Translation of small open reading frames in 3'UTR enhances translation of canonical open reading frames

3UTR 中小型开放阅读框的翻译增强了规范开放阅读框的翻译

• 批准号: 10064919
• 负责人: Qiushuang Wu
• 金额: $ 3.1万
• 依托单位: STOWERS INSTITUTE FOR MEDICAL RESEARCH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10064919
• 关键词: 3' Untranslated Regions; 5' Untranslated Regions; Affect; Award; Bioinformatics; Biological; Biological Assay; Cancer Biology; Cancer Etiology; Candidate Disease Gene; Cells; Cellular biology; Clinical; DNA; Data; Databases; Development; Disease; Drug Design; Drug Targeting; Embryo; Eukaryotic Cell; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genomics; Health; Human; Human Cell Line; Kidney Neoplasms; Kinetics; Knowledge; Light; Malignant Neoplasms; Measures; Mediating; Messenger RNA; Methodology; MicroRNAs; Molecular; Molecular Biology; Mutation; Open Reading Frames; Orthologous Gene; Outcome; Pathogenesis; Pathologic; Patients; Pattern; Peptide Initiation Factors; Peptides; Play; Polyadenylation; Population; Post-Transcriptional Regulation; Process; Proteins; Proteomics; Publishing; Regulation; Regulatory Element; Regulatory Pathway; Reporter; Reporting; Research; Research Project Grants; Ribosomes; Role; Site; Techniques; The Cancer Genome Atlas; Training; Translating; Translations; Untranslated RNA; Untranslated Regions; Vertebrates; Work; Zebrafish; base; cancer cell; career; genome-wide; genomic profiles; human disease; innovation; insight; interest; mRNA Stability; machine translation; molecular imaging; novel; novel diagnostics; ribosome profiling; single molecule; transcriptome sequencing; tumor

Project Summary Ribosome and proteomic profiling have revealed a large number of small translated open reading frames (ORF) within previously described “untranslated regions” (UTRs) and long non-coding RNAs. While some of the small ORFs depend on the encoded peptide to function in various fundamental processes (e.g., development). Translation of small ORFs in the 5’UTR, known as upstream-ORFs (uORFs), usually represses gene expression, independent of the encoded peptide. Small ORFs have also been reported in 3'UTR, termed downstream ORF (dORF). However, the dORF function and their relationship to human health and disease remain unknown. I characterized dORFs from human and zebrafish using ribosome profiling data. My preliminary data indicates, contrary to uORFs, translation of dORFs (small ORF in the 3’UTR) strongly enhances translation of the canonical ORFs and remains an uncharacterized regulatory mechanism across vertebrates. The objectives are: 1) Dissect at the single molecular level how dORF enhances translation of the canonical CDS. And 2) Determine whether alternative polyadenylation in cancer influences dORF regulation to cause cancer. The rationale for the proposed research is to gain a mechanistic understanding of dORF-mediated regulation and to assess the possible biological importance of dORF dysregulation under disease conditions (e.g. Cancer). This proposal is conceptually innovative as it is based on the exploration of a novel, yet widespread translation regulatory mechanism conserved across vertebrates. Technically, this proposal will combine single molecular imaging, genomic profiles (RNA-seq, Ribosome profiling), and reporter approaches in different human cell lines (including cancer cells) and published patient data. The outcomes from this project will emphasize the role of ribosome as a master gene expression regulator, and shield light on the importance of small ORFs. This translation kinetics work about dORF will provide critical insights into the molecular mechanism of this uncharacterized regulatory pathway. Exploring dORF dysregulation in cancer due to APA will highlight the mRNA itself as disease driver even without any mutation in DNA, and it also indicates possible clinical impact of dORF to detect and even cure cancer. My long-term interest is to study gene expression dysregulation in cancer. This training award will increase my knowledge background of cancer biology, molecular biology and bioinformatics. It will also promote the technical training of single molecular imaging, ribosome profiling, cell biology assays for cancer. Overall, this proposal will help me for future independent cancer molecular/genomic career.

项目概要 核糖体和蛋白质组分析揭示了大量小型翻译开放阅读框 (ORF) 在先前描述的“非翻译区”（UTR）和长非编码 RNA 中，而一些小的。 ORF 依赖于编码的肽在各种基本过程（例如发育）中发挥作用。 5’UTR 中小 ORF 的翻译，称为上游 ORF (uORF)，通常会抑制基因表达， 独立于编码肽的小 ORF 也已在 3'UTR 中报道，称为下游 ORF。 (dORF)。然而，dORF 的功能及其与人类健康和疾病的关系仍然未知。 我使用核糖体分析数据对人类和斑马鱼的 dORF 进行了表征，我的初步数据表明， 与uORF相反，dORF（3'UTR中的小ORF）的翻译强烈增强了 规范的 ORF 仍然是脊椎动物中一种未表征的调节机制。 目标是： 1) 在单分子水平上剖析 dORF 如何增强规范 CDS 的翻译。 2) 确定癌症中的选择性聚腺苷酸化是否会影响 dORF 调节从而导致癌症。 拟议研究的基本原理是获得对 dORF 介导的调控的机制理解 并评估疾病条件下（例如癌症）dORF 失调可能的生物学重要性。 该提案在概念上具有创新性，因为它基于对新颖但广泛的翻译的探索 从技术上讲，该提案将结合单分子。 不同人类细胞系的成像、基因组图谱（RNA-seq、核糖体图谱）和报告方法 （包括癌细胞）和已发表的患者数据。 该项目的成果将强调核糖体作为主要基因表达调节剂的作用，以及 这项关于 dORF 的翻译动力学工作将提供关键的信息，以阐明小 ORF 的重要性。 深入了解这种未知调节途径的分子机制。 即使 DNA 没有任何突变，由于 APA 导致的癌症也会突出 mRNA 本身作为疾病驱动因素，而且它 还表明 dORF 对检测甚至治愈癌症可能产生的临床影响。 我的长期兴趣是研究癌症中的基因表达失调，这个培训奖将增加我的兴趣。 癌症生物学、分子生物学和生物信息学的知识背景也将促进技术的发展。 总体而言，该提案检测将提供单分子成像、核糖体分析、癌症细胞生物学的培训。 帮助我未来独立的癌症分子/基因组职业。