High-throughput sequencing of chromatin regulatory elements

描述（由申请人提供）：人类基因组表征的一个关键目标是获得染色质调节元件和染色质状态序列决定簇的完整目录。在本申请中，我们建议开展一个大规模项目，通过在Solexa平台上将染色质IP与双通量测序相结合，在>20种人类细胞类型中绘制>35种组蛋白修饰和相关蛋白的全基因组位置。我们的初步数据表明，这种方法是高度准确的，并且在细胞要求、基因组覆盖率、通量和成本效益方面比现有技术有重大进步。将应用测序管道，通过对>1000个样品进行测序来生成500多个染色质结构的全基因组数据集。然后，计算管道将测序读数转换为高分辨率的全基因组图谱，这些图谱可以在基因组浏览器中可视化并用于下游分析。比较基因组分析和基序发现工具将被应用于分类相关的染色质结构的基础上的基因组位点，并确定潜在的序列决定因素。细胞和分子生物学方法将用于验证所发现元素的代表性子集的推断功能。 染色质调节广泛涉及人类发育和疾病的许多方面。特别是，癌细胞可能普遍表现出异常的染色质状态。人类基因组中染色质调控元件的系统鉴定和表征将为染色质的结构和功能提供前所未有的见解，并为染色质，基因组学，癌症和许多其他研究领域的研究人员提供宝贵的资源。 在拟议项目范围内收集的所有数据，一旦可靠性得到确认，将在出版前提供给广大科学界。

DESCRIPTION (provided by applicant): A key goal in characterizing the human genome is to acquire a complete catalog of chromatin regulatory elements and sequence determinants of chromatin state. In this application, we propose to undertake a large-scale project to map the genomewide locations of >35 histone modifications and related proteins in >20 human cell types by coupling chromatin IP with massive-throughput sequencing on the Solexa platform. Our preliminary data demonstrate that this approach is highly accurate and a major advance over existing technologies in terms of cell requirements, genome coverage, throughput and cost-effectiveness. A sequencing pipeline will be applied to generate more than 500 genomewide datasets of chromatin structure by sequencing >1000 samples. A computational pipeline will then convert the sequencing reads into high resolution, genomewide maps that can be visualized in genome browsers and used for downstream analysis. Comparative genomic analysis and motif-finding tools will be applied to classify genomic sites based on associated chromatin structures and to identify underlying sequence determinants. Cell and molecular biology methods will be used to validate inferred functions for a representative subset of discovered elements. Chromatin regulation is extensively implicated in many aspects of human development and disease. In particular, cancer cells may universally exhibit aberrant chromatin states. The proposed systematic identification and characterization of chromatin regulatory elements in the human genome will offer unprecedented insight into the structure and function of chromatin, and provide an invaluable resource for investigators in chromatin, genomics, cancer and many other fields of research. All data collected in the context of the proposed project will be made available pre-publication to the greater scientific community once reliability has been confirmed.