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.

（与原文相同） 自从十年前人类基因组首次测序以来，研究人员在以下方面取得了长足的进步： 确定许多种功能元件的基因组位置，包括控制 基因调控尽管如此，迄今为止的主要重点一直是对单个监管机构进行分类， 元素，而不考虑它们的动态行为或相互作用。在这份提案中，我们概述了一个 用于鉴定对基因调控至关重要的序列并表征其特征的创新方法 动态互动我们的建议包括结合一个强大的方法，直接测量 基因的表达，称为PRO-seq，与DNase-seq的适应，用于识别位置的方法 基因调控转录因子结合的基因组中。我们建议应用这些 方法在诱导系统刺激后的时间过程中， 关于结合和表达的信息，特别侧重于由蛋白质诱导的应激反应。 小分子雷公藤红素在永生化K562白血病细胞系中的作用。因为无论是PRO-seq还是 DNase-seq依赖于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因子通用和ChIP免费。我们的建议有三个 主要目的：（1）使用PRO-seq鉴定和表征转录单位;（2）鉴定和 使用DNase-seq表征许多转录因子的结合位点;以及（3）整合这些结合位点。 转录和结合的动态模式，以揭示调控之间的相互作用网络 序列和转录单位。这些目标中的每一个都涉及新的统计模型的开发 和计算方法。我们新生成的数据、我们的预测和我们的软件都将由 公开可用。