The cell cycle is among the most basic phenomena in biology. Despite advances in single‐cell analysis, dynamics and topology of the cell cycle in high‐dimensional gene expression space remain largely unknown. We developed a linear analysis of transcriptome data which reveals that cells move along a planar circular trajectory in transcriptome space during the cycle. Non‐cycling gene expression adds a third dimension causing helical motion on a cylinder. We find in immortalized cell lines that cell cycle transcriptome dynamics occur largely independently from other cellular processes. We offer a simple method (“Revelio”) to order unsynchronized cells in time. Precise removal of cell cycle effects from the data becomes a straightforward operation. The shape of the trajectory implies that each gene is upregulated only once during the cycle, and only two dynamic components represented by groups of genes drive transcriptome dynamics. It indicates that the cell cycle has evolved to minimize changes of transcriptional activity and the related regulatory effort. This design principle of the cell cycle may be of relevance to many other cellular differentiation processes.

中文翻译：

---

细胞周期中单细胞的转录组动态

细胞周期是生物学中最基本的现象之一。尽管单细胞分析取得了进展，但高维基因表达空间中细胞周期的动力学和拓扑结构仍然很大程度上未知。我们对转录组数据进行了线性分析，揭示了细胞在循环过程中沿着转录组空间中的平面圆形轨迹移动。非循环基因表达增加了三维，导致圆柱体上的螺旋运动。我们发现在永生化细胞系中，细胞周期转录组动态很大程度上独立于其他细胞过程。我们提供了一种简单的方法（“Revelio”）来及时订购不同步的单元。从数据中精确去除细胞周期影响变得非常简单。轨迹的形状意味着每个基因在周期中仅上调一次，并且只有由基因组代表的两个动态成分驱动转录组动态。它表明细胞周期已经进化到最大限度地减少转录活性和相关调节工作的变化。细胞周期的这种设计原理可能与许多其他细胞分化过程相关。