Ribothrypsis: mechanisms and implications for gene expression regulation

核密码：基因表达调控的机制和意义 项目摘要/摘要 信使RNA传递决定蛋白质生产的遗传信息，是一种 Nexus提供了许多调节基因表达的途径。规范信使核糖核酸的主流观点 衰变是通过去死烯化和脱去帽，然后从3‘端核外裂解而来的。 和5‘末端。我们最近描述了核密码，一种共翻译的mRNA的核内溶解途径。 在离开核糖体通道时，由核糖体阶段切割的信使核糖体介导的衰变。我们假设 核破译是一种统一和进化保守的机制，是协译的基础 所有mRNAs的衰变：通过监测机制降解的规范和异常的mRNAs，如 不停止衰变(NGD)或不停止衰变(NSD)。从这个意义上说，核破译可以被视为 “类固醇上的NGD/NSD”；或者相反，NGD/NSD可被视为核密码的子集。这个 在核密码中，mRNA衰变的中心积分器是翻译核糖体，它在一定的条件下 条件激活或招募一种未知的内切酶(核蛋白)，以在mrna退出时将其切割。 核糖体。在这项提案中，我们将研究核密码对基因表达的影响 分析；以及核密码在基因表达调控中的机制和影响。我们发现 内源性产生的信使核糖核酸片段在总信使核糖核酸池中占相当大的比例。 这一发现使用目前所有分析mRNA的方法获得的结果的解释变得复杂， 这不考虑核破译，因此有必要发展新的实验 以及用于RNA测序的计算工具，我们将在Aim1中开发。在AIM2中，我们将 研究核密码的触发因素和核密码在基因表达调控中的意外作用 上游开放阅读框架(UORF)，以及长非编码RNA(LncRNAs)的衰变。我们 还将在体外和体内研究核密码的分子机制，并鉴定核密码。

Ribothrypsis: mechanisms and implications for gene expression regulation PROJECT SUMMARY / ABSTRACT Messenger RNAs transmit the genetic information that dictates protein production and are a nexus for numerous pathways that regulate gene expression. The prevailing view of canonical mRNA decay is that it is mediated by deadenylation and decapping followed by exonucleolysis from the 3' and 5' ends. We recently described ribothrypsis, an endonucleolytic pathway of cotranslational mRNA decay, mediated by ribosome-phased cleavages of the mRNA as it exits the ribosome channel. We posit that ribothrypsis is a unifying and evolutionary conserved mechanism that underlies cotranslational decay of all mRNAs: canonical and aberrant mRNAs that degrade via surveillance mechanisms, such as No-Go Decay (NGD) or Non-Stop Decay (NSD). In that sense, ribothrypsis may be viewed as “NGD/NSD on steroids”; or conversely NGD/NSD may be viewed as a subset of ribothrypsis. The central integrator of mRNA decay in ribothrypsis is the translating ribosome that under certain conditions activates or recruits an unknown endonuclease (ribothrypsin) to cleave the mRNA as it exits the ribosome. In this proposal, we will investigate the impact of ribothrypsis in gene expression analysis; and mechanisms and impact of ribothrypsis in gene expression regulation. We discovered that endogenously generated mRNA fragments represent a sizable fraction of the total mRNA pool. This finding complicates interpretation of results obtained with all current methods that assay mRNAs, which do not take ribothrypsis into account, and necessitates the development of new experimental and computational tools for RNA sequencing, which we will develop in Aim1. In Aim2, we will investigate ribothrypsis triggers and unexpected roles of ribothrypsis in gene expression regulation via upstream Open Reading Frames (uORFs), and in the decay of long noncoding RNAs (lncRNAs). We will also study molecular mechanisms of ribothrypsis in vitro and in vivo and identify ribothrypsin.