Research Project: Genome-Wide Atlas of Craniofacial Transcriptional Enhancers

研究项目：颅面转录增强子全基因组图谱

基本信息

批准号：
8465756
负责人：
Axel Visel
金额：
$ 39.9万
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：
2009
资助国家：
美国
起止时间：
2009-09-21 至 2015-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8465756
关键词：
Address Affect Alleles Anatomic Models Atlases Binding Sites Biological Assay Candidate Disease Gene Clinical Clinical Research Code Communities Comparative Genomic Analysis Complement Complex Congenital Abnormality DNA Data Data Coordinating Center Data Set Databases Development Disease Distant E1A-associated p300 protein EP300 gene Elements Embryo Enhancers Etiology Face Functional RNA Future Gene Expression Gene Expression Profile Gene Targeting Genes Genetic Genomics Haplotypes Human Human Genetics Human Genome Image Individual Laboratories LacZ Genes Link Location Maps Medical Mission Molecular Mus Mutation Optics Palate Patients Pattern Property Proteins Quality Control RNA Reagent Regulatory Element Reporter Research Research Personnel Research Project Grants Resolution Resources Risk Role Sampling Scanning Specimen Staging Staining method Stains Suggestion Symptoms Testing Time Tissues Transgenic Mice Transgenic Organisms Variant base cleft lip and palate clinically relevant comparative genomics craniofacial data portal genome wide association study genome-wide in vivo interest malformation member next generation sequencing orofacial programs public health relevance research study tomography transcriptome sequencing user-friendly

项目摘要

DESCRIPTION (provided by applicant): Clefts of the lip and palate are among the most common craniofacial birth defects. They can co-occur with other symptoms as part of Mendelian disorders, but the majority of cases are non-syndromic and have a complex etiology. In some cases disrupted protein-coding genes have been identified as contributors to orofacial clefting risk. However, accumulating evidence from genome-wide association studies (GWAS) indicates that sequence variation in non-coding regions also strongly contributes to a variety of clinical disorders including orofacial clefting. While it is speculated that many of these variants affect disease through impacting on functional properties of distant-acting transcriptional enhancers, only very few isolated examples of such regulatory variation have been identified. This is likely due to the fact that the genomic location and function of the vast majority of distant-acting enhancers in the human genome remains unknown. To address the pressing need to identify on a genomic scale enhancers that are involved in face and palate development and likely relevant for clefting etiology, we propose here an integrated genomic and transgenic mouse strategy to identify craniofacial enhancers and characterize their activities. Specifically, we will use a ChlP-seq approach to identify genome-wide sets of enhancers that are active in mouse face and palate tissues at embryonic stages that are relevant for orofacial clefting. We will use a transgenic mouse enhancer screen to validate and characterize 130 of these enhancer predictions in detail by determining their in vivo activity patterns. Furthermore, we will identify disease-associated GWAS variants that map to craniofacial enhancers that we will have discovered. We will then test and compare the variant and normal sequences in the transgenic enhancer assay for differences in their in vivo activities. All of the genomic and in vivo datasets, as well as molecular reagents developed through these experiments will be made available to other investigators through the Face Base program in order to maximize their availability and accelerate the progress of biomedical and clinical studies of mid-face and palate development and orofacial clefting.

描述（由申请人提供）：嘴唇和口感的裂缝是最常见的颅面先天缺陷之一。作为孟德尔疾病的一部分，它们可以与其他症状同时发生，但大多数病例是非综合性疾病的，并且具有复杂的病因。在某些情况下，破坏的蛋白质编码基因已被确定为造成口面裂风险的贡献者。然而，从全基因组关联研究（GWAS）中积累的证据表明，非编码区域的序列变化也强烈促进各种临床疾病，包括口面裂。虽然据推测，其中许多变体通过影响遥远的转录增强子的功能性能来影响疾病，但仅确定了这种调节变异的很少的孤立示例。这很可能是由于人类基因组中绝大多数远处增强子的基因组位置和功能仍然未知。为了满足识别面部和口感开发及其可能与病因相关的基因组量表增强子的紧迫需求，我们在这里提出了一种综合的基因组和转基因小鼠策略，以识别颅面增强剂并表征其活性。具体而言，我们将使用CHLP-SEQ方法来鉴定在小鼠面部和pape骨组织中活跃的胚胎阶段中与口腔裂裂相关的增强剂的集合。我们将使用转基因小鼠增强子屏幕来验证和通过确定其体内活性模式来详细描述这些增强器预测的130个。此外，我们将确定与疾病相关的GWAS变体，这些变体将其映射到我们将发现的颅面增强剂。然后，我们将测试并比较转基因增强剂测定中的变体和正常序列是否在其体内活性中存在差异。所有基因组和体内数据集以及通过这些实验开发的分子试剂将通过面部基础计划提供给其他研究人员，以最大程度地提高其可用性，并加速中纹和pape酸和pape酸的生物医学和临床研究的进展。