Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA.
Genes Dev. 2012 Jul 1;26(13):1498-507. doi: 10.1101/gad.192732.112.
Prokaryotic and eukaryotic RNA polymerases can use 2- to ∼4-nt RNAs, "nanoRNAs," to prime transcription initiation in vitro. It has been proposed that nanoRNA-mediated priming of transcription can likewise occur under physiological conditions in vivo and influence transcription start site selection and gene expression. However, no direct evidence of such regulation has been presented. Here we demonstrate in Escherichia coli that nanoRNAs prime transcription in a growth phase-dependent manner, resulting in alterations in transcription start site selection and changes in gene expression. We further define a sequence element that determines, in part, whether a promoter will be targeted by nanoRNA-mediated priming. By establishing that a significant fraction of transcription initiation is primed in living cells, our findings contradict the conventional model that all cellular transcription is initiated using nucleoside triphosphates (NTPs) only. In addition, our findings identify nanoRNAs as a previously undocumented class of regulatory small RNAs that function by being directly incorporated into a target transcript.
原核生物和真核生物 RNA 聚合酶可以使用 2 到 ∼4 个核苷酸的 RNA（“纳米 RNA”），在体外启动转录。有人提出，纳米 RNA 介导的转录起始同样可以在体内生理条件下发生，并影响转录起始位点选择和基因表达。然而，尚未提出这种调控的直接证据。在这里，我们在大肠杆菌中证明，纳米 RNA 以生长阶段依赖的方式启动转录，导致转录起始位点选择的改变和基因表达的变化。我们进一步定义了一个序列元件，该元件部分决定了启动子是否会被纳米 RNA 介导的启动所靶向。通过确定在活细胞中有相当一部分转录起始是由引物启动的，我们的发现与传统模型相矛盾，传统模型认为所有细胞转录仅使用核苷三磷酸 (NTP) 启动。此外，我们的发现将纳米 RNA 鉴定为一类以前未被记录的调控小 RNA，其功能是通过直接整合到靶转录本中。
