Computational Approaches for RNA StructureFunction Determination

RNA 结构功能测定的计算方法

• 批准号: 8763015
• 负责人: Bruce Shapiro
• 金额: $ 30.93万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 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/8763015
• 关键词: 3' Untranslated Regions; 5' Untranslated Regions; Acylation; Algorithms; Atomic Force Microscopy; Beryllium; Binding; Biological; Biological Assay; Biology; Carrier Proteins; Catalysis; Categories; Cell membrane; Cell physiology; Cells; Characteristics; Classification; Complex; Computer Simulation; Computer software; Computing Methodologies; Cyclization; Cytoskeleton; DNA; DNA Structure; Dengue; Dengue Virus; Dependency; Detection; Development; Developmental Process; Dimerization; Disease; Drosophila genome; Elements; Enhancers; Exons; Frequencies; Functional RNA; Gene Expression; Gene Silencing; Genes; Genetic Enhancer Element; Genetic Programming; Genome; Genome Scan; Genomics; HIV-1; Higher Order Chromatin Structure; Hydrolysis; Ions; Knowledge; Label; Lead; Length; Life Cycle Stages; Light; Machine Learning; Mechanics; Membrane; Messenger RNA; Methods; MicroRNAs; Mining; Modeling; Molecular Conformation; Motion; Mutation; Nucleic Acids; Nucleotides; Organism; Pathway interactions; Pattern; Proteins; RNA; RNA Folding; RNA Sequences; RNA analysis; Reporting; Research; Resolution; Ribonucleoproteins; Ribosomes; Role; Shapes; Site-Directed Mutagenesis; Sodium Chloride; Structure; Structure-Activity Relationship; System; Techniques; Testing; Time; Training Support; Transcript; Transcriptional Regulation; Transfer RNA; Translating; Translations; Trees; Turnip - dietary; Untranslated Regions; Variant; Viral; Virus; base; cancer cell; cis acting element; combinatorial; computerized tools; drug development; indexing; inorganic phosphate; magnesium ion; molecular dynamics; monomer; multi-scale modeling; novel; pea enation mosaic virus; pre-miRNA; programs; relating to nervous system; retinal rods; stem; three dimensional structure; viral RNA; web site

-Computational Detection of Abundant Long-range Nucleotide Co-variation in Genomes- A novel computational methodology was developed to detect long-range co-variation on a genomic scale producing high and medium confidence interactinos networks. To test the algorithm, it was applied to a set of aligned drosophila genomes where it was found that there are prevalent long-range co-variations between exons of mRNAs and non-coding RNAs, including endo-siRNAs. Most of the co-variations appear to be the result of synchronized mutations, not reverse complementarity. The genes found to co-vary are enriched for functions related to regionalization as well as neural and developmental processes. In a lower confidence interaction network there is a bias towards genes that have cellular component annotations such as plasma membrane or cytoskeleton. This may be an indicator of a widespread phenomenon of hitchhiking, in which transcripts bind to other RNAs that are part of ribonucleoprotein complexes which are transported along the cytoskeleton. These interactions may occur in a statistical size dependent manner. These results indicate that RNA-RNA long-range interactions are a widespread phenomenon that is important to a variety of cellular processes. - Discovery and Characterization of a Novel Translational Enhancers - 3' UTRs of cellular and viral mRNAs harbor elements that function in gene expression by enhancing translation using unknown mechanisms. To determine the function of these elements we previously used the Turnip crinkle virus (TCV). TCV is translated in a cap-independent fashion and contains a 3' region that together with the 5' UTR synergistically enhances translation. We recently discovered another element of this type in the Pea enation mosaic virus, however, this translational enhancer element acts in a somewhat different way. We used a set of computational tools, including RNA2D3D for 3D RNA modeling, developed in our lab, and experimental methods to show that this element is T-shaped, which is reminiscent of TCV's similarity to tRNA. We showed that it binds ribosomes and engages in a long range kissing loop RNA-RNA interaction. Its functionality suggests a means for RNA 5'/3' cyclization and thus a mechanism for translational enhancement. It appears that the existence of these novel elements is suggesting alternate translational mechanisms that may be found in eukaryotic organisms. - Understanding the Structure and Function of the Dengue Virus - It has recently been reported that there are over 400 million cases of dengue fever in the world, 4 times more than previously reported with 10% leading to severe forms of the disease. Using our massively parallel genetic algorithm for RNA folding we showed that the core region of the 3' untranslated region of dengue virus RNA can form 2 dumbell structures of unequal frequencies of occurrence. It was experimentally shown that structural motifs formed from these dumbells are important for viral replication. Also it was shown that there is a cooperative synergy with both dumbells for translation. Thus, the cis-acting elements in the core region of dengue virus are required for both replication and optimal translation. Recently, we performed a detailed structural analysis of the dengue minigenome using acylation techniques (SHAPE), lead induced hydrolysis and site directed mutagenesis. Results indicate protein independent interactions between the 5' and 3' terminal regions corroborating many of the predicted interactions and shedding light on the pseudoknot interactions found in the 3' UTR and the sequence dependency on the 5' cyclization region. -The Role of Ions and Flanking Bases in the Dimerization of HIV-1- Experimentally it has been shown that the characterization of HIV-1 kissing loop formation differs depending on the subtype of the virus. It has been shown that subtype-B monomers dimerize at high salt concentrations or in the presence of magnesium ions while subtype-A monomers will only dimerize with a magnesium ion bound to the flanking G273 phosphate group or the phosphate group of G274 regardless of the salt concentration. We found using computer simulations that at low concentrations both types of monomer hairpin loops were significantly deformed and the bases in the hairpin loop that are associated with dimerization were turned inward. At high salt concentrations the subtype-B monomer maintained a shape conducive to dimerization, while subtype-A still showed significant deformations. Also the flanking bases in subtype-B helped to stabilize the conformation while the flanking base G273 in subtype-A caused deformation. However, when magnesium ions were present and bound to the G273 or G274 phosphate groups, base G273 maintained a conformation that stabilized the loop for dimerization. These results are important for understanding the mechanisms that are involved in the HIV-1 virus life cycle. -Classifying Pre-miRNA via Combinatorial Feature Mining and Boosting MicroRNAs are non-coding RNAs consisting of about 22 nucleotides that are derived from precursor molecules. These precursors usually fold into stem-loop hairpin structures. When scanning genomes it is difficult to distinguish false positive pre-miRNAs from the real thing. In this research a new method was developed for identifying and classifying pre-miRNAs. A combinatorial feature mining approach was used to discover a good set of features. These feature sets were then used to train support vector machines to obtain classification models. A boosting algorithm was then applied to further enhance the accuracy. Results indicate significant improvement over previous methods. -Discovering Common Folding Patterns in two RNA Sequences- An efficient dynamic programming algorithm was developed that uses ordered labeled trees for discovering the largest common RNA substructures given 2 RNA sequences. This algorithm can also be used to discover repeated regions of RNA secondary structure. -Multiscale Modeling of Double Helical DNA and RNA Unified through Lie Groups- In order to further understand motions that are inherent in nucleic acid helices, several means of mechanical modeling, continuous and discrete, of double-stranded nucleic acid helical structures (DNA and RNA)were reviewed and a new analysis method using Lie groups was used to reconcile the models. Rigid body motions were analyzed. At the most coarse level worm-like chains were used with anisotropic bending stiffness. It was then shown that bi-rod models converge to this for long enough lengths. We then showed how full atomic resolution molecular dynamics and experimental results obtained from atomic force microscopy relate to the models.

-基因组中丰富的长程核苷酸共变的计算检测-开发了一种新的计算方法来检测基因组规模上的长程共变，产生高和中等置信度的相互作用网络。为了测试该算法，将其应用于一组对齐的果蝇基因组，发现 mRNA 和非编码 RNA（包括内切 siRNA）的外显子之间存在普遍的长程共变。大多数共变似乎是同步突变的结果，而不是反向互补性的结果。发现共变的基因丰富了与区域化以及神经和发育过程相关的功能。在置信度较低的交互网络中，存在对具有细胞成分注释（例如质膜或细胞骨架）的基因的偏见。这可能是搭便车现象广泛存在的一个指标，即转录物与其他 RNA 结合，这些 RNA 是沿着细胞骨架运输的核糖核蛋白复合物的一部分。这些相互作用可以以统计大小相关的方式发生。这些结果表明 RNA-RNA 长程相互作用是一种普遍现象，对多种细胞过程很重要。 - 新型翻译增强子的发现和表征 - 细胞和病毒 mRNA 的 3' UTR 含有通过使用未知机制增强翻译而在基因表达中起作用的元件。为了确定这些元件的功能，我们之前使用了芜菁皱纹病毒（TCV）。 TCV 以不依赖帽子的方式进行翻译，并包含一个 3' 区域，与 5' UTR 一起协同增强翻译。我们最近在豌豆花叶病毒中发现了这种类型的另一种元件，然而，这种翻译增强子元件的作用方式有些不同。我们使用了一套计算工具，包括我们实验室开发的用于 3D RNA 建模的 RNA2D3D，以及实验方法来表明该元素是 T 形的，这让人想起 TCV 与 tRNA 的相似性。我们证明它与核糖体结合并参与长距离接吻环 RNA-RNA 相互作用。它的功能表明了一种 RNA 5'/3' 环化方法，从而提供了一种翻译增强机制。这些新元件的存在似乎暗示了真核生物中可能存在的替代翻译机制。 - 了解登革热病毒的结构和功能 - 最近有报道称，全球有超过 4 亿登革热病例，是之前报告的 4 倍，其中 10% 会导致严重的疾病。使用我们的大规模并行遗传算法进行RNA折叠，我们发现登革热病毒RNA 3'非翻译区的核心区域可以形成2个出现频率不等的哑铃结构。实验表明，这些哑铃形成的结构基序对于病毒复制很重要。还表明，两个哑铃在翻译方面具有协同作用。因此，登革热病毒核心区的顺式作用元件是复制和最佳翻译所必需的。最近，我们使用酰化技术（SHAPE）、铅诱导水解和定点诱变对登革热小基因组进行了详细的结构分析。结果表明 5' 和 3' 末端区域之间存在蛋白质独立的相互作用，证实了许多预测的相互作用，并揭示了 3' UTR 中发现的假结相互作用以及对 5' 环化区域的序列依赖性。 -离子和侧翼碱基在 HIV-1 二聚化中的作用- 实验表明，HIV-1 接吻环形成的特征因病毒亚型而异。研究表明，B 亚型单体在高盐浓度或存在镁离子的情况下会发生二聚，而 A 亚型单体只会与与侧翼 G273 磷酸基团或 G274 磷酸基团结合的镁离子发生二聚，而与盐浓度无关。我们通过计算机模拟发现，在低浓度下，两种类型的单体发夹环都显着变形，并且发夹环中与二聚化相关的碱基向内转。在高盐浓度下，B 亚型单体保持有利于二聚化的形状，而 A 亚型仍然表现出明显的变形。此外，B 亚型中的侧翼碱基有助于稳定构象，而 A 亚型中的侧翼碱基 G273 会导致变形。然而，当镁离子存在并与 G273 或 G274 磷酸基团结合时，碱基 G273 保持稳定环二聚化的构象。这些结果对于理解 HIV-1 病毒生命周期中涉及的机制非常重要。 -通过组合特征挖掘和增强对 Pre-miRNA 进行分类 MicroRNA 是由约 22 个源自前体分子的核苷酸组成的非编码 RNA。这些前体通常折叠成茎环发夹结构。扫描基因组时，很难区分假阳性 pre-miRNA 和真实的 pre-miRNA。在这项研究中，开发了一种用于识别和分类 pre-miRNA 的新方法。使用组合特征挖掘方法来发现一组好的特征。然后使用这些特征集来训练支持向量机以获得分类模型。然后应用增强算法来进一步提高准确性。结果表明比以前的方法有显着改进。 -发现两个RNA序列中的共同折叠模式-开发了一种高效的动态编程算法，该算法使用有序标记树来发现给定2个RNA序列的最大共同RNA子结构。该算法还可用于发现 RNA 二级结构的重复区域。 -通过李群统一的双螺旋DNA和RNA的多尺度建模-为了进一步了解核酸螺旋固有的运动，回顾了双链核酸螺旋结构（DNA和RNA）的连续和离散机械建模的几种方法，并使用使用李群的新分析方法来协调模型。分析了刚体运动。在最粗的水平上，使用具有各向异性弯曲刚度的蠕虫状链条。然后表明，双杆模型在足够长的长度下会收敛到此。然后，我们展示了从原子力显微镜获得的全原子分辨率分子动力学和实验结果与模型的关系。