High throughput CRISPR-mediated functional validation of regulatory elements

高通量 CRISPR 介导的调控元件功能验证

基本信息

批准号：
9420657
负责人：
Bing Ren
金额：
$ 156.5万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-02-01 至 2021-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9420657
关键词：
Address Alleles Base Pairing Binding Biological Biological Assay Biological Process Biology Biomedical Engineering CRISPR/Cas technology Candidate Disease Gene Catalogs Cell Line Cell model Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Collection DNA Sequence Data Data Set Disease Elements Funding Gene Expression Gene Expression Regulation Gene Targeting Genes Genetic Genetic Transcription Genetic Variation Genome Genomic approach Genomics Genotype Goals Health Human Illinois Individual Knowledge Link Mammalian Cell Maps Mediating Methods Mus Names Nature Nonhomologous DNA End Joining Nucleic Acid Regulatory Sequences Population Production Regulator Genes Regulatory Element Reporter Reporter Genes Research Resolution Resources Robotics Role Scanning Testing Tissues Transcriptional Regulation Untranslated RNA Validation Work base cell type chromatin modification density design embryonic stem cell epigenomics experimental study functional genomics functional group genome editing genomic data human embryonic stem cell in vivo interest mammalian genome tool trait transcription factor vector

项目摘要

Project Summary The overarching goal of the proposed study is to functionally characterize a large number of candidate functional elements in the mammalian genome. The ENCODE projects have revealed millions of putative regulatory elements across more than one hundred cell types and tissues. While these maps have significantly expanded our knowledge of non-coding sequences, there are still large gaps between having descriptive maps of functional elements and understanding the biology of these elements underlying gene regulation. These include: (a) few candidate functional elements predicted by the ENCODE experiments are functionally validated; (b) Epigenomic studies have not given/revealed information on the target genes of candidate functional elements. Therefore, it is still a challenge to interpret the biological functions of non-coding DNA sequences. To address these issues, the objective of this UM1 application is to perform large scale functional characterization of candidate functional elements in their native chromatin context. We will first identify candidate regulatory elements utilizing ENCODE data and generate reporter tagged genes of interest in cell lines utilizing a high throughput, automated platform. Second, we will interrogate candidate functional elements in their native chromatin contexts utilizing two complementary high throughput CRIPSR/Cas9 mediated genome editing approaches. We anticipate these analyses will significantly advance our knowledge of the biological functions of candidate regulatory regions and gene regulation in mammalian cells.

项目概要拟议研究的总体目标是从功能上描述大量候选者哺乳动物基因组中的功能元件。 ENCODE 项目揭示了数百万个假定的超过一百种细胞类型和组织的调节元件。虽然这些地图显着扩展了我们对非编码序列的知识，但在描述性图谱之间仍然存在很大差距功能元件并了解这些元件的基因调控生物学。这些包括： (a) ENCODE 实验预测的少数候选功能元件在功能上是有效的已验证； (b) 表观基因组研究尚未给出/揭示候选靶基因的信息功能元素。因此，解释非编码DNA的生物学功能仍然是一个挑战序列。为了解决这些问题，该 UM1 应用程序的目标是执行大规模功能候选功能元件在其天然染色质环境中的表征。我们首先会识别利用编码数据生成候选调控元件并生成细胞中感兴趣的报告基因标记基因生产线利用高吞吐量的自动化平台。其次，我们将询问候选功能元素在其天然染色质环境中利用两个互补的高通量 CRIPSR/Cas9 介导基因组编辑方法。我们预计这些分析将显着提高我们对哺乳动物细胞中候选调控区和基因调控的生物学功能。