The evolution of ultraconserved elements with different phylogenetic origins

Abstract

BackgroundUltraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined.ResultsHere, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster.ConclusionWe identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors.

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

“…To examine the intrinsic biological roles of the conserved regions, we queried the 50 most overrepresented heptamer against FlyReg motifs [23] using STAMP [24] and detected many putative TF binding sites (TFBSs) related to developmental TFs ( Figure 1C and Table S2 ). This result is consistent with previous reports showing that HCNEs harbor binding sites for developmental TFs [3] , [25] .…”

“…Coding sequences are generally under higher selective pressure than noncoding sequences, due to the essential roles that proteins play in the cell [1] . However, some noncoding regions show extreme conservation (even more than coding sequences) over very long evolutionary timeframes [2] , [3] . These extremely conserved sequences are found universally in multicellular eukaryotes of the animal and plant kingdoms [3] , [4] , indicating that such sequences have essential functions.…”

Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

“…Although their complete functional characterization is still a long way off, it is known that UCEs are not randomly distributed, and their position within the genome also seems to reflect their function. These constrained sequences are in fact mostly allocated in clusters, flanking, or embedding genes involved in important physiological processes, and act as splicing or enhancer factors [ 92 ]. Their extreme conservation could be due to the absence of annotated transposons near many UCEs during evolution [ 93 ].…”

Comparison of Ultra-Conserved Elements in Drosophilids and Vertebrates

“…None of the 481 UCEs identified by Bejerano and co-authors [7] overlap with the UCEs identified between phylogenetically distant species such as human and demosponge, hydra or sea anemone [9]. However, a recent study has described 183 CNEs conserved between mammals, fishes and tunicates, of which 145 overlap with an extended set of 5,404 vertebrate UCEs [37].…”