Developmental Regulation of Gene Expression by Long Undecoded Transcript Isoforms

项目摘要 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不同的 基因簇，以促进蛋白质组合成的必要转变。基因抑制是如何实现的 在广泛的转录激活中的作用还不是很清楚。我的实验室最近发现了一种 芽殖酵母减数分裂的调节机制，以达到这种协调。这一机制的核心是 转录因子驱动的另一种称为LUTI（长未解码）的mRNA亚型的表达 转录物同种型）。这种mRNA不能产生功能蛋白， 竞争性上游开放阅读框（uORF）。相反，它的转录服务于 通过染色质修饰抑制典型的mRNA顺式转录，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， 可以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，这取决于它是否与典型或LUTI结合 启动子，分别。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，并且在人类细胞中是保守的。重要的是，这两个基本分支 都与人类疾病有关。第一，交替转录启动的误调节 在多种癌症中广泛存在。第二，uORF表达的破坏与多种基因突变有关。 从性腺发育不全到黑色素瘤。因此，解剖机制和生物 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理状态。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 细胞在aim1中提出的实验将研究转录抑制是如何通过激活 减数分裂期间的LUTI启动子和未折叠的蛋白质反应，其中LUTI普遍表达。 目标2中提出的实验将阐明基于LUTI的调节如何被整合到更大的信号中 网络以确保精确和鲁棒的小区状态转换。最后，目标3中提出的实验将 确定基于LUTI的调节的进化保守方面，并揭示 人胚胎干细胞分化过程中的LUTI。本提案中所述的研究组合 将阐明细胞如何动态控制其基因表达程序与转录因子驱动 协调的基因激活和抑制波，在我们发现LUTI之前没有预料到。

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.