Methods for RNA structural analysis using computation and structure mapping exper

使用计算和结构作图实验进行 RNA 结构分析的方法

基本信息

  • 批准号:
    8995224
  • 负责人:
  • 金额:
    $ 23.3万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2012
  • 资助国家:
    美国
  • 起止时间:
    2012-07-23 至 2017-12-31
  • 项目状态:
    已结题

项目摘要

Project Summary Strong links between RNA structure and function, fast-paced discoveries of novel RNAs, and a growing use of RNAs in biomedical engineering underscore a pressing need to analyze RNA structural dynamics rapidly and accurately. Yet, available methods are either labor intensive and technologically complex, or rely on low- accuracy computation-based prediction. We, and two other groups, have recently begun addressing this need by coupling RNA structure mapping experiments to high-throughput sequencing platforms, to enable the generation of genome-scale structural information (Wan et al. 2011). Structure mapping is a classical approach that uses chemicals or enzymes to discriminate between paired and unpaired nucleotides, and which has recently gained widespread use, following improvements to its quality and utility. However, the method does not reveal base-pairs identities and cannot directly resolve secondary structure. Nonetheless, computational approaches can greatly benefit from this wealth of information through its proper interpretation and use. We propose to complement these advances by developing a computational framework that will improve our ability to infer RNA structural dynamics from structure mapping experiments. We will build on our previous work on a statistical method that automatically recovers structural information from chemical mapping data, which we applied to data obtained from a new assay that couples SHAPE chemistry to next-generation sequencing. We propose to extend it into a complete and statistically sound algorithmic framework for analysis of chemical mapping data and for subsequent data integration into computational prediction of RNA structure dynamics. In the R00 phase, we will design efficient algorithms that, when combined with large-scale mapping measurements, will facilitate reliable and high-throughput assessment of the impact of sequence on structure and function. The K99 phase will provide the training and experience to pursue research in the R00 phase. Specific Aim K99.1: Develop experimental expertise in chemical structure mapping assays. This will complement my computational skills and allow me to efficiently test the tools we will develop in the R00 phase. Specific Aim K99.2: Extend and further investigate our method for analysis of chemical structure mapping data. This aim includes two projects that are outlined in the proposal, one that will enable de novo and genome-wide mapping and one that will inform users of systematic inter-platform information differences. Specific Aim R00.1: Develop algorithms and software for integrating structure mapping data into ensemble-based approaches to analyzing RNA structural dynamics. This will improve the quality and resolution of computation-based structural analysis. Specific Aim R00.2: Apply the developed tools to three biological systems, to provide a proof of principle for the tools' utility. This will demonstrate the potential of the developed tools to substitute current approaches and to advance future RNA engineering efforts.
项目总结

项目成果

期刊论文数量(5)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures.
  • DOI:
    10.3390/genes9060300
  • 发表时间:
    2018-06-14
  • 期刊:
  • 影响因子:
    3.5
  • 作者:
    Radecki P;Ledda M;Aviran S
  • 通讯作者:
    Aviran S
PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.
  • DOI:
    10.1186/s13059-018-1399-z
  • 发表时间:
    2018-03-01
  • 期刊:
  • 影响因子:
    12.3
  • 作者:
    Ledda M;Aviran S
  • 通讯作者:
    Aviran S
Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.
  • DOI:
    10.1093/nar/gkx1273
  • 发表时间:
    2018-03-16
  • 期刊:
  • 影响因子:
    14.9
  • 作者:
    Watters KE;Choudhary K;Aviran S;Lucks JB;Perry KL;Thompson JR
  • 通讯作者:
    Thompson JR
Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.
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Sharon Aviran其他文献

Sharon Aviran的其他文献

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{{ truncateString('Sharon Aviran', 18)}}的其他基金

Prediction of nearest neighbor parameters for folding RNAs with modified nucleotides
预测具有修饰核苷酸的折叠 RNA 的最近邻参数
  • 批准号:
    10576175
  • 财政年份:
    2023
  • 资助金额:
    $ 23.3万
  • 项目类别:
Methods for RNA structural analysis using computation and structure mapping exper
使用计算和结构作图实验进行 RNA 结构分析的方法
  • 批准号:
    8788303
  • 财政年份:
    2012
  • 资助金额:
    $ 23.3万
  • 项目类别:
Methods for RNA structural analysis using computation and structure mapping exper
使用计算和结构作图实验进行 RNA 结构分析的方法
  • 批准号:
    8791915
  • 财政年份:
    2012
  • 资助金额:
    $ 23.3万
  • 项目类别:
Methods for RNA structural analysis using computation and structure mapping exper
使用计算和结构作图实验进行 RNA 结构分析的方法
  • 批准号:
    8354539
  • 财政年份:
    2012
  • 资助金额:
    $ 23.3万
  • 项目类别:

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