High-throughput sequencing of chromatin regulatory elements

描述（由申请人提供）：表征人类基因组的一个关键目标是获得染色质调控元件和染色质状态序列决定因素的完整目录。在本申请中，我们建议在Solexa平台上进行一项大规模的项目，通过将染色质IP与大通量测序相结合，绘制>20种人类细胞类型中>35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。测序流水线将通过测序1000个样本，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。比较基因组分析和基序寻找工具将应用于基于相关染色质结构的基因组位点分类，并确定潜在的序列决定因素。细胞和分子生物学方法将用于验证已发现元素的代表性子集的推断功能。

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.