Mapping RNA interactomes by sequencing

描述（申请人提供）：RNA-RNA相互作用是基因调控网络的重要组成部分。目前还没有技术来绘制细胞或组织中的整个RNA-RNA相互作用组。因此，虽然个人基因组正在测序，但我们解释基因组功能和预测基因组序列表型变异的能力仍然有限。我们迫切需要高通量技术来绘制任何人或组织中的分子网络。在这里，我们建议开发一种非常高通量的技术来绘制体内RNA-RNA相互作用组。其核心思想是将分子间的相互作用转化为DNA序列，然后通过DNA测序读出相互作用。所提出的RNA Hi-C技术能够在一次测定中绘制所有蛋白质辅助的RNA-RNA相互作用。这项新技术预计将普遍适用于分析任何细胞类型和组织。 我们将使用植入前发育中的细胞命运决定作为驱动生物学问题。这项新技术将用于测试两个相互竞争的假设。我们希望这些结果能够澄清哺乳动物最早的细胞命运决定背后的物理原理，从而提供有关不孕症，流产和出生缺陷的前所未有的信息。

DESCRIPTION (provided by applicant): RNA-RNA interactions are important components of gene regulatory networks. There is yet no technology to map the entire RNA-RNA interactome in cells or tissues. As a result, although personal genomes are being sequenced, our capabilities to interpret genomic functions and to predict phenotypic variation from genomic sequence remain limited. We desperately need high-throughput technologies to map the molecular networks in any person or tissue. Here, we propose to develop an extremely high-throughput technology to map RNA-RNA interactomes in vivo. The central idea is to convert molecular interactions into DNA sequences and then read out the interactions by DNA sequencing. The proposed RNA Hi-C technology is capable of mapping all protein- assisted RNA-RNA interactions in one assay. This new technology is expected to be generally applicable to analyze any cell types and tissues. We will use cell fate decisions in pre-implantation development as a driven biological question. The new technology will be applied to test two competing hypotheses. We expect the results to clarify a physical principle behind the earliest cell fate decision in mammals, and therefore offer unprecedented information regarding infertility, miscarriage, and birth defects.