Probing co-transcriptional gene regulatory logics in human transcriptomes

项目摘要 哺乳动物基因的结构使得能够通过使用替代的转录物来产生多种转录物。 启动子，替代终止位点和差异剪接外显子，这大大扩展了编码 我们基因组的能力。我们最近发现外显子剪接可以激活位于 这些新的启动子通常出现在注释的内部外显子附近，产生“杂交”外显子， 可用作不同转录物中的第一和内部外显子。对这些过程的管理 对基因表达有着深远的影响，但具体的机制却知之甚少。事实上，Key 我们对共转录基因调控的理解中的差距包括特定的机制和反式- 参与剪接依赖性转录调控的因子和剪接体组分的作用。 此外，由于外显子剪接影响从最上游和附近启动子的转录，因此它是 目前尚不清楚新启动子的激活如何影响同一细胞中替代启动子的表达， 基因.我实验室的目标是了解功能性耦合的分子过程 转录和RNA加工之间的联系，旨在揭示基因调控的新机制， 重要的背景。在这项建议中，我们将联合收割机结合遗传、分子和基因组技术， 通量计算分析，以解决两个关键方面的共转录基因调控。一是 将集中在如何剪接激活转录从杂交外显子，并确定关键的顺式和反式因子 参与杂交外显子启动子的剪接依赖性激活。同时，我们假设剪接- 依赖性启动子激活通过调节它们的转录来影响来自附近替代启动子的转录。 染色质环境然后，我们将研究启动子激活如何从替代转录调节转录。 启动子和识别启动子干扰背后的机制，对基因表达有深远的影响。 调控此外，我们将探讨启动子激活对附近其他启动子的影响， 干细胞分化，以确定其对基因调控和心脏特性的贡献。我们的研究将 导致的见解至关重要的揭露分子事件，累积建立共转录基因 监管网络。最终，我们的发现将导致新的计算工具的发展，以预测 基因调控网络和设计分子来控制具有治疗益处的基因表达。

PROJECT SUMMARY The architecture of mammalian genes enables the production of multiple transcripts by using alternative promoters, alternative termination sites, and differentially spliced exons, which greatly expand the coding capacity of our genomes. We recently discovered that exon splicing can activate cryptic promoters located nearby and that these new promoters often arise near annotated internal exons creating “hybrid” exons that can be used as both first and internal exons in different transcripts. The regulation of these processes has profound impacts on gene expression, and yet the specific mechanisms are poorly understood. Indeed, key gaps in our understanding of co-transcriptional gene regulation include the specific mechanisms and the trans- factors involved in the splicing-dependent regulation of transcription and the roles of spliceosome components. Moreover, since exon splicing influences transcription from the most upstream and nearby promoter, it is unclear how the activation of a new promoter affects the expression of alternative promoters in the same genes. The goal of my lab is to understand the molecular processes underlying the functional coupling between transcription and RNA-processing, aiming to uncover novel mechanisms of gene regulation in important contexts. In this proposal, we will combine genetic, molecular, and genomic techniques with high- throughput computational analyses to address two key aspects of co-transcriptional gene regulation. First, we will focus on how splicing activates transcription from hybrid exons and identify key cis- and trans-factors involved in the splicing-dependent activation of promoters of hybrid exons. Also, we hypothesize that splicing- dependent promoter activation affects transcription from nearby alternative promoters by modulating their chromatin environment. We will then work on how promoter activation modulates transcription from alternative promoters and discern the mechanism behind promoter interference that has profound impacts on gene regulation. Furthermore, we will explore the effects of promoter activation on other promoters nearby during stem cell differentiation to define their contribution to gene regulation and cardiac identity. Our research will result in insights crucial to uncovering the molecular events that cumulatively establish co-transcriptional gene regulatory networks. Ultimately, our findings will lead to the development of new computational tools to predict gene regulatory networks and design molecules to control gene expression with therapeutic benefits.