Comprehensive determination of the human proteins that define the splicing code

全面测定定义剪接代码的人类蛋白质

• 批准号: 8513387
• 负责人: RUSS Paul CARSTENS
• 金额: $ 20万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-18 至 2015-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8513387
• 关键词: Accounting; Affinity; Alternative Splicing; Area; Binding; Binding Sites; Bioinformatics; Biological Assay; Cells; Chimeric Proteins; Code; Collection; Complementary DNA; Complex; Couples; Databases; Destinations; Development; Disease; Enhancers; Equipment and supply inventories; Evolution; Exons; Gene Expression Profile; Gene Expression Regulation; Genes; Goals; Health; Human; Human Genome; Indium; Lead; Libraries; Ligands; Luciferases; Malignant Neoplasms; Maps; Mediating; Messenger RNA; Methods; Minority; Molecular; Outcome; Pattern; Peptides; Positioning Attribute; Process; Production; Protein Binding; Proteins; RNA; RNA Binding; RNA Sequences; RNA Splicing; RNA-Binding Proteins; Regulation; Reporter; Resources; Site; Specificity; Staging; Tissue-Specific Splicing; Tissues; Transcript; Validation; Variant; base; cDNA Library; cell type; combinatorial; disorder risk; genome-wide; high throughput screening; human disease; improved; innovation; insight; novel; preference; programs; screening; transcriptome sequencing; vector

DESCRIPTION (provided by applicant): Alternative splicing massively expands the complexity of the human transcriptome and nearly all human genes produce multiple mRNAs that encode distinct proteins. Regulation of splicing is primarily mediated by RNA binding proteins (RBPs) that bind to exonic and intronic sequences and function as splicing enhancers or silencers of nearby splice sites or exons. The net activities of a number of RBPs that bind within or near regulated exons combinatorially determine the splicing outcome. Studies of several well characterized splicing factors have revealed "RNA maps" of binding that define whether they promote or repress exon splicing. The RNA maps of a collection of splicing factors expressed in a given tissue or cell are therefore predicted to determine global splicing patterns. Such maps will thus define a "splicing code" of diverse sequence motifs and features that can confidently predict tissue-specific differences in splicing. Recent progress in this area has shown that tissue specific splicing can be predicted on the basis of RNA sequence features and revealed a vast collection of RNA sequence motifs and features that comprise this code. However, many gaps in our understanding of the complete splicing code remain. First, only a minority of the total set of splicing factors are defined. Second, the protein regulators that bindto the most of the sequence motifs that regulate splicing are unknown. Third, a more complete splicing code that can also predict more complex differences in splicing in all cell types and conditions requires substantial new inputs. A first step towards resolving these issues will be to complete the full inventory of all human proteins that directly regulate splicing and determine their cognate binding sequence motifs. We will undertake this step through the following specific aims: 1) Perform high throughput screening (HTS) splicing assays using a comprehensive library of human RNA binding proteins. We will use RNA tethering assays in conjunction with previously validated luciferase-based splicing reporters to screen a library of nearly all human RBPs for the ability to enhance or silence exon splicing from different intronic positions. This screening pipeline and subsequent validation steps will vastly expand the set of known alternative splicing regulators in the human genome. 2) Determination of RNA binding specificities for novel splicing regulators by multiplexed RNA SELEX-Seq. Using an innovative new high throughout method the high affinity binding motifs for all known and novel splicing regulators will be determined using a cell-based method to that couples systematic evolution of ligands by exponential enrichment (SELEX) with high throughput sequencing (RNA-Seq). The results from these studies will provide a comprehensive view of the cis- and trans-regulators of alternative splicing that define the splicing code. When couples with existing experimental and bioinformatics databases will substantially improve our definition of the splicing code and provide new insights into the molecular mechanisms that lead to tissue-specific splicing.

描述（由申请人提供）：选择性剪接极大地扩展了人类转录组的复杂性，几乎所有的人类基因都会产生编码不同蛋白质的多个mrna。剪接的调节主要由RNA结合蛋白（rbp）介导，rbp结合外显子和内含子序列，并作为剪接增强子或附近剪接位点或外显子的沉默子。在调控外显子内或外显子附近结合的许多rbp的净活性共同决定了剪接结果。对几个特征明确的剪接因子的研究揭示了结合的“RNA图谱”，确定了它们是促进还是抑制外显子剪接。因此，在给定组织或细胞中表达的一系列剪接因子的RNA图谱被预测为确定全局剪接模式。