Mechanism for post-transcriptional gene regulation by Ribothrypsis

核糖体转录后基因调控机制

• 批准号: 10639411
• 负责人: FADIA Fayez IBRAHIM
• 金额: $ 32.76万
• 依托单位: THOMAS JEFFERSON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2028-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10639411
• 关键词: Acceleration; Amino Acids; Biological; Biology; Cell physiology; Cells; Characteristics; Code; Consensus; Data; Development; Diagnostic; Elements; Endonuclease I; Eukaryota; Event; Excision; Exclusion; Exonuclease; Future; G-Quartets; Gene Expression; Gene Expression Regulation; Genes; Genetic Screening; Goals; Homeostasis; Human; Length; Link; Mediating; Messenger RNA; Methods; Methyltransferase; Modeling; Modification; Molecular; Mus; Names; Nature; Nucleotides; Pattern; Pennsylvania; Periodicity; Phase; Poly(A) Tail; Poly(A)+ RNA; Polyadenylation; Post-Transcriptional Regulation; Predisposition; Process; Publishing; RNA; RNA Caps; RNA Decay; RNA Sequences; Regulation; Research; Ribosomes; Role; Saccharomycetales; Site; Starvation; Stress; Textbooks; Training; Transcript; Translating; Translations; Universities; Yeasts; embryonic stem cell; endonuclease; exosome; human disease; insight; knock-down; mRNA Decay; next generation sequencing; novel; nuclease; post-doctoral training; posttranscriptional; recruit; sequencing platform; transcriptome; transcriptome sequencing

PROJECT SUMMARY/ ABSTRACT Post-transcriptional regulation of gene expression is fundamental to normal cellular homeostasis. The current model in the field of biology is that mRNAs exist primarily as ‘full-length’ molecules that are ‘protected’ from decay by ribosomes during translation. The long-established understanding is that mRNA decay is initiated by deadenylation followed by decapping and subsequent exonucleolytic decay from both ends. Co-translational mRNA decay is known to occur mainly in defective mRNAs. Existing next-generation sequencing methods that profile mRNA decay target either the 5’ or 3’ ends, thus missing information about the other end that could illuminate new insights into mRNA decay. During my post-doctoral training, I developed several novel transcriptome-wide sequencing methods that concurrently select both ends of mRNAs. I discovered a novel mechanism of co-translational decay of canonical mRNAs that involves repeated endonucleolytic cleavage events, mediated by translating ribosomes that we named “ribothrypsis”. Ribothrypsis is conserved between humans and yeast. We identified the unexpected ribosome-phased mRNAs fragmentation and found that deadenylation is not a prerequisite for mRNA decay. Our discovery of ribothrypsis revealed that co-translational mRNA decay is more widespread than previously thought. The central hypothesis of this proposal is that ribothrypsis is an evolutionarily conserved mechanism for modulating gene expression that can be triggered by numerous factors to recruit an unknown endonuclease that we termed “ribothrypsin”. We propose here to capitalize on our past discoveries and leverage cutting-edge novel RNA sequencing methods to achieve a comprehensive understanding of the mechanistic underpinnings of ribothrypsis and its regulation. In this proposal, we will investigate (i) the impact of cellular conditions that induce ribosome stalling on RNA decay intermediates; (ii) the conservation of ribothrypsis in other eukaryotes; (iii) the identity of ribothrypsin; and (iv) the role of RNA modifications in triggering ribothrypsis. These goals are mirrored by our long-term objective to understand the mechanisms that underlie RNA decay dysregulation in human diseases. The molecular insights gained in this proposal could also broaden our understanding of ribosome biology and RNA modifications.

项目概要/摘要 基因表达的转录后调控是正常细胞稳态的基础。 生物学领域的模型是，mRNA 主要作为“全长”分子存在，受到“保护” 翻译过程中核糖体的衰变 长期以来的理解是 mRNA 衰变是由核糖体引发的。 脱腺苷酸化，然后是两端的脱帽和随后的核酸外切衰变。 已知 mRNA 衰减主要发生在现有的下一代测序方法中。 配置文件 mRNA 衰减目标是 5' 或 3' 末端，因此缺少有关另一端的信息 在我的博士后培训期间，我创作了几本小说。 我发现了一种新的同时选择 mRNA 两端的转录组测序方法。 典型 mRNA 的共翻译衰变机制，涉及重复的核酸内切切割 通过翻译核糖体介导的事件，我们将其命名为“核糖体”。 我们鉴定了意想不到的核糖体定相 mRNA 片段，并发现 去腺苷酸化不是 mRNA 衰变的先决条件。我们对核糖体的发现揭示了共翻译。 mRNA 衰变比之前想象的更为普遍。该提议的中心假设是： ribothrypsis 是一种进化上保守的调节基因表达的机制，可以通过 招募一种未知核酸内切酶的因素有很多，我们在此建议将其称为“核酶”。 利用我们过去的发现并利用尖端的新型 RNA 测序方法来实现 全面了解核糖体的机械基础及其调节。 根据提议，我们将研究 (i) 诱导核糖体停滞的细胞条件对 RNA 衰变的影响 中间体；(ii) 其他真核生物中核酶的保存；(iii) 核酶的特性；以及 (iv) RNA 修饰在引发核糖体裂解中的作用反映在我们的长期目标中。 了解人类疾病中 RNA 衰变失调的机制。 该提案中获得的成果还可以拓宽我们对核糖体生物学和 RNA 修饰的理解。