SINGLE-CELL CHEMICAL TRANSCRIPTOMIC DISSECTION OF AN ESSENTIAL TRANSCRIPTION FACTOR NETWORK

必需转录因子网络的单细胞化学转录组解剖

• 批准号: 10244771
• 负责人: Vijay Ramani
• 金额: --
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-10 至 2021-11-03
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10244771
• 关键词: Address; Atlases; Cells; Chemicals; Chromatin; Decision Making; Development; Dissection; Dose; Genes; Genetic Transcription; Genome; Genomics; Health; Helix-Turn-Helix Motifs; Homeostasis; Leucine Zippers; Link; Malignant Neoplasms; Metabolism; Methods; Output; Play; Proteins; Publishing; Regulator Genes; Role; Seminal; Stem cell pluripotency; Techniques; cell growth; chemical genetics; computerized tools; dosage; embryonic stem cell; epigenome; experimental study; in vivo; insight; novel; pluripotency; protein degradation; screening; single-cell RNA sequencing; transcription factor; transcriptional reprogramming; transcriptomics

SINGLE-CELL CHEMICAL TRANSCRIPTOMIC DISSECTION OF AN ESSENTIAL TRANSCRIPTION FACTOR NETWORK PROJECT SUMMARY / ABSTRACT Basic helix-loop-helix leucine zipper transcription factors (TFs) in the extended MYC network play essential roles regulating cellular growth, differentiation, and homeostasis. Seminal studies have implicated MYC and its interacting network of TFs as drivers of proliferation and metabolism in development and cancer, but how dosage of these factors encodes transcriptional state remains contentious. Here, I propose a novel chemical genomic framework to systematically determine how TF dosage, transcriptional output, and cellular state are linked. I will combine our recently published massively multiplex single-cell RNA-seq screening method (sci-Plex) with chemical genetic degradation of protein targets to examine how embryonic stem cells are transcriptionally reprogrammed following dosed degradation of TFs. I will then employ state-of-the-art computational tools to quantify the cellular state trajectories encoded by specific dosages. Finally, I will leverage this single-cell ‘perturbation atlas’ to support genomic mapping experiments to understand how reduced dosage of these factors in vivo leads to physical redistribution across the genome. These studies will i.) illuminate mechanisms by which TF dosages encode transcriptional output, ii.) elucidate how intracellular concentrations of interacting TFs maintain chromatin, transcriptional, and cellular states, and iii.) provide mechanistic insight into how a transcription factor network interacts with the epigenome to regulate mammalian pluripotency. More generally, these approaches have the potential to address long-standing gene regulatory questions of how protein dosage controls cellular state in both health and in cancer.

原发性转移的单细胞化学透皮解剖 因子网络 项目总结/摘要 碱性螺旋-环-螺旋亮氨酸拉链转录因子（TF）在扩展的MYC网络中发挥重要作用 调节细胞生长、分化和体内平衡。精液研究表明MYC及其 TF的相互作用网络作为发育和癌症中增殖和代谢的驱动因素，但如何剂量 这些因子编码的转录状态仍然存在争议。在这里，我提出了一种新的化学基因组 该框架旨在系统地确定TF剂量、转录输出和细胞状态之间的联系。我会 联合收割机结合我们最近发表的大规模多重单细胞RNA-seq筛选方法（sci-seq）， 蛋白质靶点的化学遗传降解，以检查胚胎干细胞是如何转录的， 在TF的剂量降解后重新编程。然后我会用最先进的计算工具 量化由特定剂量编码的细胞状态轨迹。最后，我将利用这个单细胞 “扰动图谱”支持基因组作图实验，以了解如何减少这些因素的剂量 在体内会导致整个基因组的物理再分布。这些研究将（）。阐明机制， TF剂量编码转录输出，ii.）阐明相互作用TF的细胞内浓度 维持染色质、转录和细胞状态，和iii.）提供了一个机械的洞察力， 转录因子网络与表观基因组相互作用以调节哺乳动物多能性。更一般地说， 这些方法有可能解决长期存在的基因调控问题， 控制健康和癌症的细胞状态。