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: 10550144
• 负责人: Elcin Unal
• 金额: $ 31.5万
• 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/10550144
• 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; 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; TP53 gene; Testing; Transcript; Transcription Initiation Site; Transcriptional Activation; Translating; Tumor Suppressor Proteins; Yeasts; antagonist; biological adaptation to stress; chromatin modification; 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.

项目摘要 动态基因表达程序推动了基本的生物学过程，包括细胞分化和 压力反应途径。在这些过程中，细胞必须同时激活和压抑不同 基因簇促进蛋白质组合成的必要转移。如何实现基因抑制 在广泛的转录激活中，尚不清楚。我的实验室最近发现了一个 实现这种协调的酵母菌减数分裂的调节机制。这种机制的核心是 替代mRNA同工型的转录因子驱动的表达称为luti（长期未分解 远端基因启动子的转录本同工型。由于 竞争性上游的开放式阅读框架（UORFS）在其扩展的5'领导者中。相反，它的转录服务 通过染色质修饰抑制CIS中的规范mRNA转录，最终导致 抑制蛋白质合成。因此，尽管携带完整的编码区域，这些mRNA的转录， 可以直接引起基因抑制。因此，单个转录因子可以同步激活，并且 抑制蛋白质合成的不同基因集，具体取决于其与规范或luti结合 启动子分别。此外，这种机制是可调且可逆的，使其非常适合流体细胞 依赖基因表达动态变化的状态转变。 基于LUTI的机制既不局限于减数分裂，也不仅限于发芽的酵母菌，因为它发生 在展开的蛋白质反应中，在人类细胞中保守。重要的是，两个基本分支 该法规都与人类疾病有关。首先，替代转录开始 站点在多种癌症中广泛存在。其次，UORF表达的破坏与多种 从性腺发育不全到黑色素瘤的疾病。因此，解剖机制和生物学 基于LUTI的调节范围对于我们对细胞如何控制其基因表达的理解至关重要 程序，以及此过程中的错误如何导致病态状态。该建议旨在解决 关于基于酵母和人类的基于LUTI调节的机制和功能的基本问题 细胞。 AIM 1中提出的实验将研究如何通过激活来实现转录抑制 在减数分裂和展开的蛋白质反应期间的luti启动子，卢蒂斯（Lutis）普遍表达。 AIM 2中提出的实验将阐明如何将基于LUTI的调节整合到较大的信号中 网络以确保精确且健壮的单元状态过渡。最后，AIM 3中提出的实验将 确定基于LUTI的调节的进化保守方面，并发现 人类胚胎干细胞分化过程中的lutis。该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的动态控制其基因表达程序 在我们发现lutis之前，没有预料的是协调基因激活和抑制的波。