Mapping RNA interactomes by sequencing

描述（由申请人提供）：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整个RNA-RNA相互作用组的图谱。因此，尽管我们正在对个人基因组进行测序，但我们解释基因组功能和从基因组序列预测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，我们建议开发一种极高通量的技术来绘制RNA-RNA相互作用组的体内图谱。其核心思想是将分子相互作用转化为DNA序列，然后通过DNA测序读出相互作用。提出的RNA Hi-C技术能够在一次分析中绘制所有蛋白质辅助RNA-RNA相互作用。这项新技术有望普遍适用于分析任何细胞类型和组织。我们将在植入前发育中使用细胞命运决定作为一个驱动的生物学问题。这项新技术将用于测试两个相互竞争的假设。我们期望这一结果能够阐明哺乳动物最早细胞命运决定背后的物理原理，从而为不孕、流产和出生缺陷提供前所未有的信息。

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.