High-throughput sequencing of chromatin regulatory elements

描述(由申请人提供)：描述人类基因组的一个关键目标是获得染色质状态的染色质调节元件和序列决定因素的完整目录。在这项应用中，我们建议进行一个大规模的项目，通过将染色质IP与Solexa平台上的海量测序相结合，绘制&gt；35组蛋白修饰和相关蛋白质在&gt；20人类细胞类型中的全基因组位置。我们的初步数据表明，该方法具有很高的准确性，在细胞需求、基因组覆盖、吞吐量和成本效益方面比现有技术有了重大进步。测序流水线将被应用于通过对1000个样本进行测序来生成500多个全基因组染色质结构数据集。然后，计算管道将把测序读数转换成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。将应用比较基因组分析和基序发现工具，根据相关的染色质结构对基因组位置进行分类，并确定潜在的序列决定因素。细胞和分子生物学方法将被用来验证所发现的具有代表性的元素子集的推断功能。 染色质调节广泛参与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。对人类基因组中染色质调控元件的系统鉴定和鉴定将提供对染色质结构和功能的前所未有的洞察，并为染色质、基因组学、癌症等许多研究领域的研究人员提供宝贵的资源。 一旦可靠性得到确认，在拟议项目范围内收集的所有数据将在出版前提供给更大的科学界。

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.