Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.
Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai 200092, China.
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3473-3478. doi: 10.1073/pnas.1617636114. Epub 2017 Mar 13.
Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.
细胞周期中稳定的基因表达已经得到了广泛的研究。然而，在不同的细胞周期阶段，转录基因调控和组蛋白修饰的动态变化在很大程度上仍是未知的。通过应用全局核转录测序（GRO-seq）、RNA 测序（RNA-seq）和组蛋白修饰芯片测序（ChIP-seq）的组合，我们描绘了乳腺癌 MCF-7 细胞在 G0/G1、G1/S 和 M 期的全面转录图谱。重要的是，GRO-seq 和 RNA-seq 分析鉴定了不同的细胞周期调控基因，这表明在细胞周期中，转录和稳态表达之间存在滞后。有趣的是，我们鉴定了在早期 M 期活跃转录的基因，这些基因的长度较长，表达水平较低，并伴随着组蛋白 3 赖氨酸 4 甲基化（H3K4me2）和组蛋白 3 赖氨酸 27 乙酰化（H3K27ac）修饰的整体增加。此外，我们鉴定了 2440 个细胞周期调控增强子 RNA（eRNAs），它们与差异活跃转录密切相关，但与整个细胞周期的稳定表达水平无关。动态 eRNAs 的基序分析预测 Kruppel-like factor 4（KLF4）是 G1/S 转换的关键调节因子，这一鉴定得到了实验验证。总之，我们的综合分析描绘了人类细胞周期的转录和组蛋白修饰特征，并鉴定了细胞周期中动态的转录特征。
