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.

项目总结 动态基因表达程序驱动基本的生物过程，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DISTINCT 基因簇以促进蛋白质组合成中必要的转变。基因抑制是如何实现的 在广泛的转录激活中，人们还没有很好地理解。我的实验室最近发现了一种 实现这种协调的芽期酵母减数分裂的调节机制。这一机制的核心是 转录因子驱动的另一种名为LUTI(Long Undected)的mRNA亚型的表达 来自远端基因启动子的转录异构体)。这种信使核糖核酸不能产生功能蛋白 竞争性上游开放阅读框(UORF)位于其延伸的5‘端。相反，它的转录服务于 通过染色质修饰抑制顺式基因中规范的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， 会直接导致基因抑制。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，这取决于它是与规范的还是与Luti结合的 分别为启动子。此外，这种机制是可调的和可逆的，使其成为流体电池的理想选择。 依赖于基因表达的动态变化的状态转换。 这种基于Luti的机制既不局限于减数分裂，也不局限于萌芽酵母。 在未折叠的蛋白质反应中，它在人类细胞中是保守的。重要的是，这两个基本分支 这两种调控方式都与人类疾病有关。第一，对替代转录启动的错误调控 肿瘤部位广泛存在于多种癌症中。第二，uORF表达的中断与多种 疾病范围从性腺发育不全到黑色素瘤。因此，剖析其发病机制和生物学意义 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是至关重要的 程序，以及这个过程中的错误如何导致病态。这项提案旨在解决 酵母和人体中基于LUTI的调控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 Luti启动子在减数分裂和未折叠的蛋白反应中，Lutis在那里广泛表达。 目标2中提出的实验将阐明基于LUTI的调节如何整合到更大的信号中 网络，以确保准确和可靠的小区状态转换。最后，目标3中提出的实验将 确定基于LUTI的调节在进化上保守的方面，并揭示LUTI的生物学作用 人类胚胎干细胞分化过程中的狼疮。本提案中描述的研究的组合 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 一波协调的基因激活和抑制，在我们发现Lutis之前没有预料到。