Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.

中文翻译：

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大肠杆菌 5' UTR 和 ORF 内部 rna 的调节作用通过 3' 末端映射检测

许多细菌基因受其 5' 非翻译区 (UTR) 中的 RNA 元件调节。然而，即使在模型细菌大肠杆菌中，这些元素的完整补充也是未知的。使用互补 RNA 测序方法，我们在 5' UTR 和开放阅读框 (ORF) 中检测到大量 3' 末端，表明通过提前终止转录进行广泛调控。我们记录了多个转录物的调节，包括涉及 Rho 的亚精胺诱导和编码亚精胺流出泵的 mRNA 的上游 ORF 的翻译。除了发现新的调控位点外，我们还检测到源自 5' UTR 和 ORF 内部序列的短而稳定的 RNA 片段。其中三个转录本的特征，包括一个基本细胞分裂基因内部的 RNA，揭示它们具有作为sRNA海绵的独立功能。因此，这些数据揭示了细菌 5'UTR 和 ORF 内部的大量顺式和反式作用 RNA 调节剂。