Insulator-mediated chromatin organization during neural lineage commitment

神经谱系定型过程中绝缘体介导的染色质组织

基本信息

批准号：
7870494
负责人：
Jennifer Elizabeth Phillips-Cremins
金额：
$ 5.43万
依托单位：
EMORY UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-06-01 至 2012-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7870494
关键词：
Adult Base Sequence Behavior Binding Binding Sites Biological Models CCCTC-binding factor Cell Cycle Cell Nucleus Cell division Cells Characteristics Chimeric Proteins Chromatin Chromatin Fiber Chromatin Loop Chromatin Modeling Chromatin Structure Chromosomes Confocal Microscopy Cues Development Developmental Biology Diffuse ES Cell Line Embryo Embryonic Development Epigenetic Process Figs - dietary Foundations Gene Expression Gene Targeting Genes Genome Genomics Heterochromatin Higher Order Chromatin Structure Histocompatibility Testing Human Insulator Elements Knowledge Life Location Maintenance Malignant Neoplasms Malignant neoplasm of brain Maps Mediating Methylation Modeling Modification Molecular Molecular Conformation Molecular Profiling Monitor Morphology Mus Neurodegenerative Disorders Neurons Nuclear Pattern Phenotype Play Pluripotent Stem Cells Population Proteins Regenerative Medicine Research Research Personnel Role Somatic Cell Stem cells Stimulus Structure System Testing Therapeutic Time Work base brain cell cell type chromatin immunoprecipitation comparative demethylation embryonic stem cell gene repression genome wide association study genome-wide histone modification insight mRNA Differential Displays next generation pluripotency programs promoter public health relevance relating to nervous system response self-renewal stem stem cell differentiation

项目摘要

DESCRIPTION (provided by applicant): Emerging evidence supports a central role for chromatin insulators in genome-wide organization of higher- order chromosome loop structures. The overall objective of this proposal is to examine the consequences of insulator-mediated chromatin organization during mouse embryonic stem (ES) cell differentiation and development. Our central hypothesis is that the vertebrate insulator CTCF partitions the genome into lineage-specific domains of co-expressed genes by facilitating the formation of higher-order chromatin loop structures in response to developmental cues. This hypothesis will be tested according to three specific aims. In Aim 1, live cell confocal microscopy will be leveraged to investigate CTCF distribution and dynamics in real time during ES cell commitment along the neural lineage. In Aim 2, genome-wide CTCF binding sites will be identified in ES cells using chromatin immunoprecipitation in combination with high- throughput, next generation sequencing (ChlP-Seq). Global CTCF occupancy maps for pluripotent ES cells will be compared to multipotent neuroprogenitors and terminally-differentiated neurons. Finally, in Aim 3, the structural organization of CTCF-based chromatin loops will be characterized using Chromosome- Conformation-Capture (3C) at genomic loci displaying differential insulator occupancy during neural lineage commitment. Correlation of these CTCF-based structures with recent genome-wide analyses of 'traditional' epigenetic modifications and lineage-specific gene expression profiles will provide a more global understanding of how the genome and the epigenome act in concert to regulate the formation of a diverse array of tissue-types during development. Completion of the proposed work will provide significant insight into the mechanisms that govern the commitment of pluripotent stem cells toward neuroectodermal lineages. This knowledge will enable advances in understanding the causes and consequences of higher- order chromatin structure during the onset of cancer and neurodegenerative diseases. Public Health Relevance: Embryonic stem cells have enormous potential for regenerative medicine due to their capacity for indefinite self-renewal while remaining poised for differentiation into all adult cell-types. The proposed research will enhance our understanding of the molecular mechanisms that regulate commitment of stem cells along the neural lineage during embryonic development. This knowledge will provide a foundation for the development of robust strategies which harness the therapeutic potential of stem cells for treatment of neurodegenerative diseases and brain cancer.

描述（由申请人提供）：新兴证据支持染色质绝缘子在全基因组层组织中的核心作用。该提案的总体目的是检查小鼠胚胎茎（ES）细胞分化和发育过程中绝缘子介导的染色质组织的后果。我们的中心假设是，脊椎动物绝缘子CTCF通过促进高阶染色质环路结构的形成以响应发育线索，将基因组分配为共表达基因的谱系特异性域。该假设将根据三个特定目的进行检验。在AIM 1中，将利用活细胞共聚焦显微镜来研究CTCF分布和动力学，并在ES细胞沿神经谱系中实时研究。在AIM 2中，全基因组CTCF结合位点将在ES细胞中使用染色质免疫沉淀与高吞吐量的下一代测序（CHLP-Seq）结合使用。将比较多能ES细胞的全局CTCF占用图与多能神经元引起剂和末端分化的神经元进行比较。最后，在AIM 3中，基于CTCF的染色质环的结构组织将使用基因组基因座的染色体构象捕获（3C）来表征，在神经谱系承诺期间显示出差异绝缘体占用率。这些基于CTCF的结构与“传统”表观遗传修饰和谱系特异性基因表达谱的最新分析的相关性将提供对基因组和表观基因组在开发过程中如何调节各种组织类型的多种多样的组织阵列的形成的更全球理解。提议的工作的完成将为控制多能干细胞对神经外胚层谱系的承诺的机制提供重大见解。这些知识将使在癌症和神经退行性疾病发作期间了解高阶染色质结构的原因和后果的进步。公共卫生相关性：胚胎干细胞由于无限期的自我更新能力而具有巨大的再生医学潜力，同时仍准备区分所有成人细胞类型。拟议的研究将增强我们对在胚胎发育过程中调节干细胞沿神经谱系的分子机制的理解。这些知识将为发展强大策略的发展提供基础，这些策略利用了干细胞治疗神经退行性疾病和脑癌的治疗潜力。