Genomic Measurement of Alternative Splicing

选择性剪接的基因组测量

• 批准号: 8006414
• 负责人: Manuel Ares
• 金额: $ 45.29万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-01-01 至 2012-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8006414
• 关键词: Address; Affect; Alternative Splicing; Cell Differentiation process; Cells; Cellular biology; Collaborations; Complex; Complex Mixtures; Data Analyses; Databases; Development; Disease; Eukaryota; Event; Exons; Funding; Gene Expression; Gene Expression Regulation; Genes; Genome; Genomics; Glues; Goals; Grant; Health; Heart; Homeostasis; Human; Inborn Genetic Diseases; Individual; Inherited; Knockout Mice; Laboratories; Laboratory Study; Lead; Link; Malignant Neoplasms; Measurement; Measures; Messenger RNA; Methods; Microarray Analysis; Modeling; Monoclonal Antibody R24; Mus; Muscle; Muscular Dystrophies; Mutation; Neuronal Differentiation; Neurons; Nucleic Acid Hybridization; Nucleic Acids; Pathway interactions; Pattern; Printing; Process; Protein Isoforms; Proteins; RNA Splicing; Regulation; Regulatory Element; Regulatory Pathway; Research Personnel; Source; System; Technology; Technology Transfer; Testing; Work; cost effective; database design; density; design; gene function; genome-wide; human disease; improved; instrument; interest; mRNA Precursor; neuromuscular system; novel strategies; programs; research study; stem cell biology

DESCRIPTION (provided by applicant): Alternative splicing is a key process in the control of mammalian gene expression and a major source of protein diversity. Errors in splicing regulation are implicated in many disease processes, including cancer and inherited disorders of the neuromuscular systems. However, the cellular circuits that control splicing regulation are mostly unknown. New methods that measure splicing changes on a genome-wide scale make possible the discovery of coordinately regulated networks of alternative splicing. The elucidation of the regulatory events underlying this coordinate control will be essential for understanding how groups of exons are controlled during development and disease. This project will support the continued development and dispersal of parallel technologies for measuring alternative splicing initiated by the Black, Fu and Ares labs through prior R24 funding. In the initial project period, several different approaches were developed. Most notably, two splicing- sensitive microarrays, one for mouse and one for human cells, each measuring splicing of about 1300 alternative splicing events in about 1000 genes, were successfully designed, printed and used to capture and analyze data. These arrays were applied to a diverse set of experiments and were successful in uncovering several systems of coordinate splicing control important in cellular differentiation and homeostasis. We propose to continue this productive collaboration with the following aims: (1) We will continue to apply the arrays and analysis methods produced during the previous funding period to questions of splicing regulation, and we will expand their use to additional laboratories studying splicing; (2) we will improve the design and analysis of splicing-sensitive arrays to make them more comprehensive, and reliable, as well as more widely available; and (3) we will develop a promising new approach to genome-wide splicing analysis using high density sequencing methods. This project will broaden the study of splicing regulation to the level of the whole genome, allowing the integration of specific splicing regulatory pathways into our understanding of gene regulation and genome function. PUBLIC HEALTH RELEVANCE Many human diseases, including both cancer and inherited diseases of the neuromuscular systems, are caused by alterations in gene function through a process called alternative pre-mRNA splicing. Although individual changes in splicing have been linked to particular disorders, it is not well understood how programs of splicing affect the larger biology of the cell, and hence how abnormalities in these programs lead to disease. This project will extend our work on methods for examining splicing regulation on a genome wide scale that will allow elucidation of these larger programs of genetic change in disease.

描述（由申请人提供）：替代剪接是控制哺乳动物基因表达和蛋白质多样性的主要来源的关键过程。剪接调节中的错误与许多疾病过程有关，包括癌症和神经肌肉系统的遗传性疾病。但是，控制剪接调节的细胞电路大多未知。测量剪接在全基因组量表上变化的新方法使得发现了替代剪接的协调调节网络。阐明该协调控制的基础调节事件对于理解外显子组如何控制发育和疾病时至关重要。该项目将支持并行技术的持续开发和分散，以测量黑色，FU和ARES实验室通过先前的R24资金发起的替代剪接。在最初的项目期间，开发了几种不同的方法。最值得注意的是，成功设计，印刷和用于捕获数据，成功设计，打印和使用了两个剪接敏感的微阵列，一个用于小鼠的剪接微阵列，每个用于人类细胞，每次测量约1300个替代剪接事件的剪接。这些阵列应用于各种实验集，并成功地发现了几种在细胞分化和稳态中重要的坐标剪接控制系统。我们建议将这种富有成效的合作与以下目的继续：（1）我们将继续将上一批资金期间产生的阵列和分析方法应用于拼接法规的问题，我们将将其用途扩展到其他研究剪接的实验室； （2）我们将改进对剪接敏感阵列的设计和分析，以使它们更全面，可靠，并且更广泛地可用； （3）我们将使用高密度测序方法开发一种有希望的新方法，用于全基因组剪接分析。该项目将将剪接调节的研究扩大到整个基因组水平，从而使特定的剪接调节途径整合到我们对基因调控和基因组功能的理解中。 公共卫生相关性许多人类疾病，包括神经肌肉系统的癌症和遗传性疾病，都是通过称为替代性mRNA剪接的过程改变了基因功能引起的。尽管剪接的个体变化与特定疾病有关，但尚不清楚剪接程序如何影响细胞的较大生物学，因此这些程序中的异常是如何导致疾病的。该项目将扩展我们在基因组大规模检查剪接调节的方法上的工作，该方法将阐明这些较大的疾病遗传变化计划。