DISSECTING THE CIS-REGULATORY ARCHITECTURE OF THE RETINA BY EPIGENOMIC PROFILING

通过表观基因组分析剖析视网膜的 CIS 调控架构

• 批准号: 9474126
• 负责人: JOSEPH CORBO
• 金额: $ 45.75万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9474126
• 关键词: ATAC-seq; Adult; Affect; Amacrine Cells; Architecture; Binding; Binding Sites; Biomedical Research; Cell Count; Cell Line; Cells; Chromatin; Complex; Cone; DNA; DNase I hypersensitive sites sequencing; Data; Development; Disease; Enhancers; Epigenetic Process; Fluorescence-Activated Cell Sorting; Future; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Targeting; Genetic Transcription; Genetic Variation; Goals; Individual; Location; Maps; Mediating; Muller' s cell; Mus; Mutation; Nucleosomes; Organ; Play; Population; Positioning Attribute; Process; Regulatory Element; Reporter; Retina; Retinal; Role; Techniques; Technology; Transgenic Mice; Transposase; Untranslated RNA; Variant; Vertebrate Photoreceptors; Work; base; cell type; disease-causing mutation; epigenomics; falls; ganglion cell; genome wide association study; genome-wide; horizontal cell; human disease; interest; mouse genome; next generation sequencing; novel; promoter; public health relevance; tool; transcription factor; transcriptome; transcriptome sequencing

 DESCRIPTION (provided by applicant): Cis-regulatory elements (CREs) play a critical role in the regulation of gene expression by mediating the interaction between transcription factors (TFs) and their target genes. Mutations within CREs can disrupt key TF binding sites, thereby altering gene expression, and thus contributing to disease. The vast majority of SNPs identified in genome-wide association studies (GWAS) of complex disease fall within non-coding regions, and is thought to affect the activity of CREs. Thus, a better understanding of the location and function of CREs is essential for interpreting the functional significance of genetic variation within non-coding regions. ENCODE and other consortium-based projects have begun to map the location of CREs in multiple cell lines and whole organs. However, our understanding of cis-regulatory architecture at the level of individual primary cell types is limited. In this proposal,we will utilize a newly developed epigenomic mapping technology, ATAC-seq, to comprehensively identify the CREs of all seven major cell classes in the mouse retina: rods, cones, horizontal cells, bipolar cells, Müller glia, amacrine cells, and ganglion cells. ATAC-seq utilizes a transposase-based approach to tag regions of open chromatin and can be applied to very small numbers of cells purified by fluorescence-activated cell sorting (FACS). This transformative approach will permit us to probe the complex interrelations between chromatin accessibility, nucleosome positioning, and TF binding on a genome-wide scale in all mouse retinal cell classes. Furthermore, we will leverage these data to probe the function of thousands of CREs within specific retinal cell types, using CRE-seq, a novel technique for high-throughput cis-regulatory analysis. Taken together, these studies will generate a comprehensive, functional map of retinal CREs that will serve as a blueprint for understanding the transcriptional networks of the retina and the effects of non-coding variants on disease. In addition, these studies will se the stage for future work that will utilize epigenomic profiling to characterize changes that occur during the process of retinal development and in the course of degeneration.

 描述（由应用程序提供）：顺式调节元件（CRE）通过介导转录因子（TFS）及其靶基因之间的相互作用来调节基因表达的作用至关重要。 CRE内的突变会破坏关键的TF结合位点，从而改变基因表达，从而改变疾病。在全基因组关联研究（GWAS）中发现的绝大多数SNP属于非编码区域内，被认为会影响CRE的活性。这是对CRE的位置和功能的更好理解对于解释非编码区域内遗传变异的功能意义至关重要。编码和其他基于财团的项目已开始绘制CRE在多个细胞系和整个器官中的位置。但是，我们对单个主要细胞类型级别的顺式调节结构的理解是有限的。在此提案中，我们将利用新开发的表观基因组映射技术ATAC-SEQ，全面地识别小鼠视网膜中所有七个主要细胞类别的CRE：杆，锥，水平细胞，双极细胞，双极细胞，müller神经胶质细胞，混血性细胞和神经节细胞。 ATAC-SEQ利用基于转座酶的方法来对开放染色质的标签区域进行标记区域，并可以应用于通过荧光激活的细胞排序纯化的非常少量的细胞（FACS）。这种变革性方法将使我们能够在所有小鼠残留细胞类别中探测染色质可及性，核小体定位和TF结合之间的复杂相互关系。此外，我们将利用CRE-Seq（一种用于高通量顺式调节分析的新技术来探测成千上万个CRE的功能。综上所述，这些研究将产生视网膜CRE的全面，功能图，该图将作为理解视网膜转录网络以及非编码变体对疾病的影响的蓝图。此外，这些研究将为将来的工作阶段，这些工作将利用表观基因组学分析来表征发生的变化 在剩余发展过程和变性过程中。