Identification of Functionally Related cis-Regulatory DNA

功能相关顺式调控 DNA 的鉴定

• 批准号: 8940133
• 负责人: WARD F ODENWALD
• 金额: $ 56.85万
• 依托单位: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8940133
• 关键词: Algorithms; Base Pairing; Beryllium; Binding Sites; Biological; Biological Models; Cell Lineage; Comparative Genomic Analysis; Computational algorithm; Computers; Conserved Sequence; DNA; DNA Binding; DNA Sequence; DNA Sequencing Facility; Databases; Development; Drosophila genome; Drosophila genus; Drosophila melanogaster; Elements; Enhancers; Equilibrium; Event; Gene Expression; Genes; Genome; Genomic DNA; Goals; Indium; Internet; Knowledge; Learning; Logic; Methodology; Methods; Modeling; Mus; Neurons; Positioning Attribute; Printing; Protocols documentation; Regulation; Scanning; Sequence Alignment; Structure; Training; Vertebrates; base; design; fly; genome-wide; improved; nerve stem cell; next generation; programs; relating to nervous system; research study; tool; transcription factor; Algorithms; Base Pairing; Beryllium; Binding Sites; Biological; Biological Models; Cell Lineage; Comparative Genomic Analysis; Computational algorithm; Computers; Conserved Sequence; DNA; DNA Binding; DNA Sequence; DNA Sequencing Facility; Databases; Development; Drosophila genome; Drosophila genus; Drosophila melanogaster; Elements; Enhancers; Equilibrium; Event; Gene Expression; Genes; Genome; Genomic DNA; Goals; Indium; Internet; Knowledge; Learning; Logic; Methodology; Methods; Modeling; Mus; Neurons; Positioning Attribute; Printing; Protocols documentation; Regulation; Scanning; Sequence Alignment; Structure; Training; Vertebrates; base; design; fly; genome-wide; improved; nerve stem cell; next generation; programs; relating to nervous system; research study; tool; transcription factor

cis-Regulatory modules (enhancers) are genomic DNA fragments that contain multiple binding sites for sequence specific DNA-binding transcription factors that collectively control the temporal and spatial expression dynamics of flanking genes. While DNA sequence alignments between Drosophila melanogaster genes and their orthologous DNAs outside the genus are of limited use in identifying enhancers, the additive evolutionary divergence among 12 Drosophila species is of great utility for identifying functional conserved sequences within enhancers. For example, all Drosophila enhancers characterized thus far contain multiple conserved sequence blocks (CSBs), made up of DNA-binding sites for known and as yet unidentified transcriptional regulators. Comparative genomic analysis among vertebrates also reveals that many of their enhancers contain CSBs. Recent studies have demonstrated that co-regulating enhancers share conserved sequence elements. We have developed computer algorithms to identify repeat sequences within CSB clusters and to search for co-regulating enhancers throughout the Drosophila genome based on their shared conserved sequence elements. Our genome-wide CSC database currently consists of over 100,000 CSB clusters obtained from evolutionary gene prints that span 90% of the Drosophila genome. Alignment-search algorithms were designed to scan this database to detect related enhancers by a multi-step protocol: Conserved repeat elements within an input enhancer are identified and then CSCs with the same repeated sequences as the input CSC are identified. Via one-on-one alignments, the database CSCs are ranked in the order of their shared sequence elements with the input enhancer. This method has several advantages over previous enhancer discovery methods: 1) it makes no assumptions about the function of the conserved sequences -- over 50% of the shared sequences do not represent DNA binding sites for known transcription factors, 2) it requires no a priori knowledge of the functional elements in a given CSB cluster, and 3) it allows the user to focus on genes that are co-expressed in any given biological event, e.g. neural stem cell lineage development, to discover functionally related neuron identity genes via their co-regulating enhancers. We believe that the CSC database and search algorithms will become part of the next generation of tools for the discovery and analysis of Drosophila cis-regulatory DNA sequences. This methodology will also serve as a model for identifying functionally related enhancers in other model systems such as mammalian cis-regulatory DNAs. To extend the use of these tools to mammalian cis-regulation, we are currently generating a mouse CSC database covering its entire genome. CSCs parsed from 1.03 million EvoPrints that span the mouse 2.6 billion base pair genome using either 400 million or 1.0 billion cumulative evolutionary divergence (CED) years can be searched independently using the alignment algorithms developed for fly enhancer recognition. Analysis of a training set of 57 known mammalian enhancers reveals that all contain CSCs with CED values of >400 My and most have ultra-conserved core sequences with CED values in excess of 1.0 By.

顺式调节模块（增强子）是基因组DNA片段，其中包含多个结合位点，用于序列特定的DNA结合转录因子，共同控制侧面基因的时间和空间表达动力学。 虽然果蝇大麻植物基因及其在属外的直系同源DNA之间的DNA序列比对在识别增强子方面的使用有限，但12种果蝇物种之间的添加剂进化差异是鉴定增强剂内功能保守序列的极大效用。例如，到目前为止，所有果蝇增强剂都包含多个保守序列块（CSB），该序列块（CSB）由已知和尚未确定的转录调节剂组成的DNA结合位点组成。脊椎动物中的比较基因组分析还表明，其许多增强剂都包含CSB。 最近的研究表明，共同调节增强剂具有保守的序列元素。 我们已经开发了计算机算法，以识别CSB簇中的重复序列，并根据其共同的保守序列元素在整个果蝇基因组中搜索共同调节增强子。我们全基因组的CSC数据库目前由超过100,000个CSB簇从跨越果蝇基因组的90％的进化基因印刷中获得。设计的对齐搜索算法旨在扫描该数据库，以通过多步协议检测相关增强剂：鉴定输入增强器中的保守重复元素，然后与输入CSC相同的重复序列的CSC进行了识别。通过一对一的对齐，数据库CSC按其与输入增强器的共享序列元素的顺序进行排名。 该方法比以前的增强剂发现方法具有多个优势：1）对保守序列的功能没有任何假设 - 超过50％的共享序列不代表已知转录因子的DNA结合位点，2）它不需要先验地了解给定CSB集群中的功能元素，并且可以允许使用E. copexpresse e. cosexection the It toce copexpressed ee E.神经干细胞谱系的发育，通过共同调节增强子发现功能相关的神经元同一性基因。 我们认为，CSC数据库和搜索算法将成为下一代的工具的一部分，用于发现和分析果蝇顺式调节性DNA序列。 该方法还将作为识别其他模型系统（例如哺乳动物顺式调节DNA）中与功能相关的增强子的模型。 为了将这些工具的使用扩展到哺乳动物的顺式调节，我们目前正在生成涵盖其整个基因组的鼠标CSC数据库。可以使用4亿或10亿累积进化差异（CED）年的CSC从1030万个evoprint分解，跨越了26亿基碱基对基因组，可以使用用于FLY增强剂识别的捕获量的比对算法进行独立搜索。对57个已知哺乳动物增强剂的训练集的分析表明，所有CSC的CED值> 400 ME和大多数的CED值具有超过1.0 by的CED值超过1.0。