Uncovering the transcription factor networks in early human cell specification

揭示早期人类细胞规范中的转录因子网络

• 批准号: 8625642
• 负责人: Alexander Minchev Tsankov
• 金额: $ 5.62万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-03-01 至 2016-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8625642
• 关键词: Address; Antibodies; Automobile Driving; Binding; Biological Models; Biology; Cardiac Myocytes; Cell Differentiation process; Cell Fate Control; Cells; Chromatin; Communities; Computer Simulation; DNA; DNA Methylation; Data; Derivation procedure; Development; Developmental Biology; Disease; Ectoderm; Elements; Endoderm; Engineering; Epiblast; Epigenetic Process; Event; Exhibits; Fibroblasts; Gene Expression; Generations; Genetic Transcription; Germ Layers; Human; Human Development; Human body; ImProv; In Vitro; Insulin-Dependent Diabetes Mellitus; Investments; Islets of Langerhans; Maps; Measurement; Mediating; Memory; Mesoderm; Methods; Modeling; Molecular; Mus; Neurons; Organ; Parkinson Disease; Pathway interactions; Play; Postdoctoral Fellow; Property; Proteins; Protocols documentation; RNA Interference; Regenerative Medicine; Regulation; Research; Resources; Role; Sensitivity and Specificity; Signal Transduction; Signaling Protein; Small Interfering RNA; Spinal cord injury; System; Testing; Therapeutic; Time; Tissue Engineering; Tissues; base; cell type; cofactor; combat; combinatorial; epigenome; fighting; gastrulation; genome-wide; histone modification; human embryonic stem cell; improved; induced pluripotent stem cell; insight; loss of function; network models; programs; public health relevance; research study; screening; small hairpin RNA; stem cell differentiation; transcription factor

DESCRIPTION (provided by applicant): Uncovering the transcription factor networks in early human cell specification. During gastrulation, pluripotent epiblast cells give rise to the three germ layers-- endoderm, mesoderm, and ectoderm. Later in development, these layers form nearly all the different tissues and organs in our body. However the molecular mechanisms that establish the transition from epiblast to the three germ layers are still largely unknown. A class of proteins known as transcription factors (TFs) can bind specific DNA elements and activate or repress gene expression. The capacity of TFs to "de-differentiate" fibroblast cells to induced pluripotent stem cells (1, 2) or to directly program cells into various lineages (3) makes them likely candidates for regulating cellular transitions during development. To gain a deeper understanding of the regulatory events that guide early human cell specification, a more comprehensive study of TF binding and their dynamics is needed. Current research on TFs in development mainly focuses on the regulatory role of single factors in steady state conditions, yet many TFs mediate gene expression downstream of signaling cascades in a dynamic and cooperative fashion that is unique to each cell type (4, 5). During my postdoctoral studies I aim to uncover the molecular events underling cellular specification. First, I will determine the genome-wide dynamics of over 30 TFs, DNA methylation, chromatin marks, and RNA expression at multiple decision time-points, during differentiation of human embryonic stem (ES) cells into endoderm, mesoderm, and ectoderm. Such comprehensive maps of TF binding dynamics will allow me to dissect the combinatorial and temporal interactions between master regulators, cofactors, and signaling proteins that establish cell identity. Second, I will combine these dynamic measurements to generate a provisional model of the network that controls cell identity in the different germ layers and dissect the interplay between TF occupancy and epigenetic state in the regulation of development. Third, I will validate and reiterate my multi-dimensional model predictions using selected RNAi perturbations of critical TFs in the network. The combination of this data will allow me to uncover the principles and players that establish cell fate. The proposed research will greatly enhance our understanding of regulatory circuits and their roles during cell differentiation in early human development, which will, in turn, improv our ability to derive therapeutic approaches, such as in vitro generation of cardiomyocytes, pancreatic islets, and neurons. This promises to have significant impact in combating number of diseases, such as spinal cord injury, juvenile diabetes, and Parkinson's disease.

描述（由申请人提供）：揭示早期人类细胞规范中的转录因子网络。在原肠胚形成过程中，多能性外胚层细胞产生三个胚层——内胚层、中胚层和外胚层。在发育的后期，这些层形成了我们身体中几乎所有不同的组织和器官。然而，建立从外胚层到三胚层过渡的分子机制在很大程度上仍然未知。一类被称为转录因子（TFs）的蛋白质可以结合特定的DNA元素并激活或抑制基因表达。tf能够将成纤维细胞“去分化”为诱导多能干细胞（1,2）或直接将细胞编程为各种谱系(3)，这使得它们可能成为调节发育过程中细胞转变的候选者。为了更深入地了解指导早期人类细胞分化的调控事件，需要对TF结合及其动力学进行更全面的研究。目前对tf在发育过程中的研究主要集中在稳态条件下单一因子的调节作用，然而许多tf以每种细胞类型特有的动态和合作方式介导信号级联下游的基因表达（4,5）。在我的博士后研究期间，我的目标是揭示细胞规范下的分子事件。首先，我将确定在人类胚胎干（ES）细胞分化为内胚层、中胚层和外胚层期间，在多个决策时间点上超过30个tf、DNA甲基化、染色质标记和RNA表达的全基因组动态。这种全面的TF结合动力学图谱将允许我剖析主调节因子、辅因子和建立细胞身份的信号蛋白之间的组合和时间相互作用。其次，我将结合这些动态测量来生成控制不同胚层细胞身份的网络的临时模型，并剖析TF占用与表观遗传状态在发育调节中的相互作用。第三，我将使用网络中关键tf的选定RNAi扰动来验证和重申我的多维模型预测。这些数据的结合将使我能够揭示决定细胞命运的原则和玩家。这项拟议的研究将极大地增强我们对调节回路及其在人类早期发育中细胞分化过程中的作用的理解，这反过来将提高我们获得治疗方法的能力，例如在体外培养心肌细胞、胰岛和神经元。这有望对对抗脊髓损伤、青少年糖尿病和帕金森病等多种疾病产生重大影响。