Developmental Regulation of Gene Expression by Long Undecoded Transcript Isoforms

长未解码转录亚型对基因表达的发育调控

• 批准号: 10322025
• 负责人: Elcin Unal
• 金额: $ 31.61万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10322025
• 关键词: Address; Affect; Binding; Biological; Biological Process; CLN1 gene; CLN2 gene; Cell Differentiation process; Cells; Chromatin; Chromatin Remodeling Factor; Code; Coin; Coupled; Cyclins; Defect; Developmental Gene Expression Regulation; Disease; Distal; Down-Regulation; Endoderm; Ensure; Event; G1/S Transition; Gene Activation; Gene Cluster; Gene Expression; Genes; Genetic Transcription; Goals; Gonadal Dysgenesis; Human; Human Development; Lead; Link; Liquid substance; MDM2 gene; Malignant Neoplasms; Measurement; Meiosis; Messenger RNA; Metabolic Diseases; Mitosis; Mitotic; Modeling; Molecular; Names; Nucleosomes; Open Reading Frames; Outcome; Pathologic; Pathway interactions; Phenotype; Positioning Attribute; Process; Production; Protein Biosynthesis; Protein Isoforms; Protein Synthesis Inhibition; Proteins; Proteome; Proto-Oncogenes; Regulation; Regulator Genes; Repression; Ribosomes; Role; Saccharomycetales; Series; Signal Transduction; Stress; Suggestion; TP53 gene; Testing; Time; Transcript; Transcription Initiation Site; Transcriptional Activation; Translating; Tumor Suppressor Proteins; Yeasts; antagonist; base; biological adaptation to stress; chromatin modification; chromatin remodeling; experimental study; gene repression; genome-wide; genome-wide analysis; human disease; human embryonic stem cell; insight; mRNA sequencing; melanoma; nervous system disorder; pluripotency factor; programs; promoter; protein expression; recruit; response; stem cell differentiation; transcription factor; trend

PROJECT SUMMARY Dynamic gene expression programs drive essential biological processes including cellular differentiation and stress response pathways. During these processes, cells must simultaneously activate and repress distinct clusters of genes to facilitate the necessary shift in proteome synthesis. How gene repression is achieved amidst widespread transcriptional activation is not well understood. My lab has recently discovered a regulatory mechanism in budding yeast meiosis that achieves such coordination. Central to this mechanism is the transcription factor-driven expression of an alternative mRNA isoform called LUTI (Long Undecoded Transcript Isoform) from a distal gene promoter. This mRNA cannot produce functional protein due to competitive upstream open reading frames (uORFs) in its extended 5' leader. Instead, its transcription serves to repress the canonical mRNA transcription in cis through chromatin modifications, ultimately leading to inhibition of protein synthesis. Therefore, transcription of these mRNAs, despite carrying a full coding region, can directly cause gene repression. Consequently, a single transcription factor can synchronously activate and repress protein synthesis for distinct sets of genes, depending whether it binds to a canonical or a LUTI promoter, respectively. Furthermore, this mechanism is tunable and reversible, making it ideal for fluid cell state transitions that rely on dynamic changes in gene expression. The LUTI-based mechanism is neither limited to meiosis nor restricted to budding yeast, as it occurs during the unfolded protein response and is conserved in human cells. Importantly, the two essential branches of this regulation are both associated with human disease. First, misregulation of alternative transcription start sites is widespread across multiple cancers. Second, disruption of uORF expression is linked to a variety of disorders ranging from gonadal dysgenesis to melanoma. Therefore, dissecting the mechanism and biological scope of LUTI-based regulation is critical for our understanding of how cells control their gene expression programs, and how mistakes in this process can lead to pathological states. This proposal seeks to address fundamental questions regarding the mechanism and function of LUTI-based regulation in yeast and human cells. Experiments proposed in aim 1 will investigate how transcriptional repression is achieved by activation of LUTI promoters during meiosis and the unfolded protein response, where LUTIs are pervasively expressed. Experiments proposed in aim 2 will elucidate how the LUTI-based regulation is integrated into larger signaling networks to ensure precise and robust cell state transitions. Finally, experiments proposed in aim 3 will determine the evolutionarily conserved aspects of LUTI-based regulation and uncover the biological roles of LUTIs during human embryonic stem cell differentiation. The combination of studies described in this proposal will illuminate how cells dynamically control their gene expression programs with transcription factor-driven waves of coordinated gene activation and repression, not anticipated prior to our discovery of LUTIs.

项目概要 动态基因表达程序驱动重要的生物过程，包括细胞分化和 应激反应途径。在这些过程中，细胞必须同时激活和抑制不同的 促进蛋白质组合成必要转变的基因簇。基因抑制是如何实现的 广泛的转录激活尚不清楚。我的实验室最近发现了一个 芽殖酵母减数分裂中的调节机制实现了这种协调。这个机制的核心是 转录因子驱动的另一种 mRNA 异构体 LUTI（长未解码）的表达 来自远端基因启动子的转录本异构体）。该 mRNA 不能产生功能性蛋白质，因为 竞争性上游开放阅读框（uORF）位于其延伸的 5' 前导序列中。相反，它的转录服务 通过染色质修饰抑制顺式的经典 mRNA 转录，最终导致 抑制蛋白质合成。因此，这些 mRNA 的转录，尽管携带完整的编码区， 可直接引起基因抑制。因此，单个转录因子可以同步激活和 抑制不同基因组的蛋白质合成，具体取决于它是否与规范或 LUTI 结合 分别是启动子。此外，该机制是可调且可逆的，使其成为流体细胞的理想选择 依赖于基因表达动态变化的状态转换。 基于 LUTI 的机制既不限于减数分裂，也不限于芽殖酵母，因为它发生 在未折叠的蛋白质反应期间并且在人类细胞中保守。重要的是，两个重要的分支 这种调节都与人类疾病有关。第一，替代转录起始的错误调控 该位点广泛存在于多种癌症中。其次，uORF 表达的破坏与多种因素有关。 从性腺发育不全到黑色素瘤的疾病。因此，剖析其机制和生物学 基于 LUTI 的调控范围对于我们理解细胞如何控制其基因表达至关重要 程序，以及这个过程中的错误如何导致病态状态。该提案旨在解决 关于酵母和人类中基于 LUTI 的调节机制和功能的基本问题 细胞。目标 1 中提出的实验将研究转录抑制是如何通过激活 减数分裂和未折叠蛋白反应期间的 LUTI 启动子，其中 LUTI 普遍表达。 目标 2 中提出的实验将阐明如何将基于 LUTI 的调节整合到更大的信号传导中 网络以确保精确和稳健的细胞状态转换。最后，目标 3 中提出的实验将 确定基于 LUTI 的调控的进化保守性并揭示其生物学作用 人类胚胎干细胞分化过程中的 LUTI。本提案中描述的研究组合 将阐明细胞如何通过转录因子驱动动态控制其基因表达程序 协调基因激活和抑制的浪潮，在我们发现 LUTI 之前是没有预料到的。