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）：心脏病是全球死亡的主要原因，但是先天性心脏缺陷和成人心脏病的遗传危险因素尚不完全了解。远处的调节序列（增强子）的变化可能通过调节基因表达对心脏发育和疾病产生重大贡献。但是，人类基因组中心脏增强子的基因组位置和体内功能在很大程度上未知，阻碍了增强子与心脏发育与临床心脏表型之间建立机械联系的努力。我们的实验室采用了通过转基因小鼠实验进行芯片序列和体内功能增强子表征的开创性技术，可通过CHIP-SEQ和体内功能增强子进行鉴定。在这里，这些技术将被利用，以解决对人类基因组中心脏增强子位置的准确注释以及心脏发育和疾病状态的活动的紧迫需求。尽管小鼠模型和人类细胞系的体外研究具有一般值，但我们表明，人和小鼠心脏增强子之间的序列和功能保护存在明显差异，并且由特定细胞系产生的增强子图捕获了有限的调节元素在异质组织（如心脏（如心脏））中有限的调节元素。本提案旨在直接从代表胎儿和成人心脏的不同发育阶段和子区域的人体组织中表征心脏增强子和相关的基因表达，目的是为基础和临床心脏研究产生重要价值的数据集。我们还建议检查心脏增强剂活性和基因表达的个体间变化，以表征健康受试者和患有心脏病的个体的差异。在原则研究中，我们证明了这种方法的一般可行性和科学影响。该提案的具体目的包括：1）我们将执行CHIP-seq靶向增强剂相关的表观基因组痕迹，以直接从人体心脏组织的比较（包括出生前和产后发育阶段，心脏子区域，心脏子区域和主要的成人心脏病状态）中直接识别体内增强子。我们还将在同一样品中通过RNA-Seq进行转录组分析。 2）我们将至少执行250种转基因小鼠测定，以表征候选发育和与疾病相关的心脏增强剂的体内活性模式，并研究假定有害的非编码序列变化的功能效应。测试的基因座将根据生物医学兴趣选择，并将包括社区提名的心脏基因座和风险变体。 3）我们将作为心脏遗传学的综合社区资源提供结果，为数据浏览和下载以及分子试剂和转基因小鼠提供网站，以实现心脏发育和疾病中调节序列的下游研究。这项研究将揭示人类心脏发展，功能和疾病的监管格局，并将满足国家对基因组资源的迫切需求，以实现和加速心脏研究的进步。（抽象的结尾）