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: 8350934
• 负责人: RUSS Paul CARSTENS
• 金额: $ 24万
• 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 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8350934
• 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; Screening procedure; 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; 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. PUBLIC HEALTH RELEVANCE: Alternative splicing allows the same gene transcript to be processed into proteins with different functions in different cell types, at different stages of development, and in numerous diseases including cancer. To understand how this process is regulated, we propose to carry out a systematic analysis to define the majority of the proteins that regulate this process and the RNA sequences that they bind. Identification of the complete inventory of protein-RNA regulatory interactions that control alternative splicing on a genome-wide scale will provide fundamental insights with broad applications to our understanding of human health and diseases.

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，几乎所有人类基因都产生编码不同蛋白质的多种mRNA。 剪接的调节主要由RNA结合蛋白（RBP）介导，所述RNA结合蛋白结合外显子和内含子序列并作为附近剪接位点或外显子的剪接增强子或沉默子起作用。 结合在受调节的外显子内或附近的许多RBP的净活性组合决定剪接结果。 对几种特征良好的剪接因子的研究揭示了结合的“RNA图谱”，其定义了它们是否促进或抑制外显子剪接。因此，预测在给定组织或细胞中表达的剪接因子集合的RNA图谱以确定全局剪接模式。 这样的图谱将因此定义不同序列基序和特征的“剪接代码”，其可以自信地预测剪接中的组织特异性差异。 在这一领域的最新进展表明，组织特异性剪接可以预测的基础上的RNA序列特征，并揭示了大量的RNA序列基序和功能，包括这个代码。 然而，在我们对完整的剪接密码的理解中仍然存在许多差距。 首先，仅定义剪接因子的总集合的少数。其次，与大多数调节剪接的序列基序结合的蛋白质调节剂是未知的。 第三，一个更完整的剪接代码，也可以预测更复杂的差异剪接在所有细胞类型和条件下，需要大量的新的输入。 解决这些问题的第一步是 完成所有直接调节剪接的人类蛋白质的全部清单，并确定它们的同源结合序列基序。 我们将通过以下具体目标进行这一步骤：1）使用人RNA结合蛋白的综合文库进行高通量筛选（HTS）剪接测定。 我们将使用RNA拴系试验结合先前验证的基于内切酶的剪接报告筛选几乎所有人类RBP的文库，以增强或沉默来自不同内含子位置的外显子剪接的能力。这种筛选管道和随后的验证步骤将极大地扩展人类基因组中已知的选择性剪接调节子的集合。2)通过多重RNA SELEX-Seq测定新型剪接调节剂的RNA结合特异性。 使用创新的新高通量方法，将使用基于细胞的方法来确定所有已知和新型剪接调节剂的高亲和力结合基序，该方法将指数富集配体的系统进化（SELEX）与高通量测序（RNA-Seq）结合起来。 从这些研究的结果将提供一个全面的看法的顺式和反式调节选择性剪接，定义剪接代码。 当与现有的实验和生物信息学数据库相结合时，将大大改善我们对剪接密码的定义，并为导致组织特异性剪接的分子机制提供新的见解。 公共卫生关系：选择性剪接允许相同的基因转录物在不同的细胞类型、不同的发育阶段和包括癌症在内的许多疾病中被加工成具有不同功能的蛋白质。 为了了解这一过程是如何调节的，我们建议进行系统分析，以确定大多数调节这一过程的蛋白质及其结合的RNA序列。 确定在全基因组范围内控制选择性剪接的蛋白质-RNA调控相互作用的完整清单将为我们理解人类健康和疾病提供具有广泛应用的基本见解。