Genome-Wide Resources for Transcriptional Enhancers Active in the Human Heart

人类心脏中活跃的转录增强子的全基因组资源

基本信息

批准号：
8756851
负责人：
Len Alexander Pennacchio
金额：
$ 77.9万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
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：
2015-03-01 至 2020-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8756851
关键词：
Address Adult Apex of the Heart Binding Biological Assay Biological Models Cardiac Cardiac development Cardiomyopathies Categories Cause of Death Cell Line ChIP-seq Chromatin Clinical Clinical Investigator Clinical Research Communities Computer Analysis Congenital Heart Defects DNA Data Data Set Development Dilated Cardiomyopathy Disease Distant EP300 gene Enhancers Gene Expression Gene Expression Profile Gene Expression Regulation Genes Genetic Genetic Research Genetic Transcription Genetic study Genomics Goals Heart Heart Diseases Heart Research Human Human Activities Human Cell Line Human Characteristics Human Chromosomes Human Genetics Human Genome Human Resources In Vitro Individual Internet Junk DNA Laboratories LacZ Genes Left Ventricular Hypertrophy Left atrial structure Left ventricular structure Link Location Maps Medical Molecular Mus Pattern Phenotype Play Population Positioning Attribute Process RNA Reagent Recording of previous events Regulator Genes Regulatory Element Reporter Research Research Infrastructure Resources Right atrial structure Right ventricular structure Role Sampling Scanning Side Slice Staging Structure Techniques Testing Tissue Stains Tissues Transgenic Mice Transgenic Organisms Untranslated RNA Variant Work abstracting base cardiogenesis cardiovascular disorder risk clinical phenotype clinical risk congenital heart disorder cost effectiveness data mining data portal differential expression epigenomics fetal genetic risk factor genome wide association study genome-wide heart function human tissue improved in vivo interest mouse model novel strategies postnatal prenatal research study risk variant transcription factor transcriptome sequencing vector

项目摘要

DESCRIPTION (provided by applicant): Heart disease is the leading cause of death worldwide, but the genetic risk factors for congenital heart defects and adult cardiac disorders are incompletely understood. Variation in distant-acting regulatory sequences (enhancers) is likely to contribute significantly to heart development and disease via regulation of gene expression. However, the genomic location and in vivo function of heart enhancers in the human genome remains largely unknown, hindering efforts to establish mechanistic links between enhancers and heart development and clinical cardiac phenotypes. Our laboratories have pioneered techniques for genome-wide enhancer identification by ChIP-seq and in vivo functional enhancer characterization via transgenic mouse experiments. Here, these techniques will be leveraged to address the pressing need for accurate annotation of heart enhancer location in the human genome and activity across heart developmental and disease states. Despite the general value of mouse models and in vitro studies of human cell lines, we have shown that there is significant divergence in sequence and functional conservation between human and mouse heart enhancers and that enhancer maps generated from specific cell lines capture a limited slice of the regulatory elements active in heterogeneous tissues such as the heart. The present proposal is aimed at characterizing heart enhancers and associated gene expression directly from human tissues representing different developmental stages and subregions of the fetal and adult heart, with the goal of generating datasets of significant value to basic and clinical cardiac research. We additionally propose to examine inter-individual variation in heart enhancer activity and gene expression, characterizing differences across healthy subjects and individuals with heart disease. In proof-of-principle studies, we have demonstrated the general feasibility and scientific impact of this approach. The specific aims of this proposal include: 1) we will perform ChIP-seq targeting enhancer- associated epigenomic marks to identify in vivo enhancers directly from comparisons of human heart tissues, including pre- and postnatal developmental stages, cardiac subregions, and major adult cardiac disease states. We will also perform transcriptome profiling by RNA-seq in the same samples. 2) We will perform at least 250 transgenic mouse assays to characterize in vivo activity patterns of candidate developmental and disease-relevant heart enhancers and study functional effects of putative deleterious non-coding sequence variation. Tested loci will be selected based on biomedical interest and will include community-nominated cardiac loci and risk variants. 3) We will present the results as an integrated community resource for heart genetics, providing a web portal for data browsing and download and molecular reagents and transgenic mice to enable downstream studies of regulatory sequences in heart development and disease. This research will reveal the regulatory landscape of human cardiac development, function, and disease, and will address the pressing national need for genomic resources to enable and accelerate the advancement of cardiac research. (End of Abstract)

描述（由申请人提供）：心脏病是全世界死亡的主要原因，但先天性心脏病和成人心脏疾病的遗传风险因素尚不完全清楚。远距离作用调控序列（增强子）的变异可能通过基因表达的调控对心脏发育和疾病产生重大影响。然而，人类基因组中心脏增强子的基因组位置和体内功能仍然很大程度上未知，这阻碍了建立增强子与心脏发育和临床心脏表型之间机制联系的努力。我们的实验室率先采用 ChIP-seq 进行全基因组增强子鉴定，并通过转基因小鼠实验进行体内功能增强子表征。在这里，这些技术将被用来满足对人类基因组中心脏增强子位置以及心脏发育和疾病状态下的活动进行准确注释的迫切需要。尽管小鼠模型和人类细胞系的体外研究具有普遍价值，但我们已经表明，人和小鼠心脏增强子之间的序列和功能保守性存在显着差异，并且从特定细胞系生成的增强子图谱捕获了有限的切片。在心脏等异质组织中活跃的调节元件。本提案旨在直接从代表胎儿和成人心脏不同发育阶段和亚区域的人体组织中表征心脏增强剂和相关基因表达，目标是生成对基础和临床心脏研究具有重要价值的数据集。我们还建议检查心脏增强剂活性和基因表达的个体间差异，以表征健康受试者和心脏病患者之间的差异。在原理验证研究中，我们证明了这种方法的总体可行性和科学影响。该提案的具体目标包括：1）我们将针对增强子相关表观基因组标记进行 ChIP-seq，直接从人类心脏组织的比较中识别体内增强子，包括出生前和产后发育阶段、心脏分区和主要成人心脏组织。疾病状态。我们还将在相同的样本中通过 RNA-seq 进行转录组分析。 2) 我们将进行至少 250 次转基因小鼠测定，以表征候选发育和疾病相关心脏增强剂的体内活性模式，并研究假定的有害非编码序列变异的功能影响。测试基因座将根据生物医学兴趣进行选择，并将包括社区提名的心脏基因座和风险变异。 3) 我们将把研究结果作为心脏遗传学的综合社区资源展示，提供数据浏览和下载的门户网站以及分子试剂和转基因小鼠，以实现心脏发育和疾病调控序列的下游研究。这项研究将揭示人类心脏发育、功能和疾病的监管格局，并将解决国家对基因组资源的迫切需求，以促进和加速心脏研究的进步。（摘要完）