Core A - Establishing the regulatory mechanisms defining cellular function

核心 A - 建立定义细胞功能的调节机制

• 批准号: 10641539
• 负责人: Jason Daniel Buenrostro
• 金额: $ 51.79万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-07 至 2028-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10641539
• 关键词: ATAC-seq; Algorithms; Alleles; Bar Codes; Binding; Biological Assay; Cell Differentiation process; Cell Nucleus; Cell physiology; Cells; Chromatin; Chromatin Structure; Collaborations; Communities; Consultations; DNA Sequence Alteration; Data; Data Analyses; Data Set; Development; Disease; Dissection; Distal; Educational workshop; Experimental Designs; Experimental Models; Functional disorder; Gene Activation; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genomics; Hematopoiesis; Hematopoietic; Heterogeneity; Human; Joints; Maps; Measurement; Measures; Mediating; Methods; Modeling; Mus; Mutation; Nucleic Acid Regulatory Sequences; Output; Process; Production; Protocols documentation; Quality Control; RNA; Regulation; Regulator Genes; Regulatory Element; Resolution; Resources; Role; Rotation; Sampling; Schedule; Series; Source; Technology; Tissues; Universities; Work; XCL1 gene; Zebrafish; causal variant; cell behavior; cell type; computational pipelines; computerized data processing; cost; cost effective; cost effectiveness; data integration; data management; data sharing; data visualization; design; epigenomics; experience; experimental study; gene regulatory network; hematopoietic differentiation; hematopoietic tissue; innovation; member; multiple omics; online resource; programs; regenerative biology; sample collection; single-cell RNA sequencing; stem; stem cell biology; stem cells; tool; transcription factor; transcriptome sequencing; transcriptomics; web interface

Project Summary The coordinated regulation of chromatin structure, transcription factor binding and RNA expression is fundamental to cellular differentiation. Methods for measuring different layers of gene regulation within single cells can be used to determine essential regulators of cell differentiation and function as sensitive markers of cellular identity and lineage potential. To this end, we (Buenrostro) have recently developed SHARE-seq (Simultaneous High-throughput ATAC and RNA Expression with sequencing), for joint measurement of chromatin accessibility and gene expression within the same single-cell, at low-cost and massive throughput. Using SHARE-seq, we have shown that co-analysis of ATAC- and RNA-seq data from the same cell can be used to associate transcription factors to their target regulatory regions and distal regulatory elements to their target genes, enabling the definition of causal gene regulatory networks. Furthermore, we have shown that changes in chromatin accessibility precedes changes in gene expression, foreshadowing lineage commitment, and identifying a role for chromatin accessibility in priming chromatin for gene activation. Here, we propose the establishment of the Gene Regulation Core (GRC), which will be led by Dr. Jason Buenrostro at Harvard University's Department of Stem Cell and Regenerative Biology. As part of this P01 proposal, the GRC will enable the P01 members with SHARE-seq and other genomic technologies established in the Buenrostro lab, which can be used to functionally annotate regulatory regions, identify key transcription factors and chromatin regulators, define gene regulatory networks and parse cellular states. The GRC will work closely with the P01 labs to design experiments, and organize and collect hematopoietic samples (Aim 1). The GRC will use SHARE-seq to jointly profile chromatin accessibility and RNA expression at the single cell level. This will include extending SHARE-seq to capabilities uniquely enabled by SHARE-seq, such as the readout of transcribed lineage barcodes and Clonal Hematopoiesis-associated mutations (Aim 2). Finally, the GRC will be responsible for the primary processing of the data, data management, developing web interface tools and organizing data discussions and workshops between the P01 labs (Aim 3). Overall, the GRC will offer a complete solution for the single-cell genomics needs of the P01 community through a unique and innovative suite of genomic technologies.

项目概要 染色质结构、转录因子结合和RNA的协调调控 表达是细胞分化的基础。不同层数的测量方法 单细胞内的基因调控可用于确定细胞的重要调控因子 分化和功能作为细胞身份和谱系潜力的敏感标记。对此 最后，我们（Buenrostro）最近开发了SHARE-seq（同步高通量 ATAC 和 RNA 表达（带测序），用于联合测量染色质可及性 以及在同一单细胞内以低成本和高通量进行基因表达。使用 SHARE-seq，我们已经证明来自同一细胞的 ATAC 和 RNA-seq 数据的共同分析 可用于将转录因子与其目标调节区域和远端相关联 对其靶基因的调控元件，从而能够定义因果基因调控 网络。此外，我们已经证明染色质可及性的变化先于变化 在基因表达中，预示谱系承诺，并确定染色质的作用 启动染色质以激活基因的可及性。在此，我们建议成立 基因调控核心 (GRC)，将由哈佛大学的 Jason Buenrostro 博士领导 干细胞和再生生物学系。作为 P01 提案的一部分，GRC 将 使 P01 成员能够使用 SHARE-seq 和其他在该领域建立的基因组技术 Buenrostro 实验室可用于对调控区域进行功能注释，识别关键 转录因子和染色质调节因子，定义基因调节网络并解析细胞 州。 GRC将与P01实验室密切合作，设计实验、组织和 收集造血样本（目标 1）。 GRC 将使用 SHARE-seq 联合分析染色质 单细胞水平的可及性和 RNA 表达。这将包括扩展 SHARE-seq SHARE-seq 独有的功能，例如转录谱系的读出 条形码和克隆造血相关突变（目标 2）。最后，GRC 将 负责数据的初级处理、数据管理、开发Web界面 工具并组织 P01 实验室之间的数据讨论和研讨会（目标 3）。总体而言， GRC将为P01社区的单细胞基因组学需求提供完整的解决方案 通过一套独特且创新的基因组技术。