Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
BMC Evol Biol. 2012 Dec 5;12:236. doi: 10.1186/1471-2148-12-236.
Ultraconserved 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.
Here, 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.
We 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.
在脊椎动物和无脊椎动物基因组中已经鉴定出了 DNA 的超保守元件。这些元件具有多种功能，包括在发育过程中的增强子活性。然而，这些元件在细胞系统中的进化起源和功能作用尚未确定。
在这里，我们鉴定了广泛存在于远缘物种中的超保守元件，从原始水生生物到具有复杂身体系统的陆地物种，包括在果蝇和人类中保守的一些新元件。除了与发育基因的已知关联外，这些 DNA 元件还与涉及基本细胞功能的基因强烈关联，如表观遗传调控、细胞凋亡、解毒、先天免疫和感觉接收。有趣的是，我们观察到超保守元件按序列相似性聚类。此外，聚类的物种组成和侧翼基因表现出线系特异性模式。超保守元件富含发育转录因子的结合位点，而不论它们如何聚类。
我们在远缘物种中鉴定出了大量的超保守元件。这些保守元件的特定类别似乎在分类群分化之前就已经产生，并在进化过程中固定下来。我们的研究结果表明，这些超保守元件并非现代高等真核生物所特有的，而是从它们的后生动物祖先那里传递而来的。
