DNA:RNA hybrids play key roles in both physiological and disease states by regulating chromatin and genome organization. Their homeostasis during cell differentiation and cell plasticity remains elusive. Using an isogenic human stem cell platform, we systematically characterize R-loops, DNA methylation, histone modifications, and chromatin accessibility in pluripotent cells and their lineage-differentiated derivatives. We confirm that a portion of R-loops formed co-transcriptionally at pluripotency genes in pluripotent stem cells and at lineage-controlling genes in differentiated lineages. Notably, a subset of R-loops maintained after differentiation are associated with repressive chromatin marks on silent pluripotency genes and undesired lineage genes. Moreover, in reprogrammed pluripotent cells, cell-of-origin-specific R-loops are initially present but are resolved with serial passaging. Our analysis suggests a multifaceted role of R-loops in cell fate determination that may serve as an additional layer of modulation on cell fate memory and cell plasticity.

DNA：RNA杂种通过调节染色质和基因组组织在生理和疾病状态中均起着关键作用。它们在细胞分化和细胞可塑性过程中的动态平衡仍然难以捉摸。使用等基因的人类干细胞平台，我们系统地表征了多能细胞及其谱系分化衍生物中的R环，DNA甲基化，组蛋白修饰和染色质可及性。我们证实，在多能干细胞中的多能性基因和分化谱系中的谱系控制基因中，R环的一部分共转录形成。值得注意的是，分化后维持的R-环的子集与沉默多能性基因和不希望的谱系基因上的抑制性染色质标记相关。此外，在重新编程的多能细胞中，最初存在特定于单元格的R环，但可以通过串行传递来解决。我们的分析表明，R环在细胞命运测定中具有多方面的作用，可作为细胞命运记忆和细胞可塑性的附加调节层。