Ribothrypsis: mechanisms and implications for gene expression regulation

核糖体破裂：基因表达调控的机制和意义 项目总结/摘要 信使RNA传递决定蛋白质产生的遗传信息， 许多调节基因表达的途径的联系。典型mRNA的流行观点 衰变是由去腺苷化和去帽介导的，随后是从3'端的外切核溶解。 5、结束。我们最近描述了核糖裂解，一种共翻译mRNA的核酸内切途径 衰变，由mRNA在离开核糖体通道时的核糖体相裂解介导。我们断定 核糖体裂解是一种统一的、进化上保守的机制， 所有mRNA的衰变：通过监视机制降解的典型和异常mRNA，如 不间断衰减（Non-Stop Decay，NSD）从这个意义上说，核糖体加密可以被视为 “类固醇上的NGD/NSD”;或者相反，NGD/NSD可以被视为核糖体裂解的一个子集。的 核糖体裂解中mRNA降解的中心整合子是翻译核糖体， 条件激活或招募一种未知的核酸内切酶（核糖蛋白酶），在mRNA存在时将其切割 核糖体在本研究中，我们将研究核糖体裂解对基因表达的影响， 分析;以及核糖体裂解在基因表达调控中的机制和影响。我们发现 内源性产生的mRNA片段在总mRNA库中占相当大的比例。 这一发现使用所有目前测定mRNA的方法获得的结果的解释复杂化， 这并没有考虑到核糖体形成，并且需要开发新的实验方法。 以及用于RNA测序的计算工具，我们将在Aim 1中开发。在AIM 2中，我们将 研究核糖体裂解触发物和核糖体裂解在基因表达调控中意想不到作用， 上游开放阅读框架（uORF），以及长非编码RNA（lncRNA）的衰变。我们 还将在体外和体内研究核糖体形成的分子机制，并鉴定核糖体形成蛋白。

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.