mTOR-regulated U2AF plasticity and alternative polyadenylation

mTOR 调节的 U2AF 可塑性和替代聚腺苷酸化

• 批准号: 10795517
• 负责人: Jeongsik Yong
• 金额: $ 19.97万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-17 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10795517
• 关键词: 3' Splice Site; Acute Myelocytic Leukemia; Alternative Splicing; Biogenesis; CRISPR/Cas technology; Cell model; Cells; Communication; Data; Disease model; Dysplasia; Elements; Environment; FRAP1 gene; Gene Expression; Gene Expression Process; Genome engineering; Goals; Heterodimerization; Histones; Link; Malignant Neoplasms; Mediating; Modeling; Mutation; Myelogenous; Outcome; Pathogenesis; Phenotype; Phosphorylation; Phosphotransferases; Physiological; Poly A; Polyadenylation; RNA Splicing; Role; Signal Pathway; Testing; bioinformatics pipeline; extracellular; mRNA Precursor; prognostic; programs; transcriptome; transcriptomics

mTOR-regulated U2AF plasticity and alternative polyadenylation PROJECT SUMMARY/ABSTRACT U2AF (U2 auxiliary factor, comprised of U2AF1 and U2AF2) is an essential splicing factor and functions in 3’splice site selection during pre-mRNA processing. U2AF has been known to form a constitutive heterodimer and is important for alternative and constitutive splicing. However, preliminary data show that mTOR (mammalian target of rapamycin) signaling pathway controls the U2AF heterodimerization by U2AF2 phosphorylation- dependent manner. These regulated interactions between U2AF1 and U2AF2 constitute the U2AF plasticity. This newly discovered U2AF plasticity is a key element in alternative splicing and alternative polyadenylation. Based on these findings, the following central hypothesis can be proposed: the U2AF plasticity is a gateway to mTOR-regulated transcriptome reprogramming. The goals of this proposal are to investigate the regulatory mechanism of U2AF plasticity by mTOR and understand how this U2AF plasticity programs the transcriptome by focusing on alternative splicing and alternative polyadenylation. To this end, two specific aims are proposed. In the first aim, the role of mTOR-U2AF plasticity in transcriptome reprogramming will be investigated. CRISPR/Cas9-mediated genome engineering will be conducted to build up cell models which will constitutively polarize the U2AF plasticity in one way or the other. These cell models will be then tested for cell phenotypic changes and the transcriptomic changes will be profiled. Mutations in U2AF1 are prognostic in acute myeloid leukemia and myeloid dysplasia. Physiological relevance of these mutations to U2AF plasticity will be tested and a current model for disease pathogenesis will be challenged. For these tasks, a new bioinformatic pipeline will be developed. In the second aim, the regulatory axis that connects mTOR, U2AF plasticity, and histone biogenesis will be dissected. A kinase(s) that controls the U2AF plasticity will be identified. Also, the mechanism by which the U2AF plasticity programs alternative splicing and alternative polyadenylation will be delineated. Finally, the outcome of mTOR-U2AF plasticity-mediated alternative polyadenylation in the histone biogenesis will be examined. Together, this project will advance the understanding of transcriptome programming by mTOR- coordinated U2AF plasticity and suggest mechanistic cascades that communicate extracellular/cellular environments to gene expression programs. It will also challenge a current model of U2AF1 mutations in cancer pathogenesis. Moreover, this project will establish a link between mTOR and histone biogenesis through U2AF plasticity.

mTOR 调节的 U2AF 可塑性和替代聚腺苷酸化 项目概要/摘要 U2AF（U2辅助因子，由U2AF1和U2AF2组成）是一个重要的剪接因子，在 3’s 剪接位点在前 mRNA 加工过程中的选择。 U2AF 已知可形成组成型异二聚体 对于选择性剪接和本构剪接很重要。然而，初步数据显示，mTOR（哺乳动物 雷帕霉素靶点）信号通路通过 U2AF2 磷酸化控制 U2AF 异二聚化 依赖方式。 U2AF1 和 U2AF2 之间的这些受调节的相互作用构成了 U2AF 可塑性。 这种新发现的 U2AF 可塑性是选择性剪接和选择性聚腺苷酸化的关键要素。 基于这些发现，可以提出以下中心假设：U2AF 可塑性是通向 mTOR 调节的转录组重编程。该提案的目标是调查监管 mTOR 的 U2AF 可塑性机制，并了解这种 U2AF 可塑性如何编程转录组 通过关注选择性剪接和选择性聚腺苷酸化。为此，提出了两个具体目标。 第一个目标是研究 mTOR-U2AF 可塑性在转录组重编程中的作用。 将进行CRISPR/Cas9介导的基因组工程来建立细胞模型，该模型将构成 以一种或另一种方式极化 U2AF 可塑性。然后将测试这些细胞模型的细胞表型 变化和转录组变化将被分析。 U2AF1 突变可预测急性髓系疾病 白血病和骨髓发育不良。将测试这些突变与 U2AF 可塑性的生理相关性 目前的疾病发病机制模型将受到挑战。对于这些任务，新的生物信息学管道将 得到开发。第二个目标是连接 mTOR、U2AF 可塑性和组蛋白的调控轴 生物起源将被剖析。将鉴定控制 U2AF 可塑性的激酶。另外，该机制 由此将描述 U2AF 可塑性程序的选择性剪接和选择性聚腺苷酸化。 最后，mTOR-U2AF 可塑性介导的替代多聚腺苷酸化在组蛋白生物发生中的结果 将接受检查。总之，该项目将增进对 mTOR 转录组编程的理解- 协调 U2AF 可塑性并提出细胞外/细胞通讯的机制级联 环境到基因表达程序。它还将挑战当前的癌症 U2AF1 突变模型 发病。此外，该项目将通过 U2AF 在 mTOR 和组蛋白生物发生之间建立联系 可塑性。

项目成果

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

• DOI: 10.1371/journal.pcbi.1004465
• 发表时间: 2015-12
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Zhang W;Chang JW;Lin L;Minn K;Wu B;Chien J;Yong J;Zheng H;Kuang R
• 通讯作者: Kuang R

53BP1-ACLY-SLBP-coordinated activation of replication-dependent histone biogenesis maintains genomic integrity.

• DOI: 10.1093/nar/gkab1300
• 发表时间: 2022-02-22
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Wu T;Jun S;Choi EJ;Sun J;Yang EB;Lee HS;Kim SY;Fahmi NA;Jiang Q;Zhang W;Yong J;Lee JH;You HJ
• 通讯作者: You HJ

Alternative Polyadenylation in Human Diseases.

• DOI: 10.3803/enm.2017.32.4.413
• 发表时间: 2017-12
• 期刊: Endocrinology and metabolism (Seoul, Korea)
• 作者: Chang JW;Yeh HS;Yong J
• 通讯作者: Yong J

APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.

• DOI: 10.1186/s12859-022-04939-w
• 发表时间: 2022-09-28
• 期刊: BMC BIOINFORMATICS
• 影响因子: 3
• 作者: Fahmi, Naima Ahmed;Ahmed, Khandakar Tanvir;Chang, Jae-Woong;Nassereddeen, Heba;Fan, Deliang;Yong, Jeongsik;Zhang, Wei
• 通讯作者: Zhang, Wei

Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies.

• DOI: 10.5483/bmbrep.2017.50.4.019
• 发表时间: 2017-04
• 期刊: BMB reports
• 影响因子: 3.8
• 作者: Yeh HS;Zhang W;Yong J
• 通讯作者: Yong J