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

基本信息

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
项目类别：
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&apos 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

项目摘要

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（由申请人提供）：顺式调节元件（CRE）通过介导转录因子（TF）与其靶基因之间的相互作用在基因表达调节中发挥关键作用。CRE内的突变可以破坏关键的TF结合位点，从而破坏转录因子（TF）及其靶基因之间的相互作用。复杂疾病的全基因组关联研究 (GWAS) 中发现的绝大多数 SNP 都属于非编码区域，并且被认为会影响 CRE 的活性。因此，更好地了解 CRE 的位置和功能对于解释非编码区域内遗传变异的功能意义至关重要，而其他基于联盟的项目已经开始绘制 CRE 在多个细胞系和整个器官中的位置。然而，我们对单个原代细胞类型水平的顺式调控架构的理解是有限的，在本提案中，我们将利用新开发的表观基因组图谱技术 ATAC-seq 来全面识别所有七种主要细胞的 CRE。小鼠视网膜中的细胞类别：视杆细胞、视锥细胞、水平细胞、双极细胞、穆勒神经胶质细胞、无长突细胞和神经节细胞 ATAC-seq 利用基于转座酶的方法来标记开放染色质区域，并且可以应用于非常小的数量。通过荧光激活细胞分选 (FACS) 纯化的细胞，这种变革性方法将使我们能够探究染色质可及性、核小体定位和染色质之间复杂的相互关系。此外，我们将利用这些数据，使用 CRE-seq（一种高通量顺式测序新技术）来探测特定视网膜细胞类型中数千个 CRE 的功能。总而言之，这些研究将生成视网膜 CRE 的全面功能图谱，该图谱将作为了解视网膜转录网络以及非编码变异对疾病的影响的蓝图。研究将为未来的工作奠定基础，利用表观基因组分析来描述发生的变化在视网膜发育过程和退化过程中。