Factor-general characterization of dynamic transcriptional stress responses

动态转录应激反应的因子一般特征

• 批准号: 8846643
• 负责人: JOHN T LIS
• 金额: $ 33.36万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-01 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8846643
• 关键词: Address; Antibodies; Base Sequence; Behavior; Binding; Binding Sites; Bioinformatics; Biological Assay; Cataloging; Catalogs; Cell Line; Cells; Cellular Stress Response; Chromatin; Classification; Computer software; Computing Methodologies; DNA; DNA Binding; DNase I hypersensitive sites sequencing; Data; Data Set; Development; Elements; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Genotype; Goals; Human; Human Genome; Indium; Individual; Joints; K-562; K562 Cells; Light; Link; Location; Maps; Massive Parallel Sequencing; Measures; Methods; Molecular; Nuclear; Pattern; Phenotype; Positioning Attribute; Regulatory Element; Research Personnel; Running; Statistical Models; System; Techniques; Technology; Therapeutic; Time; Transcriptional Regulation; base; biological adaptation to stress; cell type; chromatin immunoprecipitation; functional genomics; genome-wide; human disease; improved; innovation; insight; leukemia; novel; response; small molecule; transcription factor; tripterine

(unchanged from original) Since the human genome was first sequenced a decade ago, researchers have made great strides in identifying the genomic locations of many kinds of functional elements, including the sequences that control gene regulation. Nevertheless, the primary focus to date has been to catalog individual regulatory elements, without regard for their dynamic behavior or interactions. In this proposal, we outline an innovative approach for both identifying sequences critical for gene regulation and characterizing their dynamic interactions. Our proposal involves combining a powerful method for directly measuring the expression of genes, called PRO-seq, with an adaptation of DNase-seq, a method for identifying positions in the genome at which gene-regulating transcription factors are bound. We propose to apply these methods in a time course after stimulation of an inducible system to obtain dynamic, genome-wide information about both binding and expression, focusing in particular on stress responses induced by the small molecular celastrol in the immortalized K562 leukemia cell line. Because neither PRO-seq nor DNase-seq depends on antibodies to particular transcription factors, or on the technique of chromatin immunuprecipitation, we describe this approach as factor-general and ChIP-free. Our proposal has three main aims: (1) to identify and characterize transcription units using PRO-seq; (2) to identify and characterize the binding sites for many transcription factors using DNase-seq; and (3) to integrate these dynamic patterns of transcription and binding to reveal networks of interaction between regulatory sequences and transcription units. Each of these aims involves the development of new statistical models and computational methods. Our newly generated data, our predictions, and our software will all be made publicly available.

（与原始不变） 由于十年前首次对人类基因组进行了测序，研究人员在 识别许多功能元素的基因组位置，包括控制的序列 基因调节。然而，迄今为止的主要重点是分类个体监管 元素，不考虑其动态行为或相互作用。在此提案中，我们概述了 识别对基因调节至关重要的序列的创新方法和表征其表征 动态相互作用。我们的建议涉及结合一种有力的方法，用于直接测量 基因的表达，称为Pro-Seq，具有DNase-Seq的适应性，一种识别位置的方法 在基因组调节转录因子的基因组中。我们建议应用这些 刺激诱导系统以获得动态，全基因组的刺激后，时间过程中的方法 有关结合和表达的信息，尤其集中于由 永生的K562白血病细胞系中的小分子celastrol。因为既不是pro-seq也不 DNase-Seq取决于对特定转录因子的抗体或染色质技术 免疫沉淀，我们将这种方法描述为无因素和无芯片。我们的建议有三个 主要目的：（1）使用Pro-Seq识别和表征转录单元； （2）识别和 使用DNase-seq来表征许多转录因子的结合位点； （3）整合这些 转录和结合的动态模式，以揭示调节之间相互作用的网络 序列和转录单元。这些目的中的每一个都涉及开发新的统计模型 和计算方法。我们的新生成的数据，我们的预测和软件将全部制定 公开可用。