Institute of Plant Biology & Zürich-Basel Plant Science Center, University Zürich, CH-8008 Zürich, Switzerland.
Genome Res. 2012 Dec;22(12):2455-66. doi: 10.1101/gr.129346.111. Epub 2012 Sep 17.
Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.
超保守元件 (UCEs) 是指在远缘物种之间完全相同的 DNA 片段，是基因组中一种神秘的特征，其功能尚未被很好地理解。UCEs 最初在哺乳动物中被发现并加以描述，它们被认为在基因调控、RNA 加工和维持基因组完整性方面发挥着重要作用。然而，由于所有这些功能都可以容忍一定程度的序列变异，因此它们的超保守和超选择性质无法得到解释。我们研究了在远缘植物基因组中是否存在没有基因功能的高度保守的 DNA 元件。我们比较了拟南芥 (Arabidopsis thaliana) 和葡萄 (Vitis vinifera) 的基因组；这两个物种在大约 1.15 亿年前 (Mya) 就已经分化了。我们鉴定出了 36 个具有至少 85%相似性且长度超过 55bp 的高度保守元件。有趣的是，这些元件表现出与哺乳动物 UCEs 相似的特性，因此我们将它们命名为 UCE-like elements (ULEs)。ULEs 位于基因间或内含子区，并且从片段重复中缺失。与 UCEs 一样，ULEs 受到强烈的净化选择，表明这些元件具有功能作用。与哺乳动物的 UCEs 类似，ULEs 在其边界处 A+T 含量急剧下降，并且在编码转录因子的基因和参与发育的基因附近富集，后者在未分化组织中优先表达。通过比较大约 5000 万年前分化的短柄草 (Brachypodium distachyon) 和水稻 (Oryza sativa) 的基因组，我们在单子叶植物中鉴定出了具有类似特性的另一组 ULEs。在植物基因组中鉴定出 ULEs 为研究它们在基因组功能、完整性和调控中的可能作用提供了新的机会。
