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: 8729397
• 负责人: JOHN T LIS
• 金额: $ 33.55万
• 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 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8729397
• 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; Data; Data Set; Deoxyribonucleases; 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

DESCRIPTION (provided by applicant): 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 immunoprecipitation, 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.

描述（由申请人提供）： 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（包括控制基因调节的序列）方面取得了长足的进步。然而，迄今为止的主要重点是对单个调节元素进行分类，而无需考虑其动态行为或相互作用。在此提案中，我们概述了一种创新方法，以识别对基因调节至关重要的序列和表征其动态相互作用的序列。我们的建议涉及将一种强大的方法与直接测量称为Pro-Seq的基因表达的强大方法与DNase-Seq的适应性结合，这是一种识别基因组中基因调节转录因子的基因组中位置的方法。我们建议在刺激诱导系统后的时间课程中应用这些方法，以获得有关结合和表达的动态，全基因组的信息，尤其集中在永生的K562白血病细胞系中小分子celastrol引起的应力反应。因为Pro-Seq和DNase-Seq都不取决于对特定转录因子的抗体或染色质免疫沉淀的技术，因此我们将这种方法描述为无因子和无因素。我们的建议具有三个主要目的：（1）使用Pro-Seq识别和表征转录单元； （2）使用DNase-seq识别和表征许多转录因子的结合位点； （3）将这些动态的转录和结合模式整合在一起，以揭示调节序列和转录单元之间相互作用的网络。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。我们新生成的数据，我们的预测和软件都将公开可用。