Center for Functional Validation and Evaluation of ENCODE Enhancer Regions, Grant Number 5UM1HG009426-03

ENCODE 增强区域功能验证和评估中心，授权号 5UM1HG009426-03

基本信息

批准号：
10049145
负责人：
KEVIN P. WHITE
金额：
$ 24.46万
依托单位：
TEMPUS LABS, INC.
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-11-01 至 2021-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10049145
关键词：
3-Dimensional Bioinformatics Biological Biological Assay Biological Models CRISPR/Cas technology Cancer cell line Cell Differentiation process Cell Line Cell model Cells Chicago Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Complex Computer Analysis Coronary Arteriosclerosis Coronary artery Coronary heart disease DNA DNA Sequence DNA Sequence Alteration Data Data Analyses Data Set Dimensions Disease Disease model Elements Enhancers Evaluation Gene Expression Genes Genetic Engineering Genetic Enhancer Element Genetic Risk Genetic Transcription Genetic Variation Genomics Grant Human Human Genome Inherited Malignant - descriptor Malignant Neoplasms Malignant neoplasm of pancreas Measurement Mediating Methods Modeling Mutagenesis Mutate Mutation Nucleic Acid Regulatory Sequences Organoids Pancreas Pancreatic Ductal Adenocarcinoma Phenotype Plant Roots Play Population Protocols documentation Quantitative Reverse Transcriptase PCR RNA Recurrence Regulator Genes Regulatory Element Reporter Resected Resolution Risk Factors Role Sampling Site-Directed Mutagenesis Smooth Muscle Smooth Muscle Myocytes Somatic Mutation System Technology Testing Tissue Model Tissues Transgenic Mice Transgenic Model Universities Untranslated RNA Validation Variant base biological systems cancer genetics cell immortalization disease phenotype droplet sequencing genome sequencing genome wide association study high risk human disease human model immortalized cell in vivo induced pluripotent stem cell pancreatic cancer model pancreatic neoplasm risk variant screening tool trait whole genome working group

项目摘要

Project Summary The purpose of each ENCODE Functional Characterization Center is “to develop and apply generalizable approaches to characterize the role of candidate functional elements identified the ENCODE project in specific biological contexts”. Our proposed Center will focus on characterization of candidate enhancer elements. We will develop, refine and apply experimental methods for functional assays of enhancers. We will use two very different biological models chosen for their high potential to act as generalizable exemplars for the study of enhancers in the context of (i) inherited risk factors for disease, and (ii) somatic mutations involved in cancers. We will also develop and refine our experimental methods in ENCODE cell lines, and we will reserve 25% of our efforts for testing candidate genomic elements that will be studied in common across all of the ENCODE Functional Characterization Centers. Using STARR-seq, and variations thereof, we will test for sufficiency of candidate enhancer elements to modulate gene expression. Using CRISPR-Cas9 methods we will edit the human genome, testing for necessity of candidate enhancer elements in their endogenous context. We will utilize these methods to examine the effects of inherited DNA variation on enhancer function in models of coronary artery disease (CAD), and to examine the effects of acquired somatic DNA mutations on enhancer function in models of pancreatic cancer (Pancreatic Ductal Adenocarcinoma – PDAC). While our approach necessarily requires a bioinformatics component to utilize ENCODE and other existing data sets in order to define the best candidate enhancer elements for testing in the specific biological models we will assay, our Center will be focused on experimental characterization of enhancers, testing different combinations of approaches in order to create extensible and generalizable protocols for systematic and accurate characterization of enhancer function.

项目摘要每个编码功能表征中心的目的是“开发和应用可推广的表征候选功能元素的作用的方法生物学环境”。我们提出的中心将集中于候选增强子元素的表征。我们将开发，完善和应用实验方法来评估增强剂。我们将非常使用两个选择的不同生物模型是因为其高潜力作为可概括的典范研究在（i）遗传的疾病风险因素以及（ii）取消涉及的体细胞突变的背景下的增强剂。我们还将在编码细胞系中开发和完善我们的实验方法，我们将保留25％我们在测试所有编码中都将研究的候选基因组元素的努力功能表征中心。使用starr-seq及其变化，我们将测试足够的功能候选增强子元素调节基因表达。使用CRISPR-CAS9方法，我们将编辑人类基因组，在内源性环境中测试候选增强子元素的必要性。我们将利用这些方法检查遗传的DNA变异对增强子功能的影响冠状动脉疾病（CAD），并检查获得的体细胞DNA突变对增强剂的影响胰腺癌模型（胰腺导管腺癌 - PDAC）的功能。而我们的方法一定需要一个生物信息学组件来利用编码和其他现有数据集来定义最佳的候选增强子元素，用于在我们将要测定的特定生物学模型中测试，中心将集中于增强剂的实验表征，测试不同的组合方法是为了创建可扩展且可推广的协议以进行系统和准确增强子功能的表征。