Assembly of a dynamic spatio-temporal map of gene expression regulation during intestinal stem cell differentiation to enterocytes

肠道干细胞分化为肠上皮细胞过程中基因表达调控动态时空图的组装

• 批准号: 453309976
• 负责人: Dr. Nike Walther
• 金额: --
• 依托单位: Department of Molecular and Cell Biology
• 依托单位国家: 德国
• 项目类别: WBP Fellowship
• 财政年份: 2020
• 资助国家: 德国
• 起止时间: 2019-12-31 至 2023-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/453309976?language=en
• 关键词: Assembly; dynamic; spatio; temporal; map

Loss of transcriptional control and concomitant aberrant gene expression are hallmarks of cancer and developmental disorders. Precise gene expression regulation throughout development ensures cell fate specification and differentiation towards the formation of healthy tissues. Transcription regulation is achieved by lineage-determining transcription factors (TFs) binding to cis-regulatory DNA elements of their target genes, thereby inducing cell type-specific gene expression programs. In the multicellular context of developing embryos or renewing adult tissues, gene expression is influenced by the cellular position and signaling environment. To understand the regulatory mechanisms ensuring healthy tissue formation, it is therefore essential to resolve cell type-specific developmental gene regulation spatially and temporally in such a multicellular system.In the mammalian intestinal epithelium, a spatial differentiation hierarchy guides directional movement of differentiating intestinal stem cells (ISCs). Recapitulating this behavior in vitro, mouse small intestinal organoids provide a well-defined 3D tissue model to study spatiotemporal gene expression regulation during ISC differentiation. Building upon recent developments in sequencing-based Micro-C and lattice light-sheet microscopy, this proposal combines cutting-edge genomics with live-cell imaging from the tissue to the single-molecule level to probe space and time dimensions of gene expression regulation during differentiation in intestinal organoids. Focusing on the differentiation pathway from ISCs to enterocytes, which are responsible for nutrient uptake, this project addresses the following aims:1) Characterization of cell type-specific chromatin organization in the intestinal epithelium to reveal changes in chromatin structure during differentiation.2) Long-term visualization of TFs driving cell-fate decisions and correlation with target gene expression to reveal their dynamics relative to cell type and position within intestinal organoids.3) Dynamic biophysical and quantitative TF characterization relative to cell type and position within intestinal organoids to conclude a data-driven model for cell fate-determining gene regulatory mechanisms.This work will provide the first spatiotemporal map of lineage-determining TFs inducing cell type-specific gene expression programs to drive ISC differentiation to enterocytes. It will further reveal how cell fate specification is modulated by chromatin reorganization, TF abundance and DNA-binding behavior within the multicellular environment of intestinal organoids. Furthermore, this work will set the technological groundwork for future studies to understand the mechanisms causing disease during tissue formation and renewal.

转录控制的丧失和伴随的异常基因表达是癌症和发育障碍的标志。在整个发育过程中精确的基因表达调控确保了细胞命运的特异性和分化，以形成健康的组织。转录调节是通过谱系决定转录因子（TF）与其靶基因的顺式调节DNA元件结合，从而诱导细胞类型特异性基因表达程序来实现的。在发育胚胎或更新成体组织的多细胞背景下，基因表达受到细胞位置和信号环境的影响。因此，在哺乳动物的肠上皮中，空间分化层次引导着分化中的肠干细胞（ISCs）的定向运动。在体外重述这种行为，小鼠小肠类器官提供了一个定义明确的3D组织模型，以研究ISC分化过程中的时空基因表达调控。基于基于测序的Micro-C和点阵光片显微镜的最新发展，该提案将尖端基因组学与从组织到单分子水平的活细胞成像相结合，以探测肠道类器官分化过程中基因表达调控的空间和时间维度。该项目关注从ISCs到肠上皮细胞的分化途径，负责营养摄取，旨在实现以下目标：1）表征肠上皮中的细胞类型特异性染色质组织以揭示分化期间染色质结构的变化。2）长期可视化TF驱动细胞命运决定以及与靶基因表达的相关性，以揭示其相对于肠类器官内的细胞类型和位置的动态。3）相对于肠类器官内的细胞类型和位置的动态生物物理和定量TF表征，以得出数据-这项工作将提供第一个时空图谱的谱系决定TF诱导细胞类型特异性基因表达程序，以驱动ISC分化为肠上皮细胞。它将进一步揭示细胞命运的规范是如何通过染色质重组，TF丰度和DNA结合行为在肠道类器官的多细胞环境中调节的。此外，这项工作将为未来的研究奠定技术基础，以了解组织形成和更新过程中引起疾病的机制。