Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals.
Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals.
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DOI：
10.1186/s12862-015-0499-6
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发表时间：
2015-10-19
影响因子：
3.4
通讯作者：
Ott S
中科院分区：
文献类型：
--
作者：
Davies NJ;Krusche P;Tauber E;Ott S
系统发育足迹法是一种比较方法，其原理是功能性序列元件随时间的推移比非功能性序列获得更少的突变。因此，成功地比较远亲物种将产生非常重要的序列元件，可能服务于基本的生物学作用。RNA调控元件不如DNA中的调控元件那么好理解。在这项研究中，我们使用了新出现的模式生物Nasonia vitripennis，一种寄生蜂，对12种昆虫基因组进行比较分析，以确定在大型昆虫群体中保守的高度保守的非编码元件（CNE），重点是5'UTR和启动子序列。我们报告了322个CNE的鉴定，这些CNE在广泛的昆虫目中是保守的。所确定的区域与调控和发育基因相关，并且包含揭示其在翻译调控中可能功能的短足迹。在我们的分析中确定的最古老的区域都被发现重叠的基因转录区域，反映了更强的保护翻译调控元件比转录元件。进一步扩大序列分析，以非昆虫物种，我们还报告发现，据我们所知，两个最古老的和最普遍的CNE的动物王国（7亿年）。这些古老的保守非编码元件与两个核糖体茎基因RPLP 1和RPLP 2相关，并且很可能在一些最早的动物中起作用。我们报告了迄今为止发现的最高度保守的CNE的鉴定，以及其他几个高度保守的元件，这些元件无一例外地是转录本5'非翻译区的一部分，并且出现在许多关键的翻译调节基因中，突出了翻译调节因子的翻译调节作为昆虫基因组的保守特征。本文的在线版本（doi：10.1186/s12862-015-0499-6）包含补充材料，可供授权用户使用。
Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences. Successful comparisons of distantly related species will thus yield highly important sequence elements likely to serve fundamental biological roles. RNA regulatory elements are less well understood than those in DNA. In this study we use the emerging model organism Nasonia vitripennis, a parasitic wasp, in a comparative analysis against 12 insect genomes to identify deeply conserved non-coding elements (CNEs) conserved in large groups of insects, with a focus on 5’ UTRs and promoter sequences. We report the identification of 322 CNEs conserved across a broad range of insect orders. The identified regions are associated with regulatory and developmental genes, and contain short footprints revealing aspects of their likely function in translational regulation. The most ancient regions identified in our analysis were all found to overlap transcribed regions of genes, reflecting stronger conservation of translational regulatory elements than transcriptional elements. Further expanding sequence analyses to non-insect species we also report the discovery of, to our knowledge, the two oldest and most ubiquitous CNE’s yet described in the animal kingdom (700 MYA). These ancient conserved non-coding elements are associated with the two ribosomal stalk genes, RPLP1 and RPLP2, and were very likely functional in some of the earliest animals. We report the identification of the most deeply conserved CNE’s found to date, and several other deeply conserved elements which are without exception, part of 5’ untranslated regions of transcripts, and occur in a number of key translational regulatory genes, highlighting translational regulation of translational regulators as a conserved feature of insect genomes. The online version of this article (doi:10.1186/s12862-015-0499-6) contains supplementary material, which is available to authorized users.