Mining open chromatin to define molecular mechanisms of CF modifier genes

挖掘开放染色质以定义 CF 修饰基因的分子机制

基本信息

批准号：
9384447
负责人：
ANN HARRIS
金额：
$ 20.62万
依托单位：
CASE WESTERN RESERVE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-07-15 至 2018-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9384447
关键词：
APAF1 gene Abnormal ion transport Address Alleles Apoptotic Bacterial Infections Beryllium Binding Binding Sites Biological Biological Assay Biology Cell Lineage Cells Cessation of life ChIP-seq Chromatin Chromosomes Chronic Clinical Control Locus Cystic Fibrosis Cystic Fibrosis Transmembrane Conductance Regulator Data Disease Disease Progression Distal Elements Enhancers Epithelial Epithelial Cells Gene Expression Genes Genetic Genetic Polymorphism Genome Genomic Segment Genomics Goals Health Heart Diseases Hematological Disease Human Hypoxia Indium Individual Inflammation Inflammatory Injury Insulator Elements Intercistronic Region Ion Transport Location Lung Lung diseases Mendelian disorder Metaplasia Mining Minor Molecular Monitor Mucociliary Clearance Mucous body substance Mutation National Heart, Lung, and Blood Institute Nucleic Acid Regulatory Sequences Other Genetics Pathology Pathway interactions Phenotype Process Property Proteins Public Health Pulmonary Cystic Fibrosis Pulmonary Pathology Regulator Genes Regulatory Element Reporter Genes Respiratory Failure Respiratory physiology Severities Severity of illness Side Single Nucleotide Polymorphism Site Small Interfering RNA Therapeutic Intervention Trans-Activators Untranslated RNA Writing base cell type chromosome conformation capture cis acting element cystic fibrosis airway epithelia genetic association genetic element genome wide association study genome-wide genome-wide analysis knock-down promoter research study response transcription factor transcriptome sequencing

项目摘要

DESCRIPTION (provided by applicant): Variability in lung disease severity in cystic fibrosis (CF) is a significant clinical problem. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause CF, a devastating, recessive, monogenic disease. CF is characterized by abnormal ion transport, reduced mucociliary clearance, chronic bacterial infection, inflammatory airway disease with mucus hyper/metaplasia, respiratory failure, and early death. However, the variability in lung phenotype is profoundly influenced by genetic factors that lie outside the CFTR locus. Recent genome-wide association studies (GWAS), led by co-PIs on this proposal, identified a robust association at chromosome 11p13 with lung disease severity. The genomic region encompassing the single nucleotide polymorphisms (SNPs) with highest p-values is located within a ~219kb intergenic region flanked by the Ets homologous factor 1 (EHF) gene on one side and APAF1-interacting protein (APIP) on the other. EHF encodes a protein that belongs to an Ets transcription factor subfamily characterized by epithelial specific expression. APIP is a negative regulator of hypoxic injury and has anti-apoptotic functions. Moreover, there are other genes of potential relevance to lung function close to this region. Our goal is to determine the mechanism whereby genetic elements at 11p13 influence CF lung disease severity, which likely involves key pathobiological pathways (ion transport, inflammation, and/or mucus metaplasia). Since the critical SNPs lie in non-coding regions of the genome it is probable that they are within or close to cis-acting regulatory elements that control the expression of one or more genes within this genomic region. We will pursue three specific aims addressing the main hypothesis that critical regulatory elements for genes at 11p13 are located at or close to the SNPs with highest p-values associating with CF lung disease severity in the replicated GWAS. Moreover, that by finding which elements interact with each gene promoter in the region we will identify genes that are critical for normal lung biology, determine how their expression is regulated and how naturally occurring polymorphisms influence these processes and alter CF disease progression. Experiments in the first aim will identify the location of critical regulatory elements in the 11p13 genomic interval and determine the physical interactions of these cis-acting elements with individual gene promoters. In the second aim, we will determine the function of the critical cis-regulatory elements in controlling expression of relevant genes at 11p13 and how SNPs may alter their properties. Finally we will elucidate the mechanism whereby lung pathology in CF is modulated by proteins encoded by critical gene(s) in the 11p13 genomic interval. The results will determine the biological basis of variability in CF lung disease severity and provide a valuable paradigm for elucidating the molecular basis of other genetic associations with heart, lung and blood diseases that involve cis-acting regulatory elements in non-coding regions distal to genes.

描述（由申请人提供）：囊性纤维化（CF）中肺部疾病严重程度的变异性是一个重大的临床问题。囊性纤维化跨膜电导调节剂（CFTR）基因的突变导致CF，这是一种毁灭性的，隐性的，单基因性疾病。 CF的特征是异常离子转运，粘膜钙清除率降低，慢性细菌感染，炎症性气道疾病伴有粘液性超/变质症，呼吸衰竭和早期死亡。但是，肺表型的变异性受到CFTR基因座以外的遗传因素的深刻影响。由Co-Pis在该提案中领导的最新基因组关联研究（GWAS）确定了11p13染色体的牢固关联与肺部疾病严重程度。涵盖具有最高p值的单核苷酸多态性（SNP）的基因组区域位于一个〜219kb的基因间区域内，一侧是ETS同源因子1（EHF）基因，一侧是另一侧，APAF1相互作用的蛋白（APIP）。 EHF编码属于ETS转录因子亚家族的蛋白质，其特征是上皮特异性表达。 APIP是低氧损伤的负调节剂，具有抗凋亡功能。此外，还有其他与肺功能接近该区域的潜在相关性的基因。我们的目标是确定11p13遗传因素会影响CF肺部疾病严重程度的机制，这可能涉及关键的病理学途径（离子转运，炎症和/或粘液化生）。由于临界SNP位于基因组的非编码区域，因此很可能它们在控制该基因组区域内一个或多个基因的表达的顺式作用调节元件内或接近。我们将追求三个特定的目标，以解决主要假设，即11p13基因的关键调节元素位于或接近SNP，其P值与CF肺部疾病严重程度最高的P值在复制的GWAS中。此外，通过发现哪些元素与该区域中的每个基因启动子相互作用，我们将确定对正常肺部生物学至关重要的基因，确定其表达的调节方式以及自然发生的多态性如何影响这些过程并改变CF疾病进展。第一个目标中的实验将确定关键调节元件在11p13基因组间隔中的位置，并确定这些顺式作用元件与单个基因启动子的物理相互作用。在第二个目标中，我们将确定关键顺式调节元素在控制相关基因在11p13处的表达以及SNP如何改变其性质的功能。最后，我们将阐明CF中肺病理学的机制，该机制由11p13基因组间隔中临界基因编码的蛋白质调节。结果将确定CF肺部疾病严重程度可变性的生物学基础，并为阐明其他遗传关联与心脏，肺和血液疾病的分子基础，这些遗传关联涉及基因远端的非编码区域的顺式作用调节元件。