High-throughput detection of transcriptomic and epitranscriptomic variation and kinetics using MarathonRT

使用 MarathonRT 高通量检测转录组和表观转录组变异和动力学

基本信息

  • 批准号:
    10470888
  • 负责人:
  • 金额:
    $ 96.63万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2021
  • 资助国家:
    美国
  • 起止时间:
    2021-08-17 至 2025-06-30
  • 项目状态:
    未结题

项目摘要

Project Summary The discovery and characterization of an efficient, ultraprocessive reverse transcriptase (MarathonRT) now makes it possible to develop high-throughput methods for accurate end-to- end sequencing of long RNA transcripts, thereby preserving information content on alternative splicing, editing and modification isoforms while conserving positional linkage information, thereby enabling one to distinguish RNA isoforms in complex mixtures without mapping to a reference genome. This type of technology is essential for deciphering the role of post- transcriptional RNA processing events during control of developmental stage, cell and tissue specificity and regulation of gene expression in higher organisms. It must be sufficiently efficient and accurate to power the long-read sequencing approaches that are used in single- cell RNAseq, particularly when transcript diversification is monitored as a function of time. The first two aims of the proposal are focused on high-throughput detection of RNA modifications (such as 2-O-methyl groups and N7-methyl guanosines). In the first aim, a unique MarathonRT primer extension protocol will be combined with a trained mutational profiling algorithm to recognize the positions and chemical identities of specific RNA modifications, reporting a modification signature that can be recognized at high throughput during long-read sequencing (MRT-ModSeq). In the second aim, MRT-ModSeq will be tested on unknown RNAs, where it will be used to predict sites of modifications on challenging long transcripts and robustness of the predictions will be directly evaluated using mass spectrometry. The second half of the proposal is focused on identification of linked alternative splicing and editing sites on long transcripts within complex cellular mixtures. In aim 3, MarathonRT will be incorporated into a workflow for accurately profiling the relative abundance and processing diversity of the highly complex paralytic (para) gene, which encodes more than 1 million possible processing variants, a subset of which are essential for the voltage-gating of a sodium channel. This sets the stage for Aim 4, in which sensitivity of the workflow must be further optimized and merged with data analysis strategies suitable for time-resolved single cell applications. The resulting method will be tested by monitoring full-length transcriptomic signatures induced by cell stress.
项目总结

项目成果

期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)

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Brenton R. Graveley其他文献

Power sequencing
电源排序
  • DOI:
    10.1038/4531197b
  • 发表时间:
    2008-06-25
  • 期刊:
  • 影响因子:
    48.500
  • 作者:
    Brenton R. Graveley
  • 通讯作者:
    Brenton R. Graveley

Brenton R. Graveley的其他文献

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{{ truncateString('Brenton R. Graveley', 18)}}的其他基金

High-throughput detection of transcriptomic and epitranscriptomic variation and kinetics using MarathonRT
使用 MarathonRT 高通量检测转录组和表观转录组变异和动力学
  • 批准号:
    10276105
  • 财政年份:
    2021
  • 资助金额:
    $ 96.63万
  • 项目类别:
High-throughput detection of transcriptomic and epitranscriptomic variation and kinetics using MarathonRT
使用 MarathonRT 高通量检测转录组和表观转录组变异和动力学
  • 批准号:
    10653940
  • 财政年份:
    2021
  • 资助金额:
    $ 96.63万
  • 项目类别:
The UConn/JAX-GM Training Program in Genomic Science
UConn/JAX-GM 基因组科学培训计划
  • 批准号:
    10378555
  • 财政年份:
    2020
  • 资助金额:
    $ 96.63万
  • 项目类别:
The UConn/JAX-GM Training Program in Genomic Science
UConn/JAX-GM 基因组科学培训计划
  • 批准号:
    10616676
  • 财政年份:
    2020
  • 资助金额:
    $ 96.63万
  • 项目类别:
A Comprehensive Functional Map of Human Protein-RNA Interactions
人类蛋白质-RNA 相互作用的综合功能图谱
  • 批准号:
    10087950
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:
A Comprehensive Functional Map of Human Protein-RNA Interactions
人类蛋白质-RNA 相互作用的综合功能图谱
  • 批准号:
    10087955
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:
A comprehensive binding and functional map of human RNA-binding proteins
人类 RNA 结合蛋白的综合结合和功能图谱
  • 批准号:
    10687988
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:
Regulation of UBE3A Imprinted Expression
UBE3A 印迹表达的调控
  • 批准号:
    10255508
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:
A Comprehensive Functional Map of Human Protein-RNA Interactions
人类蛋白质-RNA 相互作用的综合功能图谱
  • 批准号:
    10087949
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:
A Comprehensive Functional Map of Human Protein-RNA Interactions
人类蛋白质-RNA 相互作用的综合功能图谱
  • 批准号:
    10087952
  • 财政年份:
    2018
  • 资助金额:
    $ 96.63万
  • 项目类别:

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