刚被RNA聚合酶转录合成的新生RNA能形成二级结构，对转录期间发生的众多生物学事件具有潜在调节作用。前期研究中，我们在酵母报告基因系统中发现，稳定的新生RNA二级结构能减少转录诱发的DNA突变。然而由于缺乏高通量检测新生RNA二级结构的数据，新生RNA二级结构在基因组范围对突变率的调节作用尚有待证实。为此，我们拟开展以下研究：1)结合捕获新生RNA的NET-Seq技术，和测定RNA二级结构的icSHAPE技术，建立高通量测定新生RNA二级结构的NS-Seq技术，并应用于酵母基因组。2)针对NS-Seq开发高效的生物信息学分析方法，对酵母新生RNA二级结构进行全面描述。3)根据获得的NS-Seq数据，鉴定新生RNA二级结构在基因组范围对DNA突变率的调节作用。研究结果将实现高通量测定新生RNA的二级结构的创新，加深对RNA二级结构及功能的理解，也将为阐明转录和突变的调节机制提供新的理论基础。

Being synthesized by RNA polymerase, the nascent RNA molecules can fold into various biochemically-active secondary structures that is distinct from mature RNA molecules. We previously found that nascent RNA with stable secondary structure can reduce trascription-induced DNA mutation rate by shortening the R-loop structure formed during transcription. However, the genome-wide effect of nascent RNA secondary structure on transcription-induced mutation rate remain unclear due to the lack of high-throughput data describing nascent RNA secondary structure. We plan to further investigate the nascent RNA secondary structure by conducting the following researches. 1) By a combination of two high-throughput sequencing-compatible protocols, including NET-Seq, which captures nascent RNA, and icSHAPE, which measures in vivo RNA secondary structures, we will develop a new method named NS-Seq,that can probe the nascent RNA secondary structure on a genomic scale. We will apply NS-Seq to S. cerevisiae cells. 2) Develop efficient and accuracte Bioinformatic pipelines for the analyses of NS-Seq data, and provide a comprehensive genome-wide profile of yeast nascent RNA secondary structure. 3) With the measured nascent RNA secondary structure, we will assess its regulatory effect on transcription-induced mutation rate. Results of these researches will reveal the dynamics and complexity of RNA secondary structure, and improves our understanding of the regulation on transcription and mutation, as well as its underlying molecular mechanism.