Computational and Experimental Analysis of Vertebrate RNA Splicing

脊椎动物 RNA 剪接的计算和实验分析

基本信息

批准号：
8097067
负责人：
CHRISTOPHER B BURGE
金额：
$ 49.91万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-08-13 至 2012-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8097067
关键词：
3&apos Splice Site Address Algorithms Amino Acid Sequence Autoimmune Diseases Cells Code Computing Methodologies Conserved Sequence Data Data Analyses Development Elements Enhancers Evolution Exhibits Exons Financial compensation Fluorescence Functional RNA Gene Expression Profile Gene Mutation Genes Genetic Code Genetic Polymorphism Genetic Transcription Genetic Variation Genome Goals Hematological Disease Hematopoietic Hematopoietic System Human Indium Intervention Introns Knowledge Mammals Maps Messenger RNA Methods Modeling Molecular Genetics Mus Mutation Nature Nuclear RNA Oligonucleotide Microarrays Oligonucleotides Organism Pattern Peptide Sequence Determination Phenotype Proliferating Protein Isoforms Proteins RNA RNA Binding RNA Interference RNA Splicing Regulation Regulatory Element Reporter Research Personnel Screening procedure Signal Transduction Signal Transduction Pathway Simulate Site Specificity Stimulus System Testing Trans-Activators Transcript Variant Vertebrates Writing base cell type density experimental analysis flexibility functional genomics genome-wide high throughput technology human disease improved in vivo leukemia/lymphoma mRNA Precursor positional cloning programs research study response simulation synergism

项目摘要

DESCRIPTION (provided by applicant): The vast majority of human genes require RNA splicing for their expression, and at least 15% of the mutations that cause human diseases do so by disrupting splicing. The long term objective of this project remains: to understand the basis of RNA splicing specificity - the nature of the sequences in primary transcripts which are recognized by the RNA splicing machinery and used in the selection of splice sites in vertebrates and other organisms. This long-term objective is focused on four shorter-term aims: 1) to systematically identify sequences that can act as intronic splicing enhancer (ISE) and silencer (ISS) elements, to refine our knowledge of exonic splicing enhancer (ESE) and silencer (ESS) elements, and to determine rules for the context-dependent activity of these elements; 2) to identify the trans-acting factors responsible for the splicing regulatory activity of a significant proportion of the exonic splicing regulatory elements identified previously; 3) to develop and apply high-throughput technologies to map changes in expression of spliced isoforms that occur genome-wide during development and in response to external stimuli, using the murine hematopoietic system as a model; 4) to determine functional relationships - additivity, sub-additivity, synergism, etc. - between different classes of splicing regulatory elements, to develop associated scoring systems to improve algorithms that simulate splicing and predict splicing phenotypes of mutations or polymorphisms in human genes. In addressing these questions, we will use a synergistic combination of computational methods with molecular genetic and functional genomic approaches. Knowledge of splicing regulatory sequences and proteins will aid in understanding the changes that occur in the expression of RNA versions (isoforms) of genes as cells proliferate, and may identify specific protein or RNA targets for therapuetic intervention in hyperproliferative diseases of the blood such as leukemias, lymphomas and autoimmune diseases. The ability to accurately simulate splicing will enable improved genome annotation and will facilitate identification of specific genes, mutations and polymorphisms associated with human diseases.

描述（由申请人提供）：绝大多数人基因的表达需要RNA剪接，并且至少15％的引起人类疾病的突变是通过破坏剪接来做到的。该项目的长期目标仍然存在：了解RNA剪接特异性的基础 - 主要转录本中序列的性质，这些序列是由RNA剪接机械识别的，并用于选择脊椎动物和其他生物体中的剪接位点。这个长期目标的重点是四个较短的目标：1）系统地识别可以充当内含子剪接增强子（ISE）和消音器（ISS）元素的序列，以完善我们对外界剪接增强子（ESE）和消音器（ESS）元素（ESS）元素的了解，并确定依赖于这些元素的上下文活动的规则； 2）确定负责剪接调节活性的跨作用因素，这些因素是先前确定的大量外部剪接调节元件的大部分； 3）使用鼠类造血系统作为模型，开发和应用高通量技术来绘制在发育过程中发生的剪接同工型表达的变化，这些剪接的同工型在发育过程中发生的剪接同工型和对外部刺激的反应； 4）确定不同类别的剪接调节元素之间的功能关系 - 增强性，亚辅助性，协同作用等，以开发相关的评分系统，以改善人类基因中突变或多态性突变或多晶型的剪接表型的算法，以改善算法。在解决这些问题时，我们将使用计算方法与分子遗传和功能基因组方法的协同组合。剪接调节序列和蛋白质的知识将有助于理解基因的RNA版本（同工型）在细胞增殖中的表达（同工型）的变化，并且可以鉴定出特定的蛋白质或RNA靶标在血液，淋巴瘤，淋巴瘤和自身免疫性疾病的血液过度疾病中的治疗中的特定蛋白质或RNA靶标。准确模拟剪接的能力将能够改善基因组注释，并有助于鉴定与人类疾病相关的特定基因，突变和多态性。