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: 8526759
• 负责人: Alexander Minchev Tsankov
• 金额: $ 5.49万
• 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/8526759
• 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）：在早期人类细胞规范中发现转录因子网络。 在胃结构期间，多能层细胞会产生三个胚芽层 - 内胚层，中胚层和外胚层。后来，这些层几乎形成了我们体内所有不同的组织和器官。但是，建立从层细胞到三个细菌层的过渡的分子机制仍然很大程度上是未知的。一类称为转录因子（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。 TFs“去分化”成纤维细胞对诱导多能干细胞的能力（1，2）或将细胞直接编程为各种谱系（3），使它们可能候选在发育过程中调节细胞过渡的候选者。 为了更深入地了解指导早期人类细胞规范的调节事件，需要对TF结合及其动态进行更全面的研究。当前对TFS开发中TF的研究主要集中于单个因素在稳态条件下的调节作用，但是许多TFS以动态和合作的方式介导了信号级联的下游基因表达，这是每种细胞类型所独有的（4，5）。在我的博士后研究中，我旨在发现细胞规范下的分子事件。首先，我将在人类胚胎茎（ES）细胞分化为内胚层，中胚层和外胚层时，确定超过30个TF，DNA甲基化，染色质标记和RNA表达的全基因组动力学。 TF结合动力学的这种全面图将使我能够在主调节器，辅因子和建立细胞身份的信号蛋白之间剖析组合和时间相互作用。其次，我将结合这些动态测量，以生成网络的临时模型，该模型控制不同细菌层中细胞的身份，并在调节发育调节中剖析TF占用和表观遗传状态之间的相互作用。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发现建立细胞命运的原理和参与者。 拟议的研究将大大增强我们对早期人类发育中细胞分化过程中调节回路及其在细胞分化过程中的作用的理解，这反过来又可以提高我们得出治疗方法的能力，例如体外生成心肌细胞，胰岛和神经元。这有望在打击数量的疾病，例如脊髓损伤，少年糖尿病和帕金森氏病。