Methyl-7-guanosine (m⁷G) “capping” of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E (eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and increased capping efficiency of ∼100 coding and noncoding RNAs. To quantify this, we developed enzymatic (cap quantification; CapQ) and quantitative cap immunoprecipitation (CapIP) methods. The CapQ method has the further advantage that it captures information about capping status independent of the type of 5′ cap, i.e., it is not restricted to informing on m⁷G caps. These methodological advances led to unanticipated revelations: 1) Many RNA populations are inefficiently capped at steady state (∼30 to 50%), and eIF4E overexpression increased this to ∼60 to 100%, depending on the RNA; 2) eIF4E physically associates with noncoding RNAs in the nucleus; and 3) approximately half of eIF4E-capping targets identified are noncoding RNAs. eIF4E’s association with noncoding RNAs strongly positions it to act beyond translation. Coding and noncoding capping targets have activities that influence survival, cell morphology, and cell-to-cell interaction. Given that RNA export and translation machineries typically utilize capped RNA substrates, capping regulation provides means to titrate the protein-coding capacity of the transcriptome and, for noncoding RNAs, to regulate their activities. We also discovered a cap sensitivity element (CapSE) which conferred eIF4E-dependent capping sensitivity. Finally, we observed elevated capping for specific RNAs in high-eIF4E leukemia specimens, supporting a role for cap dysregulation in malignancy. In all, levels of capping RNAs can be regulated by eIF4E.

编码RNA和一些非编码RNA的甲基-7-鸟苷(m ⁷ G)“加帽”对于它们的成熟和随后的活性至关重要。在这里，我们发现真核翻译起始因子 4E (eIF4E) 本身是一种帽结合蛋白，可驱动加帽机制的表达并提高~100 种编码和非编码 RNA 的加帽效率。为了量化这一点，我们开发了酶法（上限定量；CapQ）和定量上限免疫沉淀（CapIP）方法。CapQ方法具有进一步的优点，即它捕获关于独立于5'帽的类型的加帽状态的信息，即，它不限于通知m ⁷ G帽。这些方法学进展带来了意想不到的启示：1）许多 RNA 群体在稳态时效率较低（~30% 至 50%），而 eIF4E 过表达将其增加至~60% 至 100%，具体取决于 RNA；2) eIF4E与细胞核中的非编码RNA物理结合；3) 大约一半的 eIF4E 加帽目标是非编码 RNA。eIF4E 与非编码 RNA 的关联使其在翻译之外发挥作用。编码和非编码加帽靶标具有影响存活、细胞形态和细胞间相互作用的活性。鉴于 RNA 输出和翻译机制通常利用加帽 RNA 底物，加帽调节提供了滴定转录组的蛋白质编码能力的方法，并且对于非编码 RNA，调节其活性。我们还发现了一种帽敏感性元件 (CapSE)，它赋予 eIF4E 依赖性帽敏感性。最后，我们观察到高 eIF4E 白血病样本中特定 RNA 的帽升高，支持帽子失调在恶性肿瘤中的作用。总之，加帽 RNA 的水平可以通过 eIF4E 进行调节。