干细胞是一类具有自我复制和向多种细胞分化潜能的细胞，能够分化成不同类型的组织细胞，进而组成机体的各种组织器官。同时，R-环是一种三链核酸结构，包括RNA和DNA互补配对形成的一条杂交双链和一条非模板DNA单链。研究表明R-环结构在DNA复制、基因转录和表观遗传调控等多种生物学过程中具有重要作用。然而，目前关于R-环在胚胎干细胞分化和重编程过程中的动态变化，尤其是多组学的关联分析研究尚少。本项目旨在通过体外人胚胎干细胞定向分化技术和体细胞重编程技术结合多组学高通量测序，探究在干细胞分化及重编程过程中R-环的动态变化规律，绘制多种细胞类型的R-环图谱，揭示R-环与多种表观修饰之间的关系。项目的实施将对理解人类细胞分化和细胞重编程及其内在的调节机制，揭示人细胞命运决定过程的关键因子提供重要线索。

Stem cells have the ability of self-renewal and the potential to differentiate to various cell types, which constitute a basis for various tissues and organs. Hybridization of RNA to its template DNA strand during transcription induces formation of R-loops. Previous studies indicated that R-loops play important roles in DNA replication, gene expression and numerous cellular processes. But the dynamics of R-loops in stem cell differentiation and cell reprogramming are poorly understood. In this proposal, we aim to comprehensive R-loops profiling systematically characterized R-loops, DNA modifications, chromatin signatures and the transcriptome of populations derived through directed differentiation of hESCs and hiPSCs reprogramming. Integration of strand specific DNA: RNA hybrid immunoprecipitation sequencing and multi-omics sequencing to reveal unique events associated with specification toward each lineage. This study will result in a better understanding of the molecular mechanism underlying human stem cell differentiation and cell reprogramming, and further highlight key factors during cell fate determination.