that the gene balance hypothesis better explains gene duplication retention in vertebrate genomes than the DDC model (Hufton et al, 2009). In their study of phylogenetically conserved noncoding sequences, they showed that genes retained after WGD are rather marked by many protein interaction sites than by many conserved noncoding elements, as the DDC model would predict (Hufton et al, 2009).…”

“…In their study of phylogenetically conserved noncoding sequences, they showed that genes retained after WGD are rather marked by many protein interaction sites than by many conserved noncoding elements, as the DDC model would predict (Hufton et al, 2009). Additionally, it is plausible that an increased dose of some genes is beneficial even if they are not highly interactive.…”

“…Genes where dosage is believed to be especially important are ribosomal genes, genes coding for proteins with a high number of interactions, and genes encoding proteins functioning in signaling pathways and networks. Requirement for gene dosage maintenance can lead to scenarios in which all genes of a network or pathway remain duplicated, and it has been suggested that retention of duplicate members in whole networks, can have broad evolutionary implications (Conant and Wolfe, 2007 been shown in vertebrates and plants that highly interconnected genes, such as genes involved in transcription and signaling cascades, and genes coding for proteins with more than average protein-protein interactions are over-retained after WGDs, but not after smallscale duplications (Blomme et al, 2006;Freeling, 2008;Hufton et al, 2009). …”

The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates

“…59 Ultra-Deep CNSs Are Conserved in Both Rice and Arabidopsis Animal CNEs can be detected between mammals and the early diverging chordate amphioxus, lineages that diverged ;520 mya (Hufton et al, 2009). To test whether any of the deep CNSs discovered in eudicots are also conserved in monocots (diverged ;140 mya), we added orthologous rice genes to GEvo panels containing deep eudicot CNSs (Supplemental Figure 1).…”

“…In the largest study conducted to date, more than 40% of 150 human-fugu CNEs tested had enhancer activity versus only 5% of human-rodent CNEs (Visel et al, 2007). Similarly, 45% of 22 CNEs conserved between the invertebrate amphioxus (Branchiostoma floridae) and vertebrates (mouse, fugu, and zebra fish [Danio rerio]) had enhancer activity in a transgenic zebra fish assay (Hufton et al, 2009). …”