Loke Johnny C, Stahlberg Eric A, Strenski David G, Haas Brian J, Wood Paul Chris, Li Qingshun Quinn
Department of Botany, Miami University, Oxford, Ohio 45056, USA.
Plant Physiol. 2005 Jul;138(3):1457-68. doi: 10.1104/pp.105.060541. Epub 2005 Jun 17.
Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3'-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3'-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3'-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3'-ends for gene annotation.
我们使用一个名为SignalSleuth的新程序以及一个包含经过验证的多聚腺苷酸化[poly(A)]位点的数据库，分析了拟南芥（Arabidopsis thaliana）中mRNA poly(A)信号的组成，并重新评估了先前描述的3'-非翻译（UTR）区域内的顺式元件，包括近上游元件和远上游元件。正如预期的那样，不存在高度一致的信号模式。AAUAAA信号在近上游元件模式中位居榜首，并且仅在预测位置的约10%的3'-UTR中被发现。更重要的是，我们在切割位点两侧鉴定出一组新的名为切割元件的poly(A)信号。这些顺式元件以前未通过传统诱变揭示，被认为是用于切割位点识别的一组信号。此外，对3'-UTR区域的单核苷酸谱扫描揭示了U和A核苷酸交替延伸的独特排列，这导致了二级结构形成的预测。使用RNA二级结构预测程序mFold，我们在分析的序列上鉴定出三种主要类型的二级结构。令人惊讶的是，这些观察到的二级结构在这些区域先前构建的突变中均被打断。这些结果将使我们能够修订当前的植物poly(A)信号模型，并开发用于预测基因注释3'-末端的工具。
