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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

基本信息

批准号：
8994944
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
项目类别：
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/8994944
关键词：
Accounting Address 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 Generations Genes Genetic Transcription Genome Genomic approach Genomics Genotype Goals Location Maps Mediating Methods Modeling Molecular Profiling Mutagenesis Outcome Pattern Phenotype Regulator Genes Resolution Resources Structure System Systems Biology Technology Testing Time Tissues Translating Zebrafish base blastocyst cell type computerized tools differential expression genome editing genome-wide imaging genetics in vivo mutant network models new technology programs public health relevance tool transcriptome transcriptome sequencing whole genome zebrafish development

项目摘要

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.