CAREER: Chemical Biology Approaches to Study 5-Methylcytidine Derivatives in RNA and Develop CRISPR-Tet2-Based Epitranscriptomic Tool for Gene Regulation

职业：利用化学生物学方法研究 RNA 中的 5-甲基胞苷衍生物并开发基于 CRISPR-Tet2 的基因调控表观转录组工具

• 批准号: 1845486
• 负责人: Jia Sheng
• 金额: $ 60万
• 依托单位: SUNY at Albany
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1845486&HistoricalAwards=false
• 关键词: CAREER; Chemical; Biology; Approaches; Study

Nucleotides make up ribonucleic acids (RNAs) and contain the crucial "blueprint" of genetic information that is used by cells to make proteins. With this award, the Chemistry of Life Processes Program in the Division of Chemistry is funding Dr. Jia Sheng, from the State University of New York at Albany, to develop tools to incorporate modified nucleotides into RNA with high precision. These modifications change the RNA structure and function. These changes help us understand the role of RNA in numerous biological processes. The research focuses on the determining the three-dimensional structure of RNAs containing the modified nucleotides, understanding how these changes affect the reactivity of the RNA and then studying the study of the nucleotides' role in gene expression. The Dr. Sheng makes the new natural nucleotides and their 3D structures available to a wide range of researchers. The strategies developed under this project may be applicable to other enzymes targeting different RNA modifications, leading to a new general approach for RNA editing and thus, this research is considered to be within the Understanding the Rules of Life initiative. The research methodologies and outcomes of the study are integrated into a new course "Nucleic Acid Chemistry". Dr. Sheng is a leader in the "World of Chemistry" program which helps freshmen chemistry majors transition to college successfully. Dr. Sheng also organizes the annual "RNA Day" in his lab for local K-12 students offering experimental demonstrations and presentations to awaken their inner scientist. Finally, the research group recruits students and teachers to participate in summer research through the "University in the High School" program.The research studies made possible by this award focus on the relatively new epigenetic significance of chemically-modified cytosines in RNA. Synthetic 5-methylcytosine (5mC) and its oxidized variants (5xrC) are systematically incorporated into RNAs to determine their impact on the stability and local and global conformations of the RNAs. In addition, studies with 5xrC-modified RNAs reveal their effects on enzyme recognition and the mechanism of enzymatic oxidation of 5mC by the ten-eleven translocation (TET) family of oxygenases. Finally, the sequence targeting the clustered regularly interspaced short palindromic repeats (CRISPR) enzyme is fused with a TET oxygenase to create a tool that site-selectively oxidizes 5mC in natural RNAs. This tool is used to determine how 5xrC nucleotides affect the efficiency of translating cellular mRNAs into proteins. The knowledge gained and new general approaches developed by Dr. Sheng may benefit other scientists who study epitranscriptomic modifications of messenger RNA and posttranscriptional regulation of gene expression in eukaryotes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

核苷酸组成核糖核酸（RNA），并包含细胞用来制造蛋白质的关键遗传信息“蓝图”。有了这个奖项，化学系的生命过程化学项目正在资助奥尔巴尼的纽约州立大学的贾胜博士开发工具，将修饰的核苷酸高精度地掺入RNA中。这些修饰改变了RNA的结构和功能。 这些变化帮助我们了解RNA在许多生物过程中的作用。研究重点是确定含有修饰核苷酸的RNA的三维结构，了解这些变化如何影响RNA的反应性，然后研究核苷酸在基因表达中的作用。 Sheng博士将新的天然核苷酸及其3D结构提供给广泛的研究人员。在该项目下开发的策略可能适用于针对不同RNA修饰的其他酶，从而为RNA编辑提供了一种新的通用方法，因此，这项研究被认为是在理解生命规则倡议范围内。研究方法和研究成果被整合到一个新的课程“核酸化学”。 盛博士是“化学世界”项目的领导者，该项目帮助化学专业的新生顺利过渡到大学。盛博士还在他的实验室为当地的K-12学生组织一年一度的“RNA日”，提供实验演示和演讲，以唤醒他们内心的科学家。最后，研究小组通过"大学在高中"计划招募学生和教师参加暑期研究，通过该奖项使研究成为可能，重点关注RNA中化学修饰胞嘧啶的相对较新的表观遗传意义。将合成的5-甲基胞嘧啶（5mC）及其氧化变体（5xrC）系统地掺入RNA中，以确定其对RNA稳定性以及局部和全局构象的影响。此外，用5xrC修饰的RNA的研究揭示了它们对酶识别的影响和通过加氧酶的10 - 11易位（泰特）家族酶促氧化5mC的机制。最后，靶向成簇的规则间隔短回文重复序列（CRISPR）酶的序列与泰特加氧酶融合，以产生位点选择性氧化天然RNA中的5mC的工具。该工具用于确定5xrC核苷酸如何影响将细胞mRNA翻译成蛋白质的效率。盛博士所获得的知识和新的通用方法可能会使其他研究真核生物中信使RNA的表转录修饰和基因表达的转录后调控的科学家受益。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响评审标准进行评估来支持。

项目成果

Synthesis and Functionality Study of Photoswitchable Hydrazone Oligodeoxynucleotides

• DOI: 10.1002/cpz1.295
• 发表时间: 2021-11
• 期刊: Current Protocols
• 作者: Z. Chang;S. Mao;Y. Zheng;J. Sheng

RNA Phosphorothioate Modification in Prokaryotes and Eukaryotes

• DOI: 10.1021/acschembio.0c00163
• 发表时间: 2020-06-19
• 期刊: ACS CHEMICAL BIOLOGY
• 影响因子: 4
• 作者: Wu, Ying;Tang, Yaning;Sheng, Jia
• 通讯作者: Sheng, Jia

Bio-Orthogonal Chemistry Conjugation Strategy Facilitates Investigation of N-methyladenosine and Thiouridine Guide RNA Modifications on CRISPR Activity

• DOI: 10.1089/crispr.2022.0065
• 发表时间: 2022-11-15
• 期刊: CRISPR JOURNAL
• 影响因子: 3.7
• 作者: Hoy, Alyssa;Zheng, Ya Ying;Royzen, Maksim
• 通讯作者: Royzen, Maksim

Surface-enhanced Raman spectroscopy for drug discovery: peptide-RNA binding.

• DOI: 10.1007/s00216-022-04190-5
• 发表时间: 2022-08
• 期刊: ANALYTICAL AND BIOANALYTICAL CHEMISTRY
• 影响因子: 4.3
• 作者: Almehmadi, Lamyaa M.;Valsangkar, Vibhav A.;Halvorsen, Ken;Zhang, Qiang;Sheng, Jia;Lednev, Igor K.
• 通讯作者: Lednev, Igor K.

DNA Functionality with Photoswitchable Hydrazone Cytidine**

具有光开关腙胞苷的 DNA 功能**

• DOI: 10.1002/chem.202100742
• 发表时间: 2021
• 期刊: Chemistry – A European Journal
• 作者: Mao, Song;Chang, Zhihua;Ying Zheng, Ya;Shekhtman, Alexander;Sheng, Jia
• 通讯作者: Sheng, Jia