Surveying transcription factor pioneer interactions with nucleosomal DNA

调查转录因子先锋与核小体 DNA 的相互作用

• 批准号: 9360141
• 负责人: MARTHA L BULYK
• 金额: $ 22.19万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-28 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9360141
• 关键词: Affect; Alpha Cell; Area; Binding; Binding Proteins; Binding Sites; Biochemical; Biological Assay; Cataloging; Catalogs; Cell Lineage; Cells; ChIP-seq; Chromatin; DNA; DNA Modification Process; DNase-I Footprinting; Data; Deoxyribonuclease I; Deposition; Development; Developmental Process; Electrophoretic Mobility Shift Assay; Engineering; Exhibits; Future; Gatekeeping; Gene Targeting; Genes; Genetic Transcription; Genome; Genomics; Goals; Grant; Human; Hypersensitivity; Investigation; Lead; Machine Learning; Maintenance; Malignant Neoplasms; Modeling; Nucleic Acid Regulatory Sequences; Nucleosomes; Property; Recruitment Activity; Regenerative Medicine; Regulator Genes; Regulatory Element; Reporting; Risk; Role; Site; Stem cells; Structure; Surveys; Technology; Therapeutic; Time; Transcript; Variant; base; cancer stem cell; cell type; ds-DNA; genome-wide; high throughput technology; histone modification; improved; in vivo; innovation; new technology; novel; pluripotency; programs; technology development; transcription factor

Numerous studies have focused on cataloging the genome `parts list', including transcripts, transcription factor (TF) binding sites, and chromatin states. Transcriptional regulatory networks have been inferred based on these data, leading to models of what TFs are master regulators at or near the top of the regulatory hierarchy versus lineage- or condition-specific TFs, which are downstream of those regulators. However, none of these approaches directly identifies which factors engage inaccessible chromatin to initiate the transcriptional regulatory cascades. Pioneer factors serve as keys to chromatin accessibility for binding by the majority of TFs in a cell, by binding stably to nucleosomal DNA (`pioneer binding') and thus increase the DNA enzymatic accessibility of the chromatin (`pioneer activity'), allowing the sequential recruitment of other TFs on inactive chromatin. By priming cis regulatory elements for subsequent transcriptional regulatory activity, pioneer factors serve as `gatekeepers' to cellular differentiation. Despite their importance, little is known about pioneer factors, and only a handful have been characterized. A major hurdle in characterization of pioneer factors is the lack of a robust, high- throughput functional assay. In this project, we will develop a new technology, termed Pioneer Interactions On Nucleosomal Engineered ARrays (PIONEAR), for high-throughput characterization of pioneer binding. We will use PIONEAR assays to survey the pioneer interactions of dozens of human TFs. TFs identified by PIONEAR assays to exhibit pioneer binding will be evaluated in vivo to examine chromatin decompaction on a broader scale. Identification of TFs that exhibit pioneer activity may lead to breakthroughs in directed cellular differentiation and reprogramming and the development of improved therapies to target cancer stem cells.

许多研究的重点是分类基因组“零件列表”，包括成绩单， 转录因子（TF）结合位点和染色质状态。转录监管网络 已经根据这些数据推断出来，导致TF是主调节器的模型 或接近法规层次结构与谱系或条件特异性TF的顶部， 这些监管机构的下游。但是，这些方法都没有直接识别 因素使染色质不可访问以启动转录调节级联反应。 先锋因素是染色质访问性的关键，以在A中大多数TF结合 细胞，通过稳定与核小体DNA结合（“先锋结合”），从而增加DNA 染色质（“先驱活动”）的酶促可及性，允许顺序募集 其他TF的非活性染色质。通过启动顺式调节元素以进行后续 转录调节活动，先锋因素是蜂窝的“守门人” 分化。 尽管它们的重要性很重要，但对开拓者的因素知之甚少，只有少数 特征。先驱因素表征的主要障碍是缺乏强大的高度 吞吐量功能分析。在这个项目中，我们将开发一项新技术，称为先驱 高通量的核小体工程阵列（Pionear）的相互作用 开拓者结合的表征。我们将使用Pionear分析来调查先锋 数十个人类TF的相互作用。由Pionear分析确定的TFS展示先驱 结合将在体内评估，以检查更广泛的染色质分解。 鉴定表现出开拓性活动的TF可能会导致定向细胞的突破 分化和重编程以及改善靶向癌症的疗法的发展 干细胞。