Embryonic gene regulatory networks from spatially resolved transcriptomes

来自空间解析转录组的胚胎基因调控网络

• 批准号: 9180711
• 负责人: ALEXANDER F SCHIER
• 金额: $ 64.35万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-12-01 至 2020-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9180711
• 关键词: Address; Anatomy; Animals; Atlases; Bayesian Modeling; Biological Models; CRISPR/Cas technology; Cells; Collaborations; Complement; Computational Biology; Computer Simulation; Congenital Abnormality; Data Set; Development; Developmental Biology; Embryo; Embryonic Development; Engineering; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Generations; Genes; Genetic Transcription; Genome; Genomic approach; Genomics; Genotype; Goals; Location; Maps; Mediating; Methods; Modeling; Modernization; Molecular Profiling; Mutagenesis; Pattern; Phenotype; Regulator Genes; Resolution; Resources; System; Systems Biology; Technology; Testing; Time; Tissues; Translating; Zebrafish; base; blastocyst; cell type; computerized tools; differential expression; gene complementation; genetic approach; genome editing; genome-wide; imaging approach; imaging genetics; in vivo; mutant; network models; new technology; outcome prediction; public health relevance; tool; transcriptome; transcriptome sequencing; whole genome; zebrafish development

 DESCRIPTION (provided by applicant): A major goal of systems developmental biology is to create datasets and models that describe, simulate and predict the full complement of gene regulatory interactions during embryogenesis. Such datasets and models are essential to fully understand how genomic information is translated into anatomical structure. Reductionist approaches have identified interactions among dozens of genes, but technical limitations have hindered the systems-wide elucidation of regulatory relationships at both high spatial resolution and whole-genome scale. This project will address this challenge and use novel technologies that enable large-scale mutagenesis and genome-wide expression profiling of single cells to generate gene regulatory network models. The zebrafish blastula will be used as a vertebrate model system, because of its similarities to mammalian embryos and the applicability of powerful genetic, imaging and genomic approaches. The project builds on a long-standing collaboration that combines the Schier lab's expertise in developmental biology, imaging and genetics with the Regev's lab expertise in computational biology, genomics and systems biology. Optimized one-generation CRISPR/Cas9 genome editing will be used to generate mutants for dozens of transcription regulators expressed during early embryogenesis. Mutants will be characterized by generating whole-genome high-resolution gene expression atlases using a novel technology called Seurat. Seurat combines single-cell RNA sequencing with computational mapping of cells to specific regions and cell types in the embryo. The resulting transcriptome maps serve as the inputs to generate models for gene regulatory network activity using clustering-based and Bayesian modeling approaches. Regulatory interactions predicted in silico will be tested in vivo by analyzing gene expression upon perturbation of transcription regulators. The project fulfills the stated purpose of PAR-15-020 "to complement the reductionist focus of modern developmental biology and provide a more comprehensive understanding of the causal relationships leading to normal and abnormal embryogenesis". The gene regulatory interactions discovered in this project will help inform programming and reprogramming approaches and will identify candidate interactions that might be involved in the development of birth defects. The project will generate extensive high-quality datasets and atlases for developmental and systems biologists and provide a framework to dissect gene regulatory networks in other systems.

 描述（由适用提供）：系统发展生物学的主要目标是创建数据集和模型，以描述，模拟和预测胚胎发生过程中基因调节相互作用的完整补体。这样的数据集和模型对于充分了解基因组信息如何转化为解剖结构至关重要。还原论的方法已经确定了数十个基因之间的相互作用，但是技术局限性阻碍了在高空间分辨率和全基因组量表上范围内的整个调节关系阐明。该项目将解决这一挑战，并使用新型技术，这些技术可以使单个细胞的大规模诱变和全基因组表达分析生成基因调节网络模型。斑马鱼囊肿将用作脊椎动物模型系统，因为它与哺乳动物的胚胎相似，并且具有强大的遗传，成像和基因组方法的适用性。项目以长期的合作为基础，该合作结合了Schier实验室在发育生物学，成像和遗传学方面的专业知识与Regev的计算生物学，基因组学和系统生物学方面的实验室专业知识。优化的一代CRISPR/CAS9基因组编辑将用于生成在早期胚胎发生过程中表达的数十个转录调节剂的突变体。突变体的特征是使用一种称为Seurat的新技术生成全基因组高分辨率基因表达地图。 Seurat将单细胞RNA测序与细胞的计算映射结合到胚胎中的特定区域和细胞类型。所得的转录组图是使用基于聚类和贝叶斯建模方法生成基因调节网络活动模型的输入。在体内将通过分析转录调节剂扰动基因表达来在体内测试中预测的调节相互作用。项目实现了PAR-15-020的既定目的“完成现代发展生物学的还原主义重点，并对导致正常和异常胚胎发生的因果关系提供了更全面的理解”。该项目中发现的基因调节互动将有助于为编程和重编程方法提供信息，并将确定可能与出生缺陷发展有关的候选互动。该项目将为发育和系统生物学家生成广泛的高质量数据集和地图集，并提供一个框架以剖析其他系统中的基因调节网络。