Genomic Measurement of Alternative Splicing

选择性剪接的基因组测量

• 批准号: 8208140
• 负责人: Manuel Ares
• 金额: $ 45.11万
• 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 2013-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8208140
• 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）：选择性剪接是哺乳动物基因表达控制的关键过程，也是蛋白质多样性的主要来源。剪接调控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。然而，控制剪接调节的细胞回路大多是未知的。在全基因组范围内测量剪接变化的新方法使得发现协调调节的选择性剪接网络成为可能。阐明这种协调控制背后的调控事件对于理解外显子组在发育和疾病过程中是如何控制的至关重要。该项目将支持Black、Fu和战神实验室通过先前的R24资金发起的测量选择性剪接的并行技术的继续开发和传播。在项目初期，开发了几种不同的方法。最值得注意的是，成功地设计、打印了两个剪接敏感的微阵列，一个用于小鼠，一个用于人细胞，每个测量约1000个基因中约1300个可变剪接事件的剪接，并用于捕获和分析数据.这些阵列被应用于一组不同的实验，并成功地发现了几个系统的协调剪接控制重要的细胞分化和稳态。我们建议继续这种富有成效的合作，目标如下：（1）我们将继续将上一个资助期产生的阵列和分析方法应用于剪接调控问题，并将其应用于研究剪接的其他实验室;（2）我们将改进拼接敏感阵列的设计和分析，使其更全面、更可靠、更广泛地适用;以及（3）我们将开发一种利用高密度测序方法进行全基因组剪接分析的有前途的新方法。该项目将剪接调控的研究扩展到全基因组水平，允许将特定的剪接调控途径整合到我们对基因调控和基因组功能的理解中。 许多人类疾病，包括癌症和神经肌肉系统的遗传性疾病，都是由基因功能的改变引起的，这种改变是通过一种称为前mRNA选择性剪接的过程引起的。尽管剪接中的个体变化与特定的疾病有关，但人们还不清楚剪接程序如何影响细胞的更大生物学，以及这些程序中的异常如何导致疾病。这个项目将扩展我们在全基因组范围内检查剪接调节的方法，这将允许阐明疾病中这些更大的遗传变化程序。

项目成果

Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD).

• DOI: 10.1371/journal.pgen.1003186
• 发表时间: 2013
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Pistoni M;Shiue L;Cline MS;Bortolanza S;Neguembor MV;Xynos A;Ares M Jr;Gabellini D
• 通讯作者: Gabellini D