Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

Ultraconserved elements (UCEs) are sequences that are identical between reference genomes of distantly related species. As they are tinder negative selection and enriched near or in specific classes of genes, one explanation for their ultraconservation may be their involvement in important functions. Indeed, many UCEs can drive tissue-specific gene expression. We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultra-conservation may reflect a mechanism of copy counting via comparison. Here, we report that nonexonic UCEs are also depleted among 10 of 11 recent genonmewide data sets Of human CNVs, including 3 obtained with Strategies permitting greater precision in determining the extents of CNVs. We further present observations suggesting that nonexonic UCEs per se may contribute to this depletion and that their apparent dosage sensitivity was in effect when they became fixed in the last common ancestor of mammals, birds, and reptiles, consistent with dosage sensitivity contributing to ultraconservation. Finally, in searching for the mechanism(s) underlying the function of nonexonic UCEs, we have found that they are enriched in TAATA, which is also the recognition sequence for the homoeodomain DNA-binding module, and bounded by a change in A + T frequency.